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Undergraduate Research Opportunities Program

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A conjunctive middleware adaptation of active and passive RFID techonologies

2011-05-11 , Rowswell, Brent

RFID technology has been split into two branches. Active RFID and passive RFID behave in very different manners, yet the theory behind them is practically the same. If the two branches were able to be merged into use under a single software system, then a number of use cases can be made that mitigate each technology's weakness with the other. The only major obstacle to using them interchangeably is the lack of a standard messaging system. Since we can't create a standard for industry, we plan on using a middleware to translate to our own standard.

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Finding Evidence of a Cancer Suppressing Mutation, rs 3814113

2011-05-09 , Small, James

For the past twenty years ovarian cancers has been one of the most well studied cancers. While many aspects of ovarian cancer are understood, scientists do not know what mutations cause tumor genesis. In recent years scientists have turned to genome wide association studies(GWAS) to determine what mutations are correlated to the disease, but these studies have not provided sufficient evidence to produce establish a causal link between a mutation and the disease. Instead of trying to create larger studies, scientists need to perform more focused smaller studies such as this one. This study will be investigating the findings of a recent GWAS performed by Dr. Song and his associates. However, instead of investigating the genetic information of thousands of individuals this study will focus on the complete profile of a twenty patients. This study will differ by including factors such as the patient and familial history of each of the cancer cases. By investigating this additional information this study will either prove or disprove the correlation between the SNP rs3814113 and ovarian cancer. after investigating genotypic ratios, onset of the disease, and risk ratios among pathological and genotypic groups this study found no evidence to support rs 3814113 as a cancer suppressing mutation.

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RNA-mediated double-stranded break repair in mammalian cells

2011-05-09 , Taylor, Matthew

This study seeks to examine the capability of RNA to introduce mutations into genomic DNA, and to provide insight into the enzyme(s) responsible for this phenomenon. To do this, a double-stranded break is induced in HEK 658D cells, and oligonucleotides containing RNA tracts with homology to the area around the break are introduced to examine if they can mediate repair of this area. In the first part of the study, oligonucleotides are introduced that contain a single-nucleotide substitution at the site of the break, and if the RNA is used as a template for repair, then this nucleotide should be incorporated into the genome of the cell. Oligonucleotides are introduced that contain either all-DNA, or DNA with a 6-nucleotide RNA tract at the break. These two classes of oligonucleotides are homologous to either the forward or reverse strands of the area around the break. This allows us to examine if there is a strand bias for repair, and if that bias is the same for DNA- and RNA-mediated repair, which will provide clues into the enzyme involved in repair.

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The Effect of Retrocues on CDA and Visual Working Memory Capacity in Young Adults

2011-05-09 , Delvin, Mary Courtney

Visual working memory is a system through which we retain information about objects in our visual environment. Through this system, information is stored so that it can be recalled or manipulated within the first few seconds of perception. Individual working memory capacity underlies numerous aspects of cognition including visual search, attentional processes, and concentration, and can predict performance on cognitive measures. Working memory is used in many everyday tasks and has implications in aging and the pathology of diseases. Contralateral Delay Activity (CDA) is a form of event-related potential measured with electroencephalography (EEG) that is thought to be modulated by the number of items held in working memory. In a related area of study, retrocues are attentional tools that are used to help individuals recall information from working memory. Retrocues are thought to improve visual working memory capacity by enhancing the active maintenance of relevant information held in working memory. This study attempts to show a relationship between retrocue usage and the CDA. We predict that retrocue trials will improve young adults’ performance on a working memory task and will enhance the CDA, showing that retrocues are an effective modulator of the CDA.

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Investigating steric protection of DNA in the presence of nucleases

2011-05-11 , Tomassi, Taylor Alexandra

In the human body, DNA-linked colloidal assemblies are prone to cleavage by nucleases, yielding the uncontrolled release of particles and any associated therapeutics. Thus, for in vivo applications, the DNA-linkages must be protected from cleavage by serum nucleases. The goal of this research is to stabilize DNA duplexes in the presence of nucleases by chemically modifying the primary target. The effects of sterically protecting DNA duplexes from nuclease activity by including a polymeric tail on oligonucleotide targets and by including LNA bases in the target sequence were investigated. The variables explored included the effect of tail chemistry as well as tail length on the kinetics and extent of nuclease activity. In DNA digests, two types of polymeric "tails" were compared: polyethylene glycol (PEG) chains and single stranded thymine-based strands (dT). Long and short PEG and thymine tails of equivalent lengths were compared. Ezymatic digests were also performed on fluorescently labeled primary targets modified with oligonucleotide analogs called LNA, locked nucleic acids. Flow cytometry was used to quantify the hybridization activity and measure the probe-target duplex density as well as to determine time-dependence of nuclease activity by monitoring the number of duplexes remaining following incubation with DNase I. Significant clipping was observed for all DNA targets tested and indicated that various polymeric tails did not significantly hinder nuclease activity. These results indicate that the relatively short polymeric tail lengths do not have appreciable effects on the hindrance of nuclease activity. LNA digests, on the other hand, showed enhanced stability of primary duplexes in the presence of nucleases after 24 hours and suggested that LNA may be used as an alternative to DNA to stabilize colloidal assemblies for drug delivery.

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Mobile Tactile Stimulation for Passive Haptic Learning of Simple Melodies

2011-05-09 , Jain, Abhishek

The phenomenon of acquiring motor skills without active attention is termed Passive Haptic Learning. This concept of learning is applied to acquiring piano melodies through vibration on each finger while users are given a 30-minute GRE test. Mobile Music Touch (MMT) is a lightweight, wireless, haptic music instruction system consisting of fingerless gloves and a Bluetooth-enabled mobile computing device. Passages to be learned are loaded onto the software on the computer and are communicated to the MMT system through Bluetooth and are played repeatedly. As each note of the music plays, vibrators on each finger in the gloves activate, indicating which finger is used to play each note. Such passive learning is complemented with an initial controlled active learning on the piano. This study present a 12-subject pilot and a 24 subject full study for measuring the efficacy of the system for retaining simple piano melodies in without active attention. The full study is currently under progress. This paper highlights significant improvement in learning curve for the conditions involving Passive Haptic Learning. The learning afforded by PHL for a compelling and fun treatment (playing piano) will help tetraplegic patients maintain interest in the system’s rehabilitative capabilities.

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Dynamic Fluid Shear Stress Measurements on the Normal Aortic Valve Leaflet Using Laser Doppler Velocimetry

2011-05-09 , Tamilselvan, Gowthami

Aortic valve (AV) calcification is a major cause of mortality and morbidity. This disease involves the chronic inflammation of the AV leaflets and calcium deposition, resulting in valve stenosis and regurgitation. The exact cause of aortic valve calcification is unknown but previous studies have shown that adverse mechanical forces play a role.1 Unfortunately, the mechanical environment of the AV is not well known. Thus, the objective of this project was to make experimental measurements of the fluid shear stress mechanical environmental of the native aortic valve. Native aortic valves were excised from porcine hearts, sutured onto stented rings, and tested in an in vitro pulsatile flow loop. Laser Doppler Velocimetry (LDV) was used to measure shear stresses on the aortic surface of the valve leaflet. Two fluid shear stress experiments were run to understand the effects of hemodynamics on fluid shear stress: varying stroke volumes at a constant heart rate and varying heart beats at a constant stroke volume. As the stroke volume increased, fluid shear stresses increased due to the stronger sinus fluid motion. As the heart rate increased, fluid shear stresses decreased due to reduced systolic duration which restricted strong sinus flow formations. These results show that a higher heart rate can potentially elicit sclerotic responses from the AV and a higher velocity may reduce sclerotic responses from the AV. This data can be used to further understand AV biological response to shear stresses and to create improved computational simulations of flow dynamics in an aortic valve.

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The Navajo Concept of Wind

2011-05-09 , Hall, Della

Wind – in Navajo language – is most commonly referred to as nilch’i. In simple terms, nilch’i may be translated as “the wind,” or as “holy wind.” But that simple translation does not capture the word’s full meaning. For the Navajo, nilch’i is considered the means of life. It represents not only a god, or holy person, but also a means of communication, the act of breathing, and every Navajo’s soul. Wind is present in virtually all aspects of Navajo culture. For this conference paper I will be focusing on three key topics: birth, the inner-wind soul, and religion. By understanding how wind fits into each of these themes, one can better understand the complexity and importance of this abstract concept of Wind – for which there is no equivalent in non-Native American Indian cultures of America. My paper will contribute a more complete grasp of the concept of Navajo Wind.

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Determining the minimal covering set of parameter spaces for phenomenological gravitational waveforms

2011-05-09 , Burns,  Dustin

Gravitational wave observatories are now trying to detect gravitational waves, ripples in space time predicted by Einstein’s theory of General Relativity, from sources such as merging binary star and black hole systems. Numerical relativists create template banks of gravitational waves from merging black hole binaries in an effort to confirm a gravitational wave detection by solving Einstein’s field equations. These waveforms are then compared to the raw data collected by gravitational wave detectors. Since it is computationally expensive to produce the full numerical relativity waveforms, theorists have created approximation techniques called phenomenological waveforms, in which analytical functions approximate the numerical solutions over a finite space of parameters. It is computationally expensive to match the waveform template banks to the data from the observatories. In an effort to minimize the number of waveforms in the template banks, I determine the minimal covering set of the parameter space for non-spinning binary black hole phenomenological waveforms. This is accomplished by marching through a very fine mesh of the parameter space, ensuring that the match between adjacent waveforms is above a given threshold. I determine this minimal covering set for the non-spinning case and discuss how to generalize the program to the full spinning case.

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RNA-mediated double-stranded break repair in mammalian cells

2011-05-09 , Taylor, Matthew Bryce

This study seeks to examine the capability of RNA to introduce mutations into genomic DNA, and to provide insight into the enzyme(s) responsible for this phenomenon. To do this, a double-stranded break is induced in HEK 658D cells, and oligonucleotides containing RNA tracts with homology to the area around the break are introduced to examine if they can mediate repair of this area. In the first part of the study, oligonucleotides are introduced that contain a single-nucleotide substitution at the site of the break, and if the RNA is used as a template for repair, then this nucleotide should be incorporated into the genome of the cell. Oligonucleotides are introduced that contain either all-DNA, or DNA with a 6-nucleotide RNA tract at the break. These two classes of oligonucleotides are homologous to either the forward or reverse strands of the area around the break. This allows us to examine if there is a strand bias for repair, and if that bias is the same for DNA- and RNA-mediated repair, which will provide clues into the enzyme involved in repair.

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