Digital Commons Network^™

Bioinformatics Study Of Mammalian Mrna Polydenylation, Haibo Zhang

Dissertations

Messenger RNA polyadenylation is one of the key post-transcriptional events in mammalian cells, which have influences on many aspects of mRNA metabolism. Several human diseases have been shown to associate with abnormal polyadenylation, highlighting the importance of this process. The availability of the complete sequence of human and mouse genomes, together with their gene expression data provides valuable resources to study mRNA polyadenylation on a system level. This dissertation addresses the following issues of mammalian mRNA polyadenylation through bioinformatics approaches: (1) the extensive documentation of several key aspects of polyadenylation sites in humans and mice on a genomic level; (2) …

Gas Fluidization Of Nanoparticles, Qun Yu

Dissertations

The primary objective of this study is to perform a systematic investigation on the gas fluidization of various nanoparticle agglomerates. Firstly, the gas fluidization characteristics and regime classifications without any additional external force fields are identified using both experimental measurements and modeling. Secondly, the effect of introducing certain external force fields on nanoparticle fluidization is experimentally investigated. Two external force fields were applied: sound waves from a loud speaker (acoustic assistance) and in-bed magnets that were excited by an external oscillating magnetic field (magnetic assistance). Thirdly, exploratory experimental research on the use of nanoparticle agglomerates as a granular filtration media …

Electromagnetic And Acoustic Propagation In Strip Lines And Porous Media, Lin Zhou

Dissertations

Wave propagation in two physical structures is described and analyzed in this dissertation. In the first problem, the propagation of a normally incident plane acoustic wave through a three dimensional rigid slab with periodically placed holes is modeled and analyzed. The spacing of the holes A and B, the wavelength λ and the thickness of the slab L are order one parameters compared to the characteristic size D of the holes, which is a small quantity. Scattering matrix techniques are used to derive expressions for the transmission and reflection coefficients of the lowest mode. These expressions depend only on the …

Algorithms And Complexity Analyses For Some Combinational Optimization Problems, Hairong Zhao

Dissertations

The main focus of this dissertation is on classical combinatorial optimization problems in two important areas: scheduling and network design.

In the area of scheduling, the main interest is in problems in the master-slave model. In this model, each machine is either a master machine or a slave machine. Each job is associated with a preprocessing task, a slave task and a postprocessing task that must be executed in this order. Each slave task has a dedicated slave machine. All the preprocessing and postprocessing tasks share a single master machine or the same set of master machines. A job may …

Just-In-Time Hypermedia, Li Zhang

Dissertations

Many analytical applications, especially legacy systems, create documents and display screens in response to user queries "dynamically" or in real time . These documents and displays do not exist in advance, and thus hypermedia must be generated 'just in time" -automatically and dynamically.

This dissertation details the idea of 'just-in-time" hypermedia and discusses challenges encountered in this research area. A fully detailed literature review about the research issues and related research work is given. A framework for the 'just-in-time" hypermedia compares virtual documents with static documents, as well as dynamic with static hypermedia functionality. Conceptual 'just-in-time" hypermedia architecture is proposed …

High-Dimensional Indexing Methods Utilizing Clustering And Dimensionality Reduction, Lijuan Zhang

Dissertations

The emergence of novel database applications has resulted in the prevalence of a new paradigm for similarity search. These applications include multimedia databases, medical imaging databases, time series databases, DNA and protein sequence databases, and many others. Features of data objects are extracted and transformed into high-dimensional data points. Searching for objects becomes a search on points in the high-dimensional feature space. The dissimilarity between two objects is determined by the distance between two feature vectors. Similarity search is usually implemented as nearest neighbor search in feature vector spaces. The cost of processing k-nearest neighbor (k-NN) queries via a sequential …

Improving Document Representation By Accumulating Relevance Feedback : The Relevance Feedback Accumulation (Rfa) Algorithm, Razvan Stefan Bot

Dissertations

Document representation (indexing) techniques are dominated by variants of the term-frequency analysis approach, based on the assumption that the more occurrences a term has throughout a document the more important the term is in that document. Inherent drawbacks associated with this approach include: poor index quality, high document representation size and the word mismatch problem. To tackle these drawbacks, a document representation improvement method called the Relevance Feedback Accumulation (RFA) algorithm is presented. The algorithm provides a mechanism to continuously accumulate relevance assessments over time and across users. It also provides a document representation modification function, or document representation learning …

The Control Of Frequency Of A Conditional Oscillator Simultaneously Subjected To Multiple Oscillatory Inputs, Christina L. Ambrosio

Dissertations

A conditional oscillator is one that requires input to oscillate. An example of such is the gastric mill network of the stomatogastric ganglion of the crab Cancer borealis which requires modulatory input from outside the stomatogastric ganglion and fast input from the pyloric network of the animal in order to become active. This dissertation studies how the frequency of the gastric mill network is determined when it is simultaneously subjected to two different rhythmic inputs whose timing may be mismatched. We derive a mathematical model of the gastric mill network and deduce that the difference in timing between the pyloric …

A Versatile Programming Model For Dynamic Task Scheduling On Cluster Computers, Dejiang Jin

Dissertations

This dissertation studies the development of application programs for parallel and distributed computer systems, especially PC clusters. A methodology is proposed to increase the efficiency of code development, the productivity of programmers and enhance performance of executing the developed programs on PC clusters while facilitating improvement of scalability and code portability of these programs. A new programming model, named the Super-Programming Model (SPM), is created. Programs are developed assuming an instruction set architecture comprised of SuperInstructions (SIs). SPM models the target system as a large Virtual Machine (VM); VM contains functional units which are underlain with sub-computer systems and SIs …

Order Scheduling In Dedicated And Flexible Machine Environments, Haibing Li

Dissertations

Order scheduling models are relatively new in the field of scheduling. Consider a facility with m parallel machines that can process k different products (job types). Each machine can process a given subset of different product types. There are n orders from n different clients. Each order requests specific quantities of the various different products that can be produced concurrently on their given subsets of machines; it may have a release date, a weight and a due date. Preemptions may be allowed. An order can not be shipped until the processing of all the products for the order has been …

Utility Of Remote Sensing Data In Retrieval Of Water Quality Consituents Concentrations In Coastal Water Of New Jersey, Ting Yu

Dissertations

Three important optical properties used for monitoring coastal water quality are the concentrations of chlorophyll (CHL), color dissolved organic matter (CDOM) and total suspended materials (TSM). Ocean color remote sensing, a technique to collect color data by detection of upward radiance from a distance (Bukata et al.,1995), provides a synoptic view for determining these concentrations from upwelling radiances. In the open ocean (Case-I), it is not difficult to derive empirical algorithms relating the received radiances to surface concentrations of water quality parameters. In coastal waters (Case-Il), there are serious unresolved problems in extracting chlorophyll concentration because of high concentration of …

Tcp Performance Enhancement In Wireless Networks Via Adaptive Congestion Control And Active Queue Management, Kai Xu

Dissertations

The transmission control protocol (TCP) exhibits poor performance when used in error-prone wireless networks. Remedy to this problem has been an active research area. However, a widely accepted and adopted solution is yet to emerge. Difficulties of an acceptable solution lie in the areas of compatibility, scalability, computational complexity and the involvement of intermediate routers and switches.

This dissertation rexriews the current start-of-the-art solutions to TCP performance enhancement, and pursues an end-to-end solution framework to the problem. The most noticeable cause of the performance degradation of TCP in wireless networks is the higher packet loss rate as compared to that …

Stereo Vision Algorithm Using Propagation Of Correspondences Along An Array Of Cameras, Danyan Ganjali

Theses

One well known problem in stereo vision is the trade-off between precision and accuracy.

In a conventional two camera model, as the baseline separating the two cameras becomes smaller, the images that both cameras produce become more identical. This results in a more accurate set of correspondences, however at the same time causing less precise depth measurement due to the small angle used for triangulation. Similarly, in a larger baseline model, the depth measurement is more precise while the correspondences are not as accurate as of the shorter baseline model. This thesis proposes a method that promises to solve the …

Sharing The Big Apple : A Survey Study Of People, Place And Locatability, Samer Nadim Karam

Theses

Over the past half century social trends and new technologies have weakened local social ties and thus, the fabric of civil society itself. Mobile location-aware community systems offer one path to redress these problems by enhancing community cohesion and the formation of social capital by helping people to meet each other and coordinate their actions. However, little is known about the general population's desire and attitude towards these systems.

The design space described by the People-to-People-to-Geographical-Places Framework (P3-Framework), was used to guide a survey study of the impact of 'place' on people's social information needs and their willingness to share …

Structure And Dynamics Of Soluble Guanylyl Cyclase, Kentaro Sugino

Theses

Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation.

From these MD simulations, a tentative mechanism of sGC activation …

Rebuild Performance Enhancement Using Onboard Caching And Delayed Vacation Termination In Clustered Raid 5, Akheel Ahmed

Theses

The Clustered Raid 5 (CRAID5) architecture with a parity group size(G) smaller than the number of disks(N) increases the load by the declustering ratio denoted by α = (G -1)/(N -1), which can be lesser than that in Raid 5 while switching to, and subsequently operating in rebuild mode. The Nearly Random Permutation (NRP) layout provides the flexibility to vary the declustering ratio (α) for a given N, and the Vacationing Server Model (VSM) of processing the rebuild requests provides acceptable rebuild and user response times.

The rebuild performance and the user response time can be improved by introducing an …

Short-Term Effects Of Bulkheads On The Bayshore Of Fire Island, New York, Dipanjali Chavan

Theses

Construction of bulkheads as a method of shore protection is common on the bay shoreline of Fire Island, New York but there are few studies that assess the effects of these structures on beach change in estuarine and lagoon environments. A short-term field study was conducted at Cherry Grove on Fire Island to assess the effect of a bulkhead on the fronting profile and to the adjacent beaches on the east side of the bulkhead. Data on winds, waves, and currents were gathered daily at high water. Data on profile change and depth of sediment activation were gathered at low …

Relationship Between The Autonomic Nervous System And The Recovering Heart Post Exercise Using Heart Rate Variability, Pierre Asselin

Theses

The goal of this thesis is to determine if a relationship exists between the activity of the autonomic nervous system (ANS) and the speed of heart rate recovery post maximal exercise. The parasympathetic branch of the ANS was assessed during rest by obtaining the high frequency (HF) component of the heart rate variability (HRV) frequency spectrum. The recovery time was estimated by fitting an exponential curve to the heart rate post exercise where the exponent was used to calculate the time constant to indicate recovery time. A regression was then performed on the HF and recovery time in order to …

Difference-Expansion Based Reversible Data Hiding And Its Steganalysis, Guangsen Tian

Theses

A novel reversible data embedding method was reported in a recent IEEE journal article. The method was based on difference expansion (DE) technique. It used redundancy in digital images to achieve a high embedding capacity, while keeping visual distortion of the stego-image low. In this thesis, this technique was studied and experimentally evaluated. An effective steganalysis scheme for this DE-based reversible data embedding method was proposed, which used 12-dimensional feature vectors and a Bayes Classifier. The proposed steganalysis scheme steadily achieved a correct classification rate of 99%.

Analysis Of Acceleration And Deceleration During Cyclic Exercise, Jeena Vadi

Theses

The Cyclic Exercise Protocol is a novel protocol that is designed to create a series of cyclic waves of exercise and recovery. This exercise protocol involves short bursts of exercise lasting for 60 seconds or less followed by a period of complete cardio recovery. This study involves the analysis of the acceleration and the deceleration regions of the cyclic exercise sessions. The objective of this study was to develop an algorithm to quantitatively analyze the acceleration and the deceleration regions of cyclic exercise sessions. The acceleration and the deceleration regions of cycles were split into three segments and each segment …

Approximation Algorithms For Variants Of The Traveling Salesman Problem, Ankur Gupta

Theses

The traveling salesman problem, hereafter abbreviated and referred to as TSP, is a very well known NP-optimization problem and is one of the most widely researched problems in computer science. Classical TSP is one of the original NP - hard problems [1]. It is also known to be NP - hard to approximate within any factor and thus there is no approximation algorithm for TSP for general graphs, unless P = NP. However, given the added constraint that edges of the graph observe triangle inequality, it has been shown that it is possible achieve a good approximation to the optimal …

Hybrid Explicit-Implicit Fdtd-Fem Time-Domain Solver For Electromagnetic Problems, Kakhkhor Abdijalilov

Dissertations

The Finite-Difference Time-Domain (FDTD) method and Finite-Element (FEM) method are numerical techniques used for solving Maxwell's electromagnetic equations. FDTD-FEM hybrid methods opt for combining the advantages of both FDTD and FEM. In this dissertation, signal processing techniques were used to analyze the FDTD stability condition. A procedure, which reduces time-sampling error yet preserves the stability of algorithm is proposed. Both explicit and implicit time-stepping schemes were treated in the framework of the developed method. An improved version of the implicit-explicit FEM-FDTD hybrid method was developed. The new method minimizes reflection from the interface between different types of grids. A class …

Characteristics Of Nanocomposites And Semiconductor Heterostructure Wafers Using Thz Spectroscopy, Hakan Altan

Dissertations

All optical, THz-Time Domain Spectroscopic (THz-TDS) methods were employed towards determining the electrical characteristics of Single Walled Carbon Nanotubes, Ion Implanted Si nanoclusters and Si_1-xGe_x HFO₂, SiO₂ on p-type Si wafers.

For the nanoscale composite materials, Visible Pump/THz Probe spectroscopy measurements were performed after observing that the samples were not sensitive to the THz radiation alone. The results suggest that the photoexcited nanotubes exhibit localized transport due to Lorentz-type photo-induced localized states from 0.2 to 0.7THz. The THz transmission is modeled through the photoexcited layer with an effective dielectric constant described by a Drude …

Negotiation Of Software Requirements In An Asynchronous Collaborative Environment, Catherine Lowry Campbell

Dissertations

The effect of task structure and negotiation sequence on collaborative software requirements negotiation is investigated. This work began with an extensive literature review that focused on current research in collaborative software engineering and, in particular, on the negotiation of software requirements and the requisite collaboration for the development of such requirements. A formal detailed experiment was then conducted to evaluate the effects of negotiation sequence and task structure in an asynchronous group meeting environment. The experiment tested the impact of these structures on groups negotiating the requirements for an emergency response information system. The results reported here show that these …

Corrosion Studies On Alpha Tantalum And Beta Tantalum Coated Steel, Sung Min Maeng

Dissertations

Tantalum coating by sputtering, one form of physical vapor deposition (PVD), has been investigated as a replacement for chromium coatings on gun bores to protect them from erosion and corrosion due to its high ductility and high corrosion resistance in aggressive environments. When deposited as a film on steel substrates by sputtering, either α-Ta, β-Ta, or a mixture of both phases have been observed under varying deposition conditions. To evaluate corrosion behavior of Ta coatings, electrochemical impedance spectroscopy and potentiodynamic polarization were conducted as a function of coating thickness. The coating porosity was observed to decrease with increasing coating thickness …

Bus Arrival Time Prediction Using Stochastic Time Series And Markov Chains, Rajat Rajbhandari

Dissertations

Public transit agencies rely on disseminating accurate and reliable information to transit users to achieve higher service quality and attract more users. With the development of new technologies, the concept of providing users with reliable information about bus arrival times at bus stops has become increasingly attractive. Due to the fact that bus operation parameters and variables are highly stochastic, modeling prediction of bus travel and arrival times has become one of the many challenging tasks.

Stochastic time series and delay propagation models to predict bus arrival times using historical information were developed. Markov models were developed to predict propagation …

Characterizing The Evolution Of Operating Systems, Yi Peng

Dissertations

Examining the development and trends in software engineering technology is a huge undertaking. It is constantly evolving and affected by a large number of factors, which are themselves driven by a wide range of sub-factors. This dissertation is part of a long term project intended to analyze software engineering technology trends and how they evolve. This project is intended to analyze operating system trends and what are the factors that drive how they evolve. Basically, the following questions will be answered: "How to watch, predict, adapt to, and affect operating system's evolution trends?"

In previous research, YF Chen used statistical …

Computational Studies Of Viscoelastic Multiphase Flows, Shriram B. Pillapakkam

Dissertations

A finite element code based on the level set method is developed for performing two and three dimensional direct numerical simulations (DNS) of viscoelastic two-phase flow problems. The Oldroyd-B constitutive equation is used to model the viscoelastic liquid. The code is used to study transient and steady state shapes of Newtonian and viscoelastic drops in simple shear and buoyancy driven flows. The roles of the governing dimensionless parameters: Capillary number (Ca), Deborah Number (De) and the polymer concentration parameter c, in determining deformation of drops and bubbles, are also analyzed.

The numerical code permits us to vary Ca, De and …

Live, Virtual, And Constructive Environments For Performance Support, John Michael Lacontora

Dissertations

As military systems become more complex, the operation and support of these systems becomes intrinsically more difficult. The U.S. Army's current procurement process relies on industry to provide embedded training and performance support tools for the systems they produce. These tools are relatively new and in the early stages of development. As yet, they have failed to meet the needs of the technicians that are required to support these complex systems. Current efforts to provide enabling technologies that enhance the capabilities of automotive maintenance technicians are concentrated in three professional communities. First is the Performance Improvement community where work is …

Pattern Discovery In Structural Databases With Applications To Bioinformatics, Sen Zhang

Dissertations

Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in structural data such as trees and graphs. FSM finds many applications in bioinformatics, XML processing, Web log analysis, and so on. In this thesis, two new FSM techniques are proposed for finding patterns in unordered labeled trees. Such trees can be used to model evolutionary histories of different species, among others.

The first FSM technique finds cousin pairs in the trees. A cousin pair is a pair of nodes sharing the same parent, the same grandparent, or the same great-grandparent, etc. Given a tree T, our …