Physical Sciences and Mathematics Commons^™

Pattern Discovery In Dna Using Stochastic Automata, Shweta Shweta

Master's Projects

We consider the problem of identifying similarities between different species of DNA. To do this we infer a stochastic finite automata from a given training data and compare it with a test data. The training and test data consist of DNA sequence of different species. Our method first identifies sentences in DNA. To identify sentences we read DNA sequence one character at a time, 3 characters form a codon and codons form proteins (also known as amino acid chains).Each amino acid in proteins belongs to a group. In total we have 5 groups’ polar, non-polar, acidic, basic and stop codons. …

A Desert In Disguise: The Resilience Of The Nebraska Sandhills, Jeff Hartman

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Sandhills are the largest sand dune system in the Western Hemisphere, and are unique because they remain relatively undisturbed from row crop agriculture. Research in the past two decades demonstrated that the Sandhills are dynamic on millennial timescales, switching between stabilized, vegetated states to non-vegetated, mobilized states. The Sandhills are currently stabilized, but understanding how ecological processes are altered as sand dunes transition from stabilized to mobilized states, provides insight into the thresholds, stability, and resilience of this grassland ecosystem. My research investigated the impacts of vegetation disturbances on ecological processes and the sand dune surface stability. For …

Phosphorus Release Potential Of Agricultural Soils Of The United States, Rebecca A. Young

School of Natural Resources: Dissertations, Theses, and Student Research

Phosphorus (P) is one of the leading causes of surface water quality decline in the United States, leading to algal blooms and hypoxia in lakes and streams. Decreasing conservation funds dictate that agencies such as the Natural Resources Conservation Service, maximizes its effectiveness and efficiency in implementing practices to address P management and runoff on agricultural lands. Additional information on P behavior in soil is needed to improve P management plans to reduce pollution risk at the watershed, farm, and field scales. This research focuses on the development of total soil P release models, to be included into assessment and …

Characterizing Far-Infrared Laser Emissions And The Measurement Of Their Frequencies, Michael Jackson, Lyndon R. Zink

All Faculty Scholarship for the College of the Sciences

The generation and subsequent measurement of far-infrared radiation has found numerous applications in high-resolution spectroscopy, radioastronomy, and Terahertz imaging. For about 45 years, the generation of coherent, far-infrared radiation has been accomplished using the optically pumped molecular laser. Once far-infrared laser radiation is detected, the frequencies of these laser emissions are measured using a three-laser heterodyne technique. With this technique, the unknown frequency from the optically pumped molecular laser is mixed with the difference frequency between two stabilized, infrared reference frequencies. These reference frequencies are generated by independent carbon dioxide lasers, each stabilized using the fluorescence signal from an external, …

Bodipy-Based Fluorescent Probes For Sensing Protein Surface-Hydrophobicity, Nethaniah Dorh, Shilei Zhu, Kamal B. Dhungana, Ranjit Pati, Fen-Tair Luo, Haiying Liu, Ashutosh Tiwari

Department of Chemistry Publications

Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors …

Computation Of A Virtual Tide Corrector To Support Vertical Adjustment Of Autonomous Underwater Vehicle Multibeam Sonar Data, Lawrence H. Haselmaier

University of New Orleans Theses and Dissertations

One challenge for Autonomous Underwater Vehicle (AUV) multibeam surveying is the limited ability to assess internal vertical agreement rapidly and reliably. Applying an external ellipsoid reference to AUV multibeam data would allow for field comparisons. A method is established to merge ellipsoid height (EH) data collected by a surface vessel in close proximity to the AUV. The method is demonstrated over multiple collection missions in two separate areas. Virtual tide corrector values are derived using EH data collected by a boat and a measured ellipsoid to chart datum separation distance. Those values are compared to measurements by a traditional tide …

Response Of Fishes To Restoration Projects In Bayou St. John Located Within The City Of New Orleans, Louisiana, Including Hydrological Characterization And Hydrodynamic Modelling, Patrick W. Smith

University of New Orleans Theses and Dissertations

Quantifying the impacts of restoration on coastal waterways is crucial to understanding their effectiveness. Here, I look at the impacts of multiple restoration projects on urban waterways within the city limits of New Orleans, LA, with an emphasis on the response of fishes. First I report the effects of two projects designed to improve exchange down estuary on the hydrologic characteristics of Bayou St. John (BSJ). Within BSJ, flow is dominated by subtidal wind driven processes. Removal of an outdated flood control structure did not appear to alter exchange in BSJ, but removal combined with sector gate openings did. I …

Optimizing A Game Of Chinese Checkers, Nicholas Fonseca

Honors Program Theses and Projects

Chinese Checkers is a multi-player strategy game in which game play can become surprising complex as the game progresses. In spite of this game's complexity, questions involving games with multiple players have received little research attention. This paper considers the three player case and discusses how to describe short games. By utilizing these tendencies for short games, a heuristic function can be defined which associates a player's possible move with a heuristic value. These heuristic values guide a search algorithm which searches through all the possible moves made in a game. To guide this discussion for three player games, the …

Speedups And Orbit Equivalence Of Finite Extensions Of Ergodic Zᵈ-Actions, Aimee S.A. Johnson, D. M. Mcclendon

Mathematics & Statistics Faculty Works

We classify n-point extensions of ergodic Zᵈ-actions up to relative orbit equivalence and establish criteria under which one n-point extension of an ergodic Zᵈ-action can be sped up to be relatively isomorphic to an n-point extension of another ergodic Zᵈ-action. Both results are characterized in terms of an algebraic object associated to each n-point extension which is a conjugacy class of subgroups of the symmetric group on n elements.

Postural Responses To Perturbations Of The Vestibular System During Walking In Healthy Young And Older Adults, Jung Hung Chien

Theses & Dissertations

It has been shown that approximate one-third of US adults aged 40 years and older (69 million US citizens) have some type of vestibular problems. These declining abilities of the vestibular system affect quality of life. Difficulties in performing daily activities (dressing, bathing, getting in and out of the bed and etc.) have been highly correlated to loss of balance due to vestibular disorders. The exact number of people affected by vestibular disorders is still difficult to quantify. This might be because symptoms are difficult to describe and differences exist in the qualifying criteria within and across studies. Thus, it …

Monitoring Biodiversity Of San Francisco Peninsula Grasslands Using Lepidoptera As A Bioindicator, Jonathan B. Sifuentes-Winter

Master's Projects and Capstones

San Francisco Peninsula grasslands have seen an influx of non-native invasive species starting in the 1500’s, threatening ecological stability by reducing biological diversity. To combat these invasive species, multiple public agencies have begun to adopt an integrated pest management (IPM) approach. This ecologically-based approach to pest management utilizes three controversial techniques, which are presently used or are under consideration for use on the San Francisco Peninsula: herbicide application, conservation grazing, and prescribed fire. In this paper, I will evaluate the use of the taxa Lepidoptera as a bioindicator of biodiversity to assess the environmental impacts of these techniques. The application …

Email Similarity Matching And Automatic Reply Generation Using Statistical Topic Modeling And Machine Learning, Zachery L. Schiller

Electronic Theses and Dissertations

Responding to email is a time-consuming task that is a requirement for most professions. Many people find themselves answering the same questions over and over, repeatedly replying with answers they have written previously either in whole or in part. In this thesis, the Automatic Mail Reply (AMR) system is implemented to help with repeated email response creation. The system uses past email interactions and, through unsupervised statistical learning, attempts to recover relevant information to give to the user to assist in writing their reply.

Three statistical learning models, term frequency-inverse document frequency (tf-idf), Latent Semantic Analysis (LSA), and Latent Dirichlet …

Los Morteros: Early Monumentality And Environmental Change In The Lower Chao Valley, Northern Peruvian Coast, Ana Cecilia Mauricio Llonto

Electronic Theses and Dissertations

This doctoral dissertation presents the results of archaeological and geoarchaeological studies carried out at the site of Los Morteros and the Archaeological Complex of Pampa de las Salinas, lower Chao Valley, North Coast of Peru, between September 2012 and July 2014. This research focuses on the study of the mound-shaped site of Los Morteros and the environmental contexts in which this site developed. Previous excavations at the site considered Los Morteros as a “stabilized dune” whose top was used as cemetery for pre-pottery people around cal. 5000 B.P (Cardenas 1995, 1999). However, geo-radar explorations of the mound in 2006 and …

A Critical Analysis Of Random Response Techniques, Emanuel Zanzerkia

Honors Program Theses and Projects

In order to understand and make informed decision on sensitive topics such as domestic violence and drug use, interviews have been used to collect data. However it is difficult to assess how truthful respondents are since they may not feel at ease revealing the truth to an interviewer. Surveyors of sensitive issues face the problem that respondents may be reluctant to answer truthfully since the respondent may feel pressured socially or may fear the repercussions of their truthful answer. Processes known as random response techniques have been introduced to allow interviewers the ability to extract information they need for a …

The Effects Of Warming Temperatures, Fire, And Landscape Change On Lake Production In Mountain Lakes, Alberta, Canada, Amber Elizabeth Gall

Electronic Thesis and Dissertation Repository

Many factors could be causing the widespread eutrophication being observed globally, including natural and human factors. In the mountainous regions of Alberta, Canada, warming temperatures, increased fire occurrence, and greater landscape disturbance could increase lake production. To determine the effects of these factors, proxies of lake production preserved in lake sediment records that span the last 1000 years were measured. These records are from two lakes that have not been affected by direct nutrient inputs from human activities; one in Jasper National Park and one from the Hinton area (Alberta). The results highlight that there is little effect of fire …

Utilizing Ecological Connectivity In California Desert Wilderness Preservation, Lauren Kahal

Master's Projects and Capstones

The Wilderness Act of 1964 gave the federal land management agencies—the National Park Service, United States Forest Service, U.S Fish and Wildlife Service, and Bureau of Land Management—the authority to identify, propose, and manage lands as wilderness. Wilderness, once approved by Congress for inclusion in the National Wilderness Preservation System, is offered the highest form of land preservation in the nation. However, the wilderness identification process used by the implementing agencies is based on a half-century old statute with an aging definition of wilderness. While designated wilderness can protect the plant and wildlife communities within its borders from direct anthropogenic …

Correction Of Verication Bias Using Log-Linear Models For A Single Binaryscale Diagnostic Tests, Haresh Rochani, Hani M. Samawi, Robert L. Vogel, Jingjing Yin

Biostatistics Faculty Publications

In diagnostic medicine, the test that determines the true disease status without an error is referred to as the gold standard. Even when a gold standard exists, it is extremely difficult to verify each patient due to the issues of costeffectiveness and invasive nature of the procedures. In practice some of the patients with test results are not selected for verification of the disease status which results in verification bias for diagnostic tests. The ability of the diagnostic test to correctly identify the patients with and without the disease can be evaluated by measures such as sensitivity, specificity and predictive …

Antiviral Peptide Nanocomplexes As Potential Therapeutics For The Treatment Of Infectious Diseases, Jinjin Zhang

Theses & Dissertations

Hepatitis C Virus (HCV) is recognized as a major burden in global public health, which can be further exacerbated by several cofactors such as human immunodeficiency virus (HIV). Currently, there is no vaccine for HCV. The emergence of potent and highly specific direct-acting antivirals (DAA) has marked a new era in HCV therapy, however, the remaining issues like affordability, genotype dependency, and potential resistance still necessitate the development of additional therapeutic approaches to be used instead or in combination with DAA.

Recently, the antiviral peptide C5A (in our studies designated as p1) and its cationic derivative p41 have been identified …

Proactive Environmental Strategies: Managing A Corporate Culture Shift Toward Sustainability, Mark E. Calub

Master's Projects and Capstones

The roles and responsibilities of Environmental, Health and Safety (EHS) professionals have expanded over the last several decades. Initially focused solely on reducing a firm's ecological impact, many EHS professionals are now tasked with managing a firm's cultural shift towards sustainability. EHS professionals need to develop proactive environmental strategies that further interconnect the environmental, social, and economic performance goals of the firm. Using a concept analysis and integrative literature review approach, the research examines the evolving role of corporate environmental management and evaluates strategic management tools for environmental compliance, environmental performance, and corporate sustainability. The research reveals that the role …

Urban Stormwater Management: Treatment Of Heavy Metals And Polycyclic Aromatic Hydrocarbons With Bioretention And Permeable Pavement Technologies, Viktoriya Sirova

Master's Projects and Capstones

Urban stormwater runoff is a major non-point source of pollutants release into the environment. Pollutants of concern include sediments; heavy metals; polycyclic aromatic hydrocarbons (PAHs); petroleum hydrocarbons; and chlorinated organic compounds, such as pesticides and polychlorinated biphenyls. Conventional stormwater management practices are designed to dispose of the runoff as quickly as possible, not to treat the pollutants. Low Impact Development (LID) concept is an alternative approach to the conventional framework that attempts to recreate hydrologically functional landscape mimicking pre-development regimes. This research paper assesses the effectiveness of two LID technologies, bioretention and permeable pavements in treating PAHs and common urban …

Adapting To Rising Sea Levels In San Francisco Bay: The Potential For Thin Layer Sediment Application To Enhance Tidal Marsh Resiliency Through This Century, Scott K. Hine

Master's Projects and Capstones

The research here focuses on two projected century sea-level rise scenarios (100 and 180 cm/century) and the potential to offset elevation loss to sea-level rise by supplying deteriorating tidal marsh habitat with a thin layer of dredge sediment via high-pressure spray disposal within San Francisco Bay. This adaptation strategy is then analyzed for potential integration into the Bay’s long term management plan for dredge material disposal. The Marsh Equilibrium Model (Morris, 2012) is used to evaluate elevation deficits for existing tidal marsh habitat around San Pablo Bay against future century sea-level rise scenarios and model marsh resiliency following elevation enhancement. …

Recent Discoveries In The Ni-Cu-Pge Bearing Trill And Parkin Offset Dykes, Sudbury Impact Structure, Canada, Adam B. Coulter

Electronic Thesis and Dissertation Repository

The Sudbury structure hosts world class Ni-Cu-PGE deposits that have been mined, explored and studied for over 130 years. The structure is widely recognized as the erosional remnant of a 1.85 Ga 200- to 250-km tectonically altered multi-ring impact basin located in central Ontario, Canada. The focus of this investigation is on the Trill and Parkin Offset dykes. This study provides updated regional scale geologic maps, detailed geologic maps of newly exposed sections, geochemistry, sulphide analysis and an analysis of the inclusion population and orientation within the dykes. We conclude, the dyke phases display remarkable geochemical homogeneity, the Ni-Cu-PGE mineralization …

Photooxidation Reactions Of Small-Chain Methyl Esters, Aerosol Photoelectron Spectroscopy, And The Photodissociation Of Ethylenediamine, Giel Muller

Master's Theses

Research conducted at the University of San Francisco is presented within this masters thesis, including the Cl-initiated photooxidation reactions of methyl propanoate, methyl butanoate, and methyl valerate (pentanoate), the aerosol photoelectron spectroscopy of isoprene and gamma-valerolactone, and the TPEPICO investigation of ethylenediamine. Experiments were conducted at the Lawrence Berkeley National Lab Advanced Light Source (ALS), the National Synchrotron Radiation Research Center in Hsinchu City (NSRRC), and the University of Stockton in California, respectively.

The Role Of The State, Multinational Oil Companies, International Law & The International Community: Intersection Of Human Rights & Environmental Degradation Climate Change In The 21st Century Caused By Traditional Extractive Practices, The Amazon Rainforest, Indigenous People And Universal Jurisdiction To Resolve The Accountability Issue, Marcela Cabrera Luna

Master's Theses

Local, national and international conventions that protect indigenous sovereignty and their territories, where many of the resources are extracted from by multinational corporations (MNCs) particularly oil, the number one commodity of the world and cause of climate change, continue to be jeopardized because of the lack of a clear international legal framework that can protect them and potentially hold multinationals accountable for their actions. These practices are causing not only environmental issues to the indigenous and surrounding communities, but climate change is in fact, the real human rights issue of the 21^st century and it affects everyone. By using …

Submarine Channel Evolution Linked To Rising Salt Dome, Mississippi Canyon, Gulf Of Mexico, Rachel C. Carter

University of New Orleans Theses and Dissertations

By examining halokinetics and channel evolution in a deep-water system, we investigate how submarine channel morphology is affected by changing seascape linked to diapirism. The study area is located in Mississippi Canyon, Gulf of Mexico (GOM), situated directly off the continental slope in a prominent salt dome region. Interactions of salt domes with submarine channels in the GOM are poorly documented. Utilizing 3D seismic data and seismic geomorphology techniques, a long-lived Plio-Pleistocene submarine channel system has been investigated to develop a relationship between variable phases of salt movement and plan-form morphology of preserved channels.

We suggest that halokinetics acts as …

Towards A Theory Of Recursive Function Complexity: Sigma Matrices And Inverse Complexity Measures, Bradford M. Fournier

University of New Orleans Theses and Dissertations

This paper develops a data structure based on preimage sets of functions on a finite set. This structure, called the sigma matrix, is shown to be particularly well-suited for exploring the structural characteristics of recursive functions relevant to investigations of complexity. The matrix is easy to compute by hand, defined for any finite function, reflects intrinsic properties of its generating function, and the map taking functions to sigma matrices admits a simple polynomial-time algorithm . Finally, we develop a flexible measure of preimage complexity using the aforementioned matrix. This measure naturally partitions all functions on a finite set by characteristics …

Parameterized Spectral Bathymetric Roughness Using The Nonequispaced Fast Fourier Transform, David H. Fabre

University of New Orleans Theses and Dissertations

The ocean and acoustic modeling community has specifically asked for roughness from bathymetry. An effort has been undertaken to provide what can be thought of as the high frequency content of bathymetry. By contrast, the low frequency content of bathymetry is the set of contours. The two-dimensional amplitude spectrum calculated with the nonequispaced fast Fourier transform (Kunis, 2006) is exploited as the statistic to provide several parameters of roughness following the method of Fox (1996). When an area is uniformly rough, it is termed isotropically rough. When an area exhibits lineation effects (like in a trough or a ridge line …

Stabilized Least Squares Migration, Graham Ganssle

University of New Orleans Theses and Dissertations

Before raw seismic data records are interpretable by geologists, geophysicists must process these data using a technique called migration. Migration spatially repositions the acoustic energy in a seismic record to its correct location in the subsurface. Traditional migration techniques used a transpose approximation to a true acoustic propagation operator. Conventional least squares migration uses a true inverse operator, but is limited in functionality by the large size of modern seismic datasets. This research uses a new technique, called stabilized least squares migration, to correctly migrate seismic data records using a true inverse operator. Contrary to conventional least squares migration, this …

Petroleum Play Study Of The Keathley Canyon, Gulf Of Mexico, Jean Pierre Malbrough

University of New Orleans Theses and Dissertations

Beneath Keathley Canyon (KC) off the Southern Coast of Louisiana and Texas, allochthonous salt bodies have attained thicknesses of over 7620 m (25000 feet), providing excellent seals and migration pathways for hydrocarbons produced by post-rift sedimentary deposition. This study analyzes a small portion of the KC area, utilizing Petrel Seismic software and well information from the KC102 (Tiber) well.

An intra-Miocene wedge, expressed beneath salt, may provide information about movement of allochthonous salt over Wilcox sands, sediment compaction, and hydrocarbon pathways. Progradational sedimentation is the driving force which leads to faulting in the early Miocene, allowing Jurassic salt to rise, …

Restoring The Mississippi River Delta In Louisiana Ecological Tradeoffs And Barriers To Action, Alison Maulhardt

University of New Orleans Theses and Dissertations

This study investigates the Louisiana 2012 Coastal Master Plan’s ability to reconcile conflicting economic and ecological demands on coastal resources. The Louisiana Coastal Master Plan was unique in combining flood control and coastal restoration under one authority. However, the objectives of flood control and coastal restoration can be in conflict. The plan was also unique in its approach of restoration from a working coast perspective. However, the objectives of ecological restoration and economic productivity do not always agree. By conducting semi-structured interviews with major coastal stakeholders, this research will explore how the planning process has accommodated the views and values …