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Multivariate Models And Algorithms For Systems Biology, Lipi Rani Acharya

University of New Orleans Theses and Dissertations

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete …

Mineralogy And Geochemistry Of Anorogenic Granitic Miarolitic Pegmatites Associated With The White Mountain Intrusive Suite, New Hampshire, Kristen F. Camp

University of New Orleans Theses and Dissertations

Subvolcanically emplaced granitic, miarolitic pegmatites associated with the White Mountain Igneous Province (WMIP), New Hampshire, were sampled and analyzed using modern analytical techniques including X-ray fluorescence, electron microprobe, scanning electron microscopy, and direct-coupled plasma spectrophotometry. Analytical results suggest that all the sampled miarolitic pegmatites from this study are petrogenetically related to the same intrusive suite, the WMIP. Based on the geochemical data, all the samples formed in an anorogenic tectonic setting and are rift-related. They are classified as NYF-type and plot in the “within plate granite” field on tectonic discrimination diagrams. The majority of the samples are peraluminous, A_{1 …}

Statistical Spectral Parameter Estimation Of Acoustic Signals With Applications To Byzantine Music, Kyriakos Michael Tsiappoutas

University of New Orleans Theses and Dissertations

Digitized acoustical signals of Byzantine music performed by Iakovos Nafpliotis are used to extract the fundamental frequency of each note of the diatonic scale. These empirical results are then contrasted to the theoretical suggestions and previous empirical findings. Several parametric and non-parametric spectral parameter estimation methods are implemented. These include: (1) Phase vocoder method, (2) McAulay-Quatieri method, (3) Levinson-Durbin algorithm,(4) YIN, (5) Quinn & Fernandes Estimator, (6) Pisarenko Frequency Estimator, (7) MUltiple SIgnal Characterization (MUSIC) algorithm, (8) Periodogram method, (9) Quinn & Fernandes Filtered Periodogram, (10) Rife & Vincent Estimator, and (11) the Fourier transform. Algorithm performance was very precise. …

Investigating The Thermal Stability And Cation Ordering In Layered Cathode Lixmo2 (X ≤ 1; M = Co, Mn, Ni) Materials For Li-Ion Rechargeable Batteries And Studying The Ferroelectric Properties Of Linbo3 Nanoparticles, Debasish Mohanty

University of New Orleans Theses and Dissertations

In recent years, transition metal oxides have drawn extensive attention because of their wide application in electronic, memory, battery, informatics, and optoelectronics devices. In this dissertation, we have studied two different types of oxide materials which are technologically important: LiMO 2 (M = Co, Mn, Ni), has served as cathode materials in the rechargeable battery, and LiNbO3, has wide application in ferroelectric devices such as electronics, non-volatile memories, and thin film capacitors. LiMO2 was synthesized and characterized to understand the correlation between capacity fading and thermal stability relating to the microstructures. Our results showed that delithiated (charged) LiCoO2, forms a …

Synthesis And Antifungal Evaluation Of Spirostane Saponins, Sunil Upadhyay

University of New Orleans Theses and Dissertations

Methods for the preparation of novel antifungal saponins have been investigated in

order to further explore their medicinal utility and provide the opportunity to synthesize

their derivatives.

Through this work, several partially protected stereoisomers of Cholestane,

Androstane and Spirostane have been prepared which could be used for the synthesis of

various saponin derivatives in order to discover novel saponin based antifungal agent.

Various mono and disaccharide derivatives of these steroids have been synthesized and

evaluated for their antifungal activity against four pathogenic fungal strains. Among the

various derivatives maltose derivatives were found to have the best antifungal activity.

However there …

Understanding Uplift Of The Ethiopian Plateau From Longitudinal Profile Analysis Of The Blue Nile Drainage System, Prabhat Chandra Neupane

University of New Orleans Theses and Dissertations

The Ethiopian Plateau is one of the few tectonically-active regions on Earth that is situated in continental rift zones. About 1.6 km deep gorge of the Nile was carved by the Blue Nile River on the Ethiopian Plateau, as the plateau has been experiencing continuous uplift and exhumation in the Cenozoic. Here, we used quantitative analysis of longitudinal rive-profile forms and parameters (knickpoint and normalized steepness-index k_sn) of the Blue Nile tributaries to tease out regional tectonic signals.

244 knickpoints were examined in the tributaries, majority (>80%) of which are unassociated with lithology or geological structures. Knickpoint …

Synthesis And Biological Evaluation Of Aeruginosin Based Compounds And Self-Assembly Of Glucosamine Based Compounds, Navneet Goyal

University of New Orleans Theses and Dissertations

Aeruginosins are a family of marine natural products containing mostly non-proteogenic amino acids. These compounds contain a common 2-carboxy-6-hydroxy-octaindole (Choi) rigid bicyclic structure. Many aeruginosins are inhibitors for enzymes involved in the blood coagulation cascade, such as thrombin and Factor VIIa. In order to understand the structure activity relationship (SAR) of the aeruginosins and to discover novel anticoagulants with potentially improved inhibitory and pharmacokinetic properties, in the first part of my thesis I have discussed, synthesis of a series of novel analogs of aeruginosin 298-A, in which the Choi will be replaced with L-proline and oxygenated Choi analogs, and the …

Android Memory Capture And Applications For Security And Privacy, Joseph T. Sylve

University of New Orleans Theses and Dissertations

The Android operating system is quickly becoming the most popular platform for mobiledevices. As Android’s use increases, so does the need for both forensic and privacy toolsdesigned for the platform. This thesis presents the first methodology and toolset for acquiringfull physical memory images from Android devices, a proposed methodology for forensicallysecuring both volatile and non-volatile storage, and details of a vulnerability discovered by theauthor that allows the bypass of the Android security model and enables applications to acquirearbitrary permissions.

Synthesis And Applications Of Luminescent Quantum Dots In Bioassays, Venkata Ramana Kethineedi

University of New Orleans Theses and Dissertations

Luminescent quantum dot (QD) based probes have gained significance in the last decade for optical imaging of cells, tissues and in bioassays as alternatives to conventional organic fluorophores. The main objective of my PhD dissertation was to develop luminescent quantum dot based bioassays for real time monitoring of enzyme activity and simultaneous detection of several biomarkers. The quantum dot based bioassays developed will be potential tools in identification and diagnosis of several ailments that interfere with normal living conditions of human beings.

In Chapter 2 new liposome encapsulated quantum dot based fluorescence resonance energy transfer (FRET) probes have been fabricated …

Development Of A Novel Electron-Transfer Secondary Reaction Matrix, Characterization Of The Site–Specificity Of Novel Bilin-Lyase, And Fundulus Grandis Protein Expression Investigation Using Mass Spectrometry, Mohamed N. Boutaghou

University of New Orleans Theses and Dissertations

Reported in this dissertation are the results of investigations performed at the New Orleans Center for Mass Spectrometry at the University of New Orleans. The projects that are detailed in the coming pages take on a variety of subjects, but a common thread is that each employs matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to solve a problem. Fundamental aspects of MALDI in-plume ionization are implicated in the introduction of a newly developed electron-transfer secondary ionization matrix. The remaining projects are related to the ever expanding field of proteomics. Mass spectrometry was used to investigate the site specificity of a newly …

A Dynamical Study Of The Evolution Of Pressure Waves Propagating Through A Semi-Infinite Region Of Homogeneous Gas Combustion Subject To A Time-Harmonic Signal At The Boundary, John Eslick

University of New Orleans Theses and Dissertations

In this dissertation, the evolution of a pressure wave driven by a harmonic signal on the boundary during gas combustion is studied. The problem is modeled by a nonlinear, hyperbolic partial differential equation. Steady-state behavior is investigated using the perturbation method to ensure that enough time has passed for any transient effects to have dissipated. The zeroth, first and second-order perturbation solutions are obtained and their moduli are plotted against frequency. It is seen that the first and second-order corrections have unique maxima that shift to the right as the frequency decreases and to the left as the frequency increases. …

Self-Assemblies Driven By The Hydrophobic Effect, Haiying Gan

University of New Orleans Theses and Dissertations

Water is a simple molecule but is an essential part of life. One key aspect of the properties of water is the hydrophobic effect, and whilst there is an appreciation of this phenomenon at the macro-scale (raindrops falling off leaves) and the micro-scale (the structure of cellular systems), a complete understanding at the molecular level still eludes science. Addressing this issue, our studies involve synthetic supramolecular compounds that assemble in water via the hydrophobic effect.

First of all, a novel water-soluble deep-cavity cavitand was synthesized. It possesses four endo methyl groups on top rim of the cavitand, eight water-solubilizing carboxylic …

Exchange Flows In An Urban Water Body: Bayou St. John Responses To The Removal Of Flood Control Structures, Future Water Elevation Control, And Water Quality, Robin L. Schroeder

University of New Orleans Theses and Dissertations

Bayou St. John, an urban water body extending south from Lake Pontchartrain, has two anthropogenic structures that regulate flow from the Lake . The City of New Orleans has plans to remove the inner control structure to improve water quality. Field and numerical methods used in this study show removing this structure increased water elevations throughout the Bayou but resulted in lower water elevation signal amplitudes that caused a lower tidal flow exchange from north to south. Bulk Richardson numbers showed mixing was inversely related to flow and the Bayou generally remains stratified. Resuspension of contaminated sediment could negatively impact …

Water In Protein Cavities: Free Energy, Entropy, Enthalpy, And Its Influences On Protein Structure And Flexibility, Hongtao Yu

University of New Orleans Theses and Dissertations

Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistantto novobiocin as well as those with a decreased affinity for novobiocin over clorobiocinboth involve a less favorable entropy of binding, which more than compensates for amore favorable enthalpy, and additional water molecules at the proteinligandinterface.Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamicintegration computer simulations. The calculations show that addition of thewater molecules is entropically unfavorable, with values that are comparable to the measuredentropy differences. The free energies and entropies correlate with the …

Towards The Synthesis Of Magnesidin, Subramanya Pingali

University of New Orleans Theses and Dissertations

Magnesidin is a magnesium chelate of the 3-hexanoyl and 3-octanoyl tetramic acid derivatives isolated from Psuedomonas magensiorubra. Its activity against grampositive bacteria was found to be a specific target for Gingivitis, a dental plaque.Although the synthesis of magnesidin has been reported earlier, it was not reproducible. The highly polar nature and it’s ability to exhibit tautomerization makes their chemical behavior complex and difficult to predict its structure. A variety of reactions and an in depth understanding of the chemical structure is necessary to attain the synthesis of these compounds. This dissertation focuses on addressing the attempts towards the synthesis …

Synthesis Of Chiral Intermediates By Deritivization Of Monosaccharides, Sanjeeva Dodlapati

University of New Orleans Theses and Dissertations

Conformationally constrained bicyclic amino acids are invaluable in the synthesis of natural products and peptidomimetics. Aeruginosins contain novel bicyclic amino acid, 2--‐carboxy--‐6--‐hydroxyl octahydrindole (Choi) as the core structure. Aeruginosins are tetra peptide serine protease inhibitors isolated from marine sponges and cyanobacterial water blooms. Rigid bicyclic amino acid(Choi)is an essential core structure, which strongly influences biological activity of aeruginosin family members. Aeruginosins showed promising inhibitory activity against thrombin, trypsin, and factor VIIa. Thrombin and factor VIIa play a major role in blood clotting cascade; excessive coagulation leads to thrombosis and other cardiovascular diseases. Several research groups have reported a number of …

Computational Pipeline For Human Transcriptome Quantification Using Rna-Seq Data, Guorong Xu

University of New Orleans Theses and Dissertations

The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently access essential information from NGS data files in SAM/BAM format, we have …

Thermoelectric Properties Of Zr0.5hf0.5ni1-Xpdxsn0.99sb0.01 And Effect Of Nanoinclusions On Transport Properties Of Half Heuslers, Rumana Yaqub

University of New Orleans Theses and Dissertations

Thermoelectric materials convert temperature gradients into electricity and vice-versa. These materials utilize the Seebeck effect for power generation and function without moving parts and are highly reliable. The efficiency of thermoelectric devices is related to the dimensionless figure of merit for the constituent materials, defined as where S is the Seebeck coefficient, is the electrical conductivity, is the thermal conductivity and T is the temperature. Maximizing ZT is very challenging because of interdependence of parameters, for example, increasing the electrical conductivity by increasing the carrier concentration invariably lowers S and vice versa. Presently numerous thermoelectric materials are being investigated by …

Synthesis And Characterization Of Nanostructures In Porous Anodic Aluminum Oxide Templates, Jin-Hee Lim

University of New Orleans Theses and Dissertations

In this study, template-based methods are used for the fabrication of various nanostructures such as nandots, nanorods, nanowires, nanotubes, and core-shell structures. Porous alumina membranes were employed as templates and metal nanostructures were synthesized in the templates by electrodeposition. By using lithography techniques, controlled patterned nanostructures were also fabricated on alumina templates. The magnetic properties of the various metal nanostructures were investigated. The pore size, interpore distance, and pore geometry highly affect magnetic properties of nanostructures grown in the templates. Hexagonally ordered porous alumina templates can be fabricated by two-step anodization. The pore diameters and interpore distances were readily controlled …

Pulsed Laser Deposition Of Thin Film Heterostructures, Ezra Garza

University of New Orleans Theses and Dissertations

Thin films of Strontium Ruthenate have been grown on Strontium Titanate and Lanthanum Aluminate (100) substrates by pulsed laser deposition. X-ray diffraction results show that the films grown on the Strontium Titanate are amorphous and polycrystalline on the Lanthanum Aluminate. Resistances versus temperature measurements show that the films exhibit semiconducting characteristics. In addition to the growth of Strontium Ruthenate thin films, multilayer heterostructures of Terfenol-D thin films on polycrystalline Lead Titanate thin films were grown by pulsed laser deposition. By using a novel experimental technique called magnetic field assisted piezoelectric force microscopy it is possible to investigate the magnetoelectric coupling …

Subsurface Controls On Mainland Marsh Shoreline Response During Barrier Island Transgressive Submergence, Mary Ellison

University of New Orleans Theses and Dissertations

Many recent studies have sought to understand the response of barrier islands and their attendant marshes to sea level rise. The Mississippi River delta plain, specifically the Chandeleur Islands and associated interior wetlands in eastern Louisiana, serves as an excellent natural laboratory for studying these responses. This region is presently undergoing the highest rates of shoreline erosion (> 15 m yr -1) in North America as wetlands are converted to open water in a regime of subsidence-driven rapid relative sea-level rise (~1 cm yr-1). Three conceptual models were developed based on the geomorphic relationships observed in the marsh that describe …

Enhancing The Verification-Driven Learning Model For Data Structures With Visualization, Yashwanth Reddy Kondeti

University of New Orleans Theses and Dissertations

The thesis aims at teaching various data structures algorithms using the Visualization Learning tool. The main objective of the work is to provide a learning opportunity for novice computer science students to gain a broader exposure towards data structure programming. The visualization learning tool is based on the Verification-Driven Learning model developed for software engineering. The tool serves as a platform for demonstrating visualizations of various data structures algorithms. All the visualizations are designed to emphasize the important operational features of various data structures. The learning tool encourages students into learning data structures by designing Learning Cases. The Learning Cases …

Sea: A Novel Computational And Gui Software Pipeline For Detecting Activated Biological Sub-Pathways, Thair Judeh

University of New Orleans Theses and Dissertations

With the ever increasing amount of high-throughput molecular profile data, biologists need versatile tools to enable them to quickly and succinctly analyze their data. Furthermore, pathway databases have grown increasingly robust with the KEGG database at the forefront. Previous tools have color-coded the genes on different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure Enrichment Analysis (SEA) thus seeks to take biological analysis to the next level. SEA accomplishes this goal by highlighting for users the sub-pathways of a biological pathways that best correspond to their molecular profile …

Topochemical Manipulation Of Layered Perovskites, Elisha A. Josepha

University of New Orleans Theses and Dissertations

Topochemical strategies, techniques that allow one to effectively manipulate the structures of nonmolecular solids once a crystal lattice is established, are effective in the low temperature (< 500 °C) modification of solid state structures, allowing the preparation of nonmolecular compounds not accessible by standard synthetic routes. Some of the techniques, ion exchange, intercalation/deintercalation, have proven to be excellent synthetic methods for preserving specific frameworks. The combination of these techniques can allow one to create a multistep approach that can be used to design new compounds with interesting properties.

As an expansion to the field of topotactic reactions, a multistep approach was developed towards the synthesis of the new compounds (A xM0.5Cly)LaNb2O7 (where A = Rb, Cs; M = Fe, Ni; x ≈ 1.5;y ≈ 1) at temperatures below 400oC. The first reaction step involved the ion exchange of the host materials (ALaNb2O7, A = Rb, Cs) to form the products M0.5LaNb2O7 (where M = Fe, Ni), a structure open to further …