Physical Sciences and Mathematics Commons^™

Examining Biomolecular Interactions And Their Significance In Toxoplasma Gondii Survival And Infection, Grace Wen

Electronic Theses and Dissertations

Elucidating biomolecular interactions that underlie the cellular processes vital to the survival and infectivity of the parasitic protozoan Toxoplasma gondii is crucial for development of effective prophylactics and therapeutics against this resilient pathogen. In the first two parts of this three-part study, the significance of protein-protein, protein-nucleic acid, and protein-lipid interactions in T. gondii pathogenicity is explored. The first part of the study presents an overview of current knowledge on the topic of liquid-liquid phase separation, which is the condensation of macromolecules driven by multivalent interactions between protein and protein or protein and nucleic acids, and its multifaceted role in …

Development Of Nanostructured Titania-Incorporated Photocatalysts For Environmental Applications, Sudheera B. Yaparatne

Electronic Theses and Dissertations

Ultraviolet (UV) radiation application in water and wastewater treatment has become a common approach for inactivation of protozoa and other pathogenic microorganisms. However, degradation of most organic compounds, such as taste and odor products prevalent in surface waters, has not been proven effective with direct UV photolysis. Advanced oxidation processes (AOPs) that involve efficient photocatalysts like TiO₂ show an advantage over direct UV photolysis providing fast reaction rates and non-selective oxidation of contaminants. However, the real-world application of TiO₂ in water and wastewater treatment is limited due to difficulties in separating the suspended nanosized particles following treatment, the …

Deep Learning Applications In Medical Bioinformatics, Ziad Omar

Electronic Theses and Dissertations

After a patient’s breast cancer diagnosis, identifying breast cancer lymph node metastases is one of the most important and critical factor that is directly related to the patient’s survival. The traditional way to examine the existence of cancer cells in the breast lymph nodes is through a lymph node procedure, biopsy. The procedure process is time-consuming for the patient and the provider, costly, and lacks accuracy as not every lymph node is examined. The intent of this study is to develop an artificial neural network (ANNs) that would map genetic biomarkers to breast lymph node classes using ANNs. The neural …

Work Order And Subassembly Identification And Tracking System, Israa El-Sabbagh

Electronic Theses and Dissertations

The research encompassed in this thesis includes the development of a work order and subassembly identification and tracking software system created in-house and tested at SPM Automation (Canada) Inc. The research is motivated by the significant losses the company is enduring and the recurring problems occurring at the facility (i.e., excess inventory, late ordering, reordering, misplaced components, etc.). These problems are critical in the progress and profits of the company.

An extensive literature review was completed, and the research gaps were presented. The optimal work order and subassembly process was created using Process Mapping Methodology, Cause-and-Effect Diagrams, and 5Why Analysis. …

Multifaceted Environmental Enrichment In Industrial Fish Hatcheries: The Influence Of Enriched Rearing On The In-Situ Behaviour And Post-Stocking Success Of Juvenile Atlantic Salmon (Salmo Salar), Justine Elizabeth Mcadrews

Electronic Theses and Dissertations

Hatchery fish reared and stocked to sustain or restore wild populations often perform poorly in novel environments compared to their wild counterparts. To combat maladaptive hatchery-acquired traits environmental enrichment is an emerging tool used to provide ‘life skills training’ to hatchery fish prior to release. Through the application of simple yet multifaceted enrichment protocols in an industrial fish hatchery, this thesis aimed to demonstrate how enrichment could be applied to improve the ecological viability of stocked fish. At a provincially-run fish hatchery, a subgroup of juvenile Atlantic salmon (Salmo salar) were subject to 10 weeks of environmental enrichment …

A Framework To Study The Impact Of Interventions On Social Isolation During Pandemics Using Multi-Agent Simulation, Simranpreet Kaur

Electronic Theses and Dissertations

The spread of Coronavirus, widely known as COVID-19, has posed detrimental effects worldwide, affecting almost every primary sector. Due to its asymptomatic behavior and non-early diagnosis, government and health organizations implemented interventions such as physical distancing, lockdown, and quarantine, to mitigate the spread of the virus. Studies have shown that a connection exists between social isolation and health risks experienced by individuals. Thus, this research proposes an agent-based model to address the impact of varying interventions in our society. For simulation purposes, the SEIR model is followed, and agents are categorized into two classes based on their pace of movement, …

Bridging The Simulation-To-Reality Gap: Adapting Simulation Environment For Object Recognition, Hardik Yogesh Sonetta

Electronic Theses and Dissertations

Rapid advancements in object recognition have created a huge demand for labeled datasets for the task of training, testing, and validation of different techniques. Due to the wide range of applications, object models in the datasets need to cover both variations in geometric features and diverse conditions in which sensory inputs are obtained. Also, the need to manually label the object models is cumbersome. As a result, it becomes difficult for researchers to gain access to adequate datasets for the development of new methods or algorithms. In comparison, computer simulation has been considered a cost-effective solution to generate simulated data …

Assessing The Adaptive Capacity Of An Arctic Seabird To Increasing Frequency In Predation Risk From Polar Bears Using Behavioural And Physiological Metrics, Erica Anne Geldart

Electronic Theses and Dissertations

Predator-prey dynamics in the Arctic are being altered with changing sea-ice phenology. The increasing frequency of predation on colonial nesting seabird eggs by a rare predator - the polar bear (Ursus maritimus), is a consequence of bears shifting to terrestrial food resources through a shortened seal-hunting season. I study a colony of nesting common eiders (Somateria mollissima) on Mitivik (East Bay) Island, Nunavut, Canada, that is exposed to established nest predators such as arctic fox (Vulpes lagopus), but has recently experienced an increase in polar bear nest predation due to the bears’ lost on-ice hunting opportunities. Given eiders’ limited eco-evolutionary …

Efficient Heuristic Solutions To Scheduling Online Courses, Rida Zaidi

Electronic Theses and Dissertations

The demand for efficient algorithms to automate (near-)optimal timetables has motivated many well-studied scheduling problems in operational research. With most of the courses moving online during the recent pandemic, the delivery of quality education has raised many new technical issues, including online course scheduling. This thesis considers the problem of yielding a near-optimal schedule of the real-time courses in an educational institute, taking into account the conflict among courses, the constraint on the simultaneous consumption of the bandwidth at the hosting servers of the courses, and the maximum utilization of the prime time for the lectures. We propose three approaches …

A Network-Based Approach For Computational Drug Repurposing On Cancer Data, Ann Reba Thomas Alexander

Electronic Theses and Dissertations

In this thesis, we are interested in finding the best drugs that can be repurposed for the disease and able to find the adverse effects such drugs that are FDA-Approved. Developing an effective drug can be a time-consuming and expensive crucible method. Network-based machine learning methods are used for predicting a given drug for A that can be used for B. It aims at finding new indications for already existing drugs and therefore increases the available therapeutic choices at a fraction of the cost of new drug development. The perturbation gene expression data corresponding to the MCF7 cell line was …

Computational Enzymology On Sulfur-Containing Enzymes: From Method To Application, Paul Meister

Electronic Theses and Dissertations

Sulfur-containing biomolecules display incredible functional diversity. Indeed, in addition to thiols and thioethers, S-nitrosothiols, 3,4-coordinate, sulfoxides, persulfides and now even polysulfides are commonly observed intermediates. Unfortunately, however, their biological synthesis and roles remain poorly understood. In addition, sulfur-containing species can access a broad range of oxidation states and thus can act as either an electrophile or nucleophile giving rise to an even more diverse set of sulfur-derived functional groups. However, these unique properties can lead to difficulties in characterizing such compounds experimentally and reinforces the need for computational studies to reliably predict their structural and energetic properties. In this dissertation, …

Improved Glove Word Embedding Using Linear Weighting Scheme For Word Similarity Tasks, Quinlan Lu

Electronic Theses and Dissertations

One of the trends in Natural Language Processing (NLP) is the use of word embedding. Its aim is to build a low dimensional vector representation of words from text corpora. Global Vectors for Word Representation (GloVe) and Sikp-Gram with Negative Sampling (SGNS) are two representative word embedding methods. Existing papers have different conclusions on the performance of these two methods. This thesis focuses on GloVe and studies its commonalities and differences with SGNS.

Word co-occurrence is the cornerstone of all word embedding algorithms. One difference between GloVe and SGNS is the definition of co-occurrence. The weight of co-occurring words tapers …

Deposition And Diagenesis Of The Blossom Sand, Panola County, Texas, Hannah Chambers

Electronic Theses and Dissertations

The Late Cretaceous Blossom Sand within the Austin Group is a historic gas reservoir in the East Texas basin, located at depths of approximately 2,000 ft below the surface. Since the discovery of the Carthage Field in 1918 in the East Texas Basin, the Blossom Sand has produced approximately 26 BCF of gas with minor amounts of oil. Despite its notoriety in the Carthage Field, there is very little research that has been conducted on this unit, although it crops out in northeast Texas and is found in the subsurface of southwest Arkansas, western Louisiana, and the East Texas Basin. …

Mineralogical Restrictions On Porosity In The Taylor Sand Of The Cotton Valley Group, Northern Louisiana Salt Basin, Claiborne Parish, Louisiana, Kaleb C. Mcclain

Electronic Theses and Dissertations

The Cotton Valley Group has been targeted for hydrocarbons since the 1940s. However, the reservoir was initially considered uneconomical to drill due to its low permeability and porosity. Since then, recent technological advances in hydraulic fracturing have allowed the Cotton Valley Sandstone members to become prolific, profitable plays, renewing interest in drilling and exploration across the northwest/northern Louisiana region.

In this research, mineralogical restrictions on the porosity in the Lower Taylor Sand of the Cotton Valley Group were studied from core (10,035’ft/3,059m -10,150’ft/3,094m) from Blackburn Field, northwest Claiborne Parish. Twelve samples were taken at intervals throughout the Taylor Sand, starting …

Precambrian Basement Influence On The Deposition Of The Upper Ordovician Utica Shale Play In East Central Ohio, William Kaleb Kirk

Electronic Theses and Dissertations

The Ordovician Utica shale play is a major oil and gas producing interval in the Appalachian Basin. The Utica shale play can be found as far as New York and Canada and to the south into Indiana and Kentucky. The play consists of the Trenton/Lexington limestones, Point Pleasant Formation, and Utica shale. The shallow marine fossiliferous limestones of the Trenton and shallow marine shaley limestones of the Lexington are overlain by an interbedded shale and limestone of the Point Pleasant Formation, which grade into the deeper marine interbedded shales and limey shales of the Utica. These formations are highly heterogeneous, …

Hydrodynamic Impacts Of Expanding Aquaculture, Zhilong Liu

Electronic Theses and Dissertations

Climate change may potentially change aquatic systems and bring certain risks for aquaculture development. Understanding interactions between aquaculture and the environment helps to ensure aquaculture expansion is sustainable in the future. It is critical to determine how farms influence tidal flow patterns, turbulence, mixing and material transport in estuaries. This research aims to determine the flow response of an oyster farm, predict how expanding farms and farm placement will alter estuarine dynamics, and understand how the design of a farm influences material transport.

The hydrodynamic response of a floating oyster aquaculture farm in a low inflow estuary (the Damariscotta River …

Eastward-Propagating Planetary Waves In The Middle Atmosphere During Major Sudden Stratospheric Warming Events, Christian Todd Rhodes

Electronic Theses and Dissertations

No abstract provided.

Evaluating Methods For Research In Physical Weed Control And Farm Asset Tracking, Johnny J. Sanchez

Electronic Theses and Dissertations

Effective weed control has long been recognized as critical for agricultural production, yet weeds remain a major constraint to production and economic return in many agroecosystems. Moreover, improvements in physical weed control are necessary to address increasing problems of herbicide resistance in weeds of grain and fiber crops and the high cost of hand weeding in vegetables. From tractor-mounted cultivation tools to autonomous weeders, weeding implements are affected by weeds, crops, soil conditions, and actuator effectiveness. In order to address these complex and often interacting factors concerning weed control, new and innovative tools must be designed and evaluated. Chapter one …

10be Chronology Of Moraines Deposited During The Last Glaciation By The Khumbu Glacier, Nepalese Himalaya, Laura Alexandra Mattas

Electronic Theses and Dissertations

Understanding the global pattern of glaciation can aid interpretation of what caused late-Pleistocene glacial cycles. Here I investigate the glacial history of the Khumbu Glacier of the Mount Everest region of Nepal. Prominent hypotheses for Himalayan glaciation suggest important roles for orbitally modulated insolation change and the Asian summer monsoon. Here I test these hypotheses by developing a 10Be surface-exposure chronology of moraines constructed by the Khumbu Glacier during the last glacial period. My chronology is underpinned by detailed glacial-geomorphic mapping constructed by use of drone and satellite imagery. The ages presented in this study indicate that the Khumbu glacier …

Radiosonde High Altitude Measurements Of Radiation Levels And Cosmic Ray Events, Ayodeji Opeyemi Akinuliola

Electronic Theses and Dissertations

Just above us, cosmic rays are hurtling in from space. These fast moving particles crash uncontrollably into molecules in the atmosphere, causing spontaneous decays of these particles. Despite the fact that we are broadly shielded from this radiation on earth, these particles can still disturb humans and electronics alike. Therefore, this research focuses on expanding the use of long-range radio transmitters such as radiosondes to transmit valuable data such as cosmic ray flux, geographical position, atmospheric temperature, pressure, etc. This can improve real-time radiation monitoring for aviation industry crew and passengers working in potentially higher radiation environments. On March 11, …

Lexicographic Sensitivity Functions For Nonsmooth Models In Mathematical Biology, Matthew D. Ackley

Electronic Theses and Dissertations

Systems of ordinary differential equations (ODEs) may be used to model a wide variety of real-world phenomena in biology and engineering. Classical sensitivity theory is well-established and concerns itself with quantifying the responsiveness of such models to changes in parameter values. By performing a sensitivity analysis, a variety of insights can be gained into a model (and hence, the real-world system that it represents); in particular, the information gained can uncover a system's most important aspects, for use in design, control or optimization of the system. However, while the results of such analysis are desirable, the approach that classical theory …

Quantification Of Persistent Organic Pollutants In Various Matrices Using Stir Bar Sorptive Extraction And Isotope Dilution Mass Spectrometry, Weier Hao

Electronic Theses and Dissertations

A method was developed to quantify persistent organic pollutants (POPs) in a wide range of matrices including wastewater, dietary supplements, and human whole blood using stir-bar sorptive extraction, GC-MS/MS, and isotope dilution mass spectrometry (IDMS). The method enabled accurate, precise, sensitive, and efficient quantification of POPs in these matrices. Compared with calibration curves, IDMS provided measurements with a higher level of accuracy and precision, especially at lower measured concentrations. The use of GC-MS/MS enabled a lower limit of quantification compared with GC-MS. A reverse-IDMS method was performed to further eliminate biases from the labelled concentrations of the commercially available standards. …

Computational And Experimental Studies Of Functionalized Phenolic Tertiary Phosphine Oxides As Organocatalysts For The Redox-Neutral Mitsunobu Reaction, Sadie Brown

Electronic Theses and Dissertations

The purpose of this thesis was the identification of a more efficient catalyst analog that could perform the redox-neutral Mitsunobu reaction, which was achieved via two synthetic pathways: elimination-addition and addition-rearrangement. Furthermore, a computational investigation was conducted on the conflicting interpretations of the catalytic cycle. Our research group replicated Houk et al. work, as well as expanded the computations to examine the influence different functional groups had on the ground state and transition state structures. Important ground state and transition state structures were determined, which provided a more energetically favorable pathway of the catalytic cycle. Experimental work demonstrated that both …

Air Pollution In The Steel City: Assessing The Influence Of Covid-19 On Air Pollution In Allegheny County, Carissa L. Lange

Electronic Theses and Dissertations

Though the novel coronavirus (COVID-19) has sickened millions of individuals, lockdown measures have provided a unique opportunity to analyze air pollution reductions. Reductions in air pollution are especially important in a city like Pittsburgh, where industrial activity has led to elevated levels of particulate matter with an aerodynamic diameter 2.5). The majority of this PM_2.5 pollution comes from two industrial facilities, the Edgar Thomson Steel Works and the Clairton Coke Works. By utilizing a natural experiment, this study sought to determine how large of a role the COVID-19 lockdowns played in improving air quality in the Pittsburgh region. Data …

Development Of Methods For Determining Water Content In Oil Using Infrared Spectroscopy, Sfoog Hamad Saleh

Electronic Theses and Dissertations

Karl Fischer Titration (KFT) is the “gold standard” method for measuring the amount of water in oils. KFT is a laborious and time-consuming method that requires expensive and hazardous chemicals which has provided the impetus to develop alternative methods. In this thesis, we investigated three approaches for determining water content in oils that are based on the use of infrared spectroscopy. In the first approach, we developed a simple method for measuring water concentrations from 1 to 5000 ppm in various types of oil that uses no hazardous, and expensive, chemical reagents or matrix specific calibrations. This approach involves capturing …

Variations In Zooplankton Communities As Indicators Of Biological Responses To Climate Change And Recovery From Acidification In Northeastern And Maine Mountain Lakes, Stephanie Dykema

Electronic Theses and Dissertations

Since the Clean Air Act Amendments of 1990, lakes in Maine and much of the Northeastern US have seen significant shifts in response to reduced atmospheric deposition as well as climate change. The organisms that inhabit lakes are susceptible to environmental change, but our understanding about how biological communities react to simultaneous changes in geochemistry and climate is incomplete. This research investigates how zooplankton communities respond to geochemical changes and warming, on both long-term and seasonal scales. These small organisms are sensitive to changes in physical lake conditions, and variation within zooplankton communities could indicate larger ecosystem shifts. We evaluated …

Deciphering The Ecology Of Aulacoseira Taxa In Alpine Lakes: Implications For Paleoclimate Reconstructions, Edna Luz Pedraza Garzon

Electronic Theses and Dissertations

Diatoms of the genus Aulacoseira are thought to bloom during enhanced lake mixing. Thus, changes in their relative abundances in lake sediment records may track lake thermal conditions and be used to reconstruct past climate. However, the lack of species-specific ecological information for the genus, and taxonomical conflicts for low-height mantle taxa, generates uncertainty about the conditions in which they occur. As many of the environmental reconstructions analyzing alpine lake sediments report species from this genus, it is relevant to understand the factors that control their growth and persistence to improve climate inferences. This research focused on low-mantle species, particularly …

Farmer Engagement Through Mental Modeling: Opportunities For Climate Change Outreach, Ruth S, Clements

Electronic Theses and Dissertations

Climate change poses a challenge to farming systems worldwide. Effective adaptation and mitigation may be facilitated by outreach that is locally tailored and framed in terms of farmers’ perceptions and values. However, existing research suggests that farmers and those providing outreach may have different climate change perspectives, and there is little understanding of how farmers consider and prioritize climate change in relation to other aspects of their farming system. Furthermore, the diverse agricultural, economic, social, and environmental challenges farmers face require agricultural research and engagement efforts that can identify and adapt to farmers’ dynamic priorities and perceptions. Mental modeling is …

Geochemical Characterization Of The Utica Shale Play Using Xrf-Based Chemostratigraphy In Ohio, Barbara Kemeh, Julie M. Bloxson

Electronic Theses and Dissertations

The Utica shale is an extensive gas shale play within the Appalachian Basin, expanding from Quebec through New York, into Pennsylvania, West Virginia and Ohio. Currently a target for gas exploration, it is also the source rock for much of the Paleozoic reservoirs throughout the basin. However, the Utica-Point Pleasant lithology varies significantly across the Appalachian Basin which can make it challenging to characterize.

The Utica shale Play consists of the Trenton/Lexington Limestones, Point Pleasant Formation and Utica shale. The Point Pleasant Formation and Utica shale are often grouped together, especially in Ohio because they are difficult to visually distinguish …

Sub-Surface Structural Analysis Of The Appalachian Basin In Morrow County, Ohio, Adrian Isaiah-Sias Valdez

Electronic Theses and Dissertations

Located in the western most region of the Appalachian Basin, Morrow County, Ohio, was once one of the largest oil-producing regions in the nation and continually produces today. To date, approximately 30 million barrels of oil and 6.5 billion cubic feet of gas have been produced, primarily from the Copper Ridge Dolomite. Past studies suggest that regional remnant doming within the Copper Ridge accounts for production, however it is hypothesized that faulting within the basement rock exerts an important control on trapping and migration of hydrocarbons. In order to gain insight into the underlying structure and the causes of significant …