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Efficient Algorithms For Improving The Accuracy In Motifs Prediction, Jerlin C. Merlin

Master's Theses

Analysis of sequence homology has always played a major role in the understanding of biological factors such as protein domain identification, gene product relationships, and gene function determination. Short contiguous protein sequences that are conserved across proteins provide important information about such factors, and are of at most 15 residues in length. These segments of proteins are known as minimotifs. Identifying minimotifs has been of much use in the formulation of the hypothesis about the biological functions that otherwise might be uncharacterized. Mechanisms of motif predictions such as Minimotif Miner are widely used for predicting minimotifs. However, due to the …

Active Storage And Ssd Caching In An Object Storage Environment, Michael T. Runde

Master's Theses

The advancing performance and lowering costs required to implement additional processing power on system peripherals such as disk drives are increasingly allowing additional computing ability to be located directly on individual drives. Active Storage attempts to take advantage of this excess by moving some computationally intensive applications directly to the disk drives. This can remove the bottlenecks seen through interconnects between the drives and the CPU of an initiating system as well as remove the need for systems to handle these applications.

The contributions of this thesis are in two areas. The first is the development of a framework designed …

Computational Modeling For Transportation Network Security, Sherif A. Tolba

Master's Theses

No abstract provided.

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …

Automation Of Orthodontic Wire Tester For Performing Three Point Bending Tests, Adithya Venkatesan

Master's Theses

Abstract

Understanding the biomechanical factors in orthodontics is important in order to improve the overall effectiveness of actual clinical treatment. An accurate method to study the threedimensional (3D) force systems and the resulting movements of teeth during orthodontic treatment is needed along with the understanding of the material properties of any orthodontic wire. Until recently, most of the orthodontic biomechanics literature was limited to twodimensional experimental studies. Recent advances in threedimensional computer modeling have also been developed but have been limited to the manual control of tooth movement. Overall, there is very little published evidence in the literature on the …

Public Transit Accessibility And Need Indices: Approaches For Measuring Service Gap, Sha Mamun

Master's Theses

The integration of transit needs into transit accessibility indexing is important for the evaluation of existing transportation systems and, service gaps, and for the identification of priority areas for future investments in transportation infrastructure. This thesis details an accessibility-based transit need indexing model that focuses on the necessity of evaluating transit needs and transit accessibility simultaneously. A need index is developed to identify areas in high need of public transit services using economic and socio-demographic information and a composite accessibility index is developed to identify levels of access to transit services and shortcomings in service provision. The need for transit …

Robust Region Tracking In Multi-Agent Systems Utilizing Sliding Mode Control: Theory And Applications, Mark Bacon

Master's Theses

This thesis presents a methodology to bring controlled agents within a moving region despite agent interaction dynamics, uncertain forces and parameter variation. The logic is derived from traditional Sliding Mode Control theory with an expanded boundary layer which allows position deviation from the region center to specified bounds. As an example of the utility of this control, multiple methods of herding (controlling passive agents by appropriate positioning of controlled agents) are presented.