Physical Sciences and Mathematics Commons^™

Methods For Single-Cell And Low-Input Proteomics, Yiran Liang

Theses and Dissertations

Single-Cell Proteomics (SCP) can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. In addition to achieving in-depth proteome coverage from single cells, higher throughput measurements enable large-scale and statistically significant features within single cell populations. This dissertation focuses on method development to improve the sensitivity and throughput of SCP based on the nanoPOTS (nanodroplet Processing in One pot for Trace Samples) platform. The methods discussed …

Chasing Transients: Constructing Local Galaxy Catalogs For Electromagnetic Follow-Up Of Gravitational Wave Events, Chaoran Zhang

Theses and Dissertations

Gravitational waves (GWs) provide a new window for observing the universe which is not possible using traditional electromagnetic (EM) wave astronomy. The coalescence of compact object binaries, such as black holes (BHs) and neutron stars (NSs) generates “loud" GW signals that are detectable by the LIGO-Virgo-KAGRA (LVK) GW Observa- tory. If the binary contains at least one NS, there is a possibility that an observable EM counterpart will be launched during and/or after the merger. The first joint detection of GW radiation (GW170817) and its EM counterpart (AT 2017gfo) greatly extended our understanding of the universe in many fields, such …

Using Anisotropy Of Magnetic Susceptibility (Ams) To Identify A Tectonic Lineation In The Pulo Do Lobo Formation In The Southern Iberian Shear Zone Near Aracena, Spain, Devin Levang

Theses and Dissertations

The Southern Iberian Shear Zone (SISZ) is a Variscan-aged suture representing the closure of a small ocean basin during the Carboniferous. The SISZ is bounded on either side by the well-studied, relatively homogeneous Beja-Acebuches Metabasites (BAM) and the complex and heterogeneous accretionary metasedimentary rocks of the Pulo do Lobo (PdL). The SISZ underwent a combination of shortening and lateral shearing known as transpression. Despite a very well-developed tectonic foliation, kinematic interpretation in the PdL is made difficult by a lack of easily identifiable lineations. Anisotropy of magnetic susceptibility (AMS), a geophysical technique measuring the relative anisotropy of magnetic susceptibility axes …

Common Ground Over Common Water: Defining The Public Interest In The Milwaukee Watershed, Thomas Anthony Gentine

Theses and Dissertations

My dissertation examines government and nongovernment entities’ attempts to restore and protect the use and health of the Milwaukee River and its watershed from 1960 to 2000. Under Mayor Henry Maier’s leadership, Milwaukee worked to reclaim the urban riverway to stimulate economic growth. However, state and federal representatives, after the passage of the 1965 Water Quality Act, demanded that the city government prioritize updating the combined storm and sewer system to lessen pollution in the Milwaukee River. At the same time, other groups worked to save rural areas from unplanned development and further degradation of the waterway. Influential groups included …

An Ethercat Based Real-Time Control System Design For Wheelchair-Mounted 6dof Assistive Robotic Arm, Ivan Alexander Rulik Cote

Theses and Dissertations

Numerous assistive robots for individuals with disabilities have been produced over the past ten years, but researchers have not completely exploited these robotic technologies to enable people with impairments to live independently, especially in respect to activities of daily living. (ADLs). For people with impairments, an assistive system can help them fulfill the requirements of typical ADLs. Assistive robots can help address future healthcare demands due to a growing need for caregivers, a scarcity of them, and an increase in the number of the elderly and people with disabilities. Enhancing functional independence while creating a superior human-machine interaction is one …

Use Of Machine Learning And Natural Language Processing To Enhance Traffic Safety Analysis, Md Abu Sayed

Theses and Dissertations

Despite significant advances in vehicle technologies, safety data collection and analysis, and engineering advancements, tens of thousands of Americans die every year in motor vehicle crashes. Alarmingly, the trend of fatal and serious injury crashes appears to be heading in the wrong direction. In 2021, the actual rate of fatalities exceeded the predicted rate. This worrisome trend prompts and necessitates the development of advanced and holistic approaches to determining the causes of a crash (particularly fatal and major injuries). These approaches range from analyzing problems from multiple perspectives, utilizing available data sources, and employing the most suitable tools and technologies …

Photo-Reactivity Of Bifunctional Naphthalene Compounds Toward Dna, Qi Zhang

Theses and Dissertations

DNA interstrand cross-link (ICL) can covalently bind two DNA strands, preventing DNA strands separation, and therefore, blocking DNA transcription and replication, which are essential biological processes for cell division. Among different methods to induce DNA interstrand cross-linking, photoinduction is an important way to activate the cross-linking reactions due to its many characteristics, such as non-invasive, controllability, selectivity and biorthogonality. My research mainly focuses on developing novel binaphthalene compounds which can be activated by 350 nm UV light to produce DNA interstrand cross-linking via alkylation. We designed and synthesized a series of binaphthalene analogues with different substituents at the position-4’ on …

Unraveling Deformation Mechanisms And Kinematics In Metasedimentary Rocks Along The Southern Iberian Shear Zone, Kayla P. Kopinski

Theses and Dissertations

The primary goal of this project is to document deformation mechanisms in quartz-rich rocks across a 100 m wide ductile shear zone to evaluate whether strain localization at the brittle-ductile transition is accompanied by variations in active or dominant deformation mechanisms. A secondary goal of this project is to evaluate whether the kinematic framework varies across a shear zone with a major rheological boundary. The Southern Iberian Shear Zone (SISZ), a major terrane bounding shear zone within the Iberian Massif, is an ideal location to study these questions because it is a regional scale shear zone currently exposed at the …

Automated Feature Extraction From Large Cardiac Electrophysiological Data Sets, And A Population Dynamics Approach To The Distribution Of Space Debris In Low-Earth Orbit, John Jurkiewicz

Theses and Dissertations

We present two applications of mathematics to relevant real-world situations.

In the first chapter, we discuss an automated method for the extraction of useful data from large file-size readings of cardiac data. We begin by describing the history of electrophysiology and the background of the work's setting, wherein a new multi-electrode array-based application for the long-term recording of action potentials from electrogenic cells makes large-scale readings of relevant data possible, opening the way for exciting cardiac electrophysiology studies in health and disease. With hundreds of simultaneous electrode recordings being acquired over a period of days, the main challenge becomes achieving …

Strain Development And Partitioning Across A Transpressional Shear Zone Along A Quartzite- Metagabbro Contact In The Black Hills Uplift, South Dakota, Eric L. Schuemann

Theses and Dissertations

The Nemo region of South Dakota’s Black Hills offers an ideal location to study transpressional shear zones because it hosts an exposed Archean lithological boundary between two contrasting rheological units, the Boxelder Creek Quartzite (BCQ), a rift-depositional quartzite, and the Blue Draw Metagabbro (BDM), a metagabbro sill, deformed within a ductile shear zone that represents the beginning of main-phase formation of the North American continent as we know it today. The tectonic setting of the Black Hills is at the eastern edge of the Archean Wyoming province, located near the Trans-Hudson Orogeny suture zone that formed between the Wyoming and …

A Protocol To Build Trust With Black Box Models, Timothy K. Thielke

Theses and Dissertations

Data scientists are more widely using artificial intelligence and machine learning (ML) algorithms today despite the general mistrust associated with them due to the lack of contextual understanding of the domain occurring within the algorithm. Of the many types of ML algorithms, those that use non-linear activation functions are especially regarded with suspicion because of the lack of transparency and intuitive understanding of what is occurring within the black box of the algorithm. In this thesis, we set out to create a protocol to delve into the black box of an ML algorithm set to predict synoptic severe weather patterns …

Internal Waves Of Port Everglades: Experimental And Numerical Studies To Characterize Ambient Magnetic Signals, Johanna Riley Evans

Theses and Dissertations

Ocean dynamics are an important contributing factor to measurable environmental magnetic noise. Seawater is conductive and as an internal wave oscillates across Earth’s magnetic field, a small yet detectable induced magnetic field develops. A significant source of underwater magnetic noise off the southeast coast of Florida comes from internal waves. Characterizing the magnetic signals present required a combination of computational modeling effort and field experiments. For this research, undersea sensors were monitored as a continuous field experiment and a computational fluid dynamic (CFD) magneto-hydrodynamic (MHD) model was customized to simulate internal wave-induced magnetic fields at the site. I developed the …

Unified Model Of Lightning & Electrostatic Discharges Across The Solar System, Annelisa Blackwell Esparza

Theses and Dissertations

As we increase the number of probes on other objects within our solar system, it becomes all the timelier to understand the physics of electrostatic discharges (ESDs). Since these probes will have sensitive instruments on-board, we will need to apply our existing knowledge of ESDs to extraterrestrial environments to protect these investments from deterioration. On Earth, even small-scale ESDs can permanently destroy critical components within electronics, while large-scale ESDs (e.g., lightning strikes) are capable of debilitating entire power grids. The characteristic timescale of an ESD is small compared to the timescales of cloud charging and storm evolution. This lets us …

Modeling Settlement And Filtration Of The Indian River Lagoon Benthic Community, With An Emphasis On Living Dock Restoration Mats, Sandra Lisette Rech

Theses and Dissertations

The Indian River Lagoon (IRL) is one of the most biologically diverse estuaries in North America. An increase in population and anthropogenic effects have led to eutrophication, a decline in water quality, and overall degradation. The Living Docks program is a citizen science initiative started at the Florida Institute of Technology for lagoon restoration. In this program, public and private docks are volunteered to become Living Docks, where oyster mats made of plastic mesh and dead, dried oyster shells are attached to dock pilings in an effort to provide a natural substrate for benthic organism growth. The community which develops …

Non-Negative Matrix Factorization In The Identification Of Co-Mutations, Michael Robert Kolar

Theses and Dissertations

One of the difficulties of genetic research is the asymmetrical relationship between data collection techniques and data analysis techniques. The goal of this research was to test a novel application of non-negative matrix factorization, which would allow researchers to more easily identify co-mutations. Those co-mutations then can then be further verified by frequency analysis. This pruning process allows researchers to identify more fruitful research opportunities, saving time, energy, and funding. Past research has utilized non-negative matrix factorization to extract factors which meaningfully express underlying data features. This study extends the depth of non-negative matrix factorization knowledge in various ways. First, …

Representation Learning For Open Set Recognition And Novel Category Discovery, Jingyun Jia

Theses and Dissertations

As machine learning models have achieved great success in various research and industry fields, the success of these models heavily relies on the massive amount of data collection and human annotations. While the real world is an open set, the daily emerged categories and the lacking of annotations have become new challenges for machine learning models. The absence of newly emerged categories in training samples can be captured by Open Set Recognition (OSR). Then, given the newly emerged samples, the process of automatically identifying the novel categories is called Novel Category Discovery (NCD). In this dissertation, we focused on learning …

The Use Of Flexible Organic And Inorganic Building Blocks In Complex Metal- Organic Frameworks, Sahar Yahia Rajeh

Theses and Dissertations

Metal organic frameworks (MOFs) are new class of hybrid materials that draw the attention of scientists to discover new properties that help in many fields. The structural diversity of MOFs is accessible by incorporating different organic linkers to the same metal cluster. In this work, we reacted seven flexible organic linkers with different lengths varying from 4-carbons to 10-carbons to a copper-paddlewheel metal cluster. The flexibility of the linkers make the confirmation of MOFs a challenge, although we were able to prepare a new crystalline MOF from a 5-carbon organic linker with two different copper-clusters. Another MOF in powder form …

Image-Based Cancer Diagnosis Using Novel Deep Neural Networks, Hosein Barzekar

Theses and Dissertations

Cancer is the major cause of death in many nations. This serious illness can only be effectivelytreated if it is diagnosed early. In contrast, biomedical imaging presents challenges to both clinical institutions and researchers. Physiological anomalies are often characterized by modest modifications in individual cells or tissues, making them difficult to detect visually. Physiological anomalies are often characterized by slight abnormalities in individual cells or tissues, making them difficult to detect visually. Traditionally, anomalies are diagnosed by radiologists and pathologists with extensive training. This procedure, however, demands the participation of professionals and incurs a substantial expense, making the classification of …

Understanding Ecological Relationships To Improve Biofouling Management Practices In The Marine Environment, Ann Catherine Wassick

Theses and Dissertations

Biofouling, the growth of benthic invertebrates on anthropogenic surfaces, impacts many industries and is a major vector of non-native species worldwide. Understanding the ecological relationships between biofouling organisms and their environment is necessary to assist management practices. This study investigates the biofouling communities at Port Canaveral, Florida, in order to potentially refine biofouling mitigation practices. Recruitment panels were used to document the temporal changes in community composition, biofouling pressure, recruitment, and growth rates. These factors were also used to assess relationships with temperature and salinity. A second component of this work provided documentation on the variation in non-native species abundance …

On Clinical Use Of Infrared Cameras For Video-Based Estimation Of 3d Facial Kinematics, William Mackenzie Harrington

Theses and Dissertations

Neurological and neurodegenerative disorders such as Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and stroke can cause speech and orofacial motor impairments with devastating effects on quality of life. Analysis of orofacial movement provides vital information for early diagnosis and tracking disease progression, but current clinical practice relies on perceptual assessments performed by clinicians, which are unreliable and insensitive to early symptoms. New methods in machine learning have enabled automatic and objective assessment of orofacial kinematics from color and depth videos, hence we introduce MEADepthCamera, a mobile application for RGB-D video and audio recording and automatic estimation of 3D facial …

Cloud Image Classification Using Machine Learning, Marcus Peter Cote

Theses and Dissertations

Machine learning is a rapidly expanding technology that has proven to be highly useful for image classification. Ground-based camera networks are an emerging resource for aviation weather information with near real-time imagery available online for public viewing and download. While raw web camera imagery can be analyzed by aviators, high pilot workload motivates the use of machine learning to autonomously interpret cloud type information from images that is relevant to aviation weather hazards. In particular, transfer learning is a machine learning approach by which elements of a pre-trained machine learning model are refitted for new tasks. By employing transfer learning …

Design Of Ethical Autonomous Agents For Unmanned Aerial Vehicles Using Fuzzy Logic, Gavin Giovanni Smith

Theses and Dissertations

Autonomous systems have, over the years become part of our everyday lives. These systems have been deployed to executed a diverse range of applications in different industries; finance, healthcare, military, and in particular, the flight industry. With the rise of UAVs, new opportunities arose, but with those opportunities came new pitfalls within any industry. For UAVs, one of the pitfalls came in the form of ethical decisionmaking, which led to a variety of questions. Can the Autonomous systems within UAVs be designed with ethics in mind? Which ethical guidelines would we use to implement such a system? How would we …

Investigating The O’Connell Effect In Kepler Eclipsing Binaries, Matthew Frederick Knote

Theses and Dissertations

The O’Connell effect – the presence of unequal maxima in eclipsing binaries – remains an unsolved riddle in the study of close binary systems. The Kepler space telescope produced high precision photometry of nearly 3,000 eclipsing binary systems, providing a unique opportunity to study the O’Connell effect in a large sample and in greater detail than in previous studies. I have characterized the observational properties – including temperature, luminosity, and eclipse depth – of a set of 212 systems (7.3% of Kepler eclipsing binaries) that display a maxima flux difference of at least 1%, representing the largest sample of O’Connell …

Dynamic Soil Properties In The Lower Rio Grande Valley: Carbon And Nitrogen Responses To Different Tillage Practices, Luzyannet Ballesteros Gonzalez

Theses and Dissertations

There has been increased attention in utilizing agriculture for carbon sequestration. Soil carbon and nitrogen are two dynamic soil properties (DSPs) that are indicators of soil health and function and have overlapping cycles. These soil properties change frequently as a result of environmental conditions and agricultural management practices. This study focuses on the impact of tillage practices in unirrigated agricultural fields in Hidalgo and Willacy counties located in South Texas on Hidalgo Sandy Clay Loam; With a particular focus on Soil Total Carbon (TC), Soil Inorganic Carbon (SIC), Permanganate Oxidizable Carbon (POXC), Carbon and Nitrogen ratio (C:N), Soil Organic Matter …

Dynamic Soil Properties In The Lower Rio Grande Valley: Understanding Responses Of Infiltration Rate, Bulk Density, Aggregate Stability To Different Tillage Practices, Temiloluwa Faith Awotoye

Theses and Dissertations

Dynamic Soil Properties (DSPs) are soil properties that change in response to both natural and human-caused interruptions and pressures such as agro-based and wildland management. These soil properties can transform for months or even years in response to the farm use and management procedures. This research project investigates the relationship between different dynamic soil physical properties and tillage practices in the Texas Hidalgo sandy clay loam benchmark soil series. Data analyses was done to compare the effect of tillage to these soil physical properties and build a discussion about relationships between on-farm practices to other aspects of farm viability. We …

Conjunctive Management For Groundwater-Surface Water Resources: Numerical Modeling And Potential Assessment Of Managed Aquifer Recharge (Mar) At Lower Rio Grande Valley In South Texas, Dwight Zedric Q. Capus

Theses and Dissertations

Texas is well known to frequent floods and droughts, and yet has mounting concerns in very imbalanced water availability and water demands from growth in population and economical activities. Capturing and storing water is essential to long-term and climate-smart management of the “already-scarce” water resources. This study aimed to apply numerical modeling to evaluate potentials and impacts of Managed Aquifer Recharge (MAR) to regional groundwater systems in the Lower Rio Grande Valley. Using Visual MODFLOW Flex 3D package, different scenarios were simulated for groundwater flow patterns and storage capacities. Water injections tested ranged between 7.30x105 ft3 to 3.65x109 ft3 , …

Salas Y Gómez Benthic Habitat And Community Assessment Of Seamounts And Oceanic Islands, Kara Eckley

Theses and Dissertations

Seamounts are essential benthic habitats that are ecologically important, providing habitat and functioning as stepping stones for dispersal and possible refugia, and economically valuable, supporting deep-sea fisheries and potential mineral mining activities. The Salas y Gómez Ridge in the southeast Pacific Ocean longitudinally contains dozens of seamounts that extend ~2,900 km across the South Pacific Subtropical Gyre. The ridge contains a range of oxygen and nutrient conditions that, along with the distance between seamounts, have led to high levels of endemism, reported in the few studies that have been conducted on seamounts of the region; this study is the first …

Search For Gravitational Waves From Core Collapse Supernovae In Ligo's Observation Runs Using A Network Of Detectors, Shahrear Khan Faisal

Theses and Dissertations

Core-Collapse Supernova (CCSN) is one of the most anticipated sources of Gravitational Waves (GW) in the fourth observation run (O4) of LIGO and other network of GW detectors. A very low rate of galactic CCSN, coupled with the fact that the CCSN waveforms are unmodeled, make detection of these signals extremely challenging. Mukherjee et. al. have developed a new burst search pipeline, the Multi-Layer Signal Enhancement with cWB and CNN or MuLaSEcC, that integrates a non-parametric signal estimation and Machine Learning. MuLaSEcC operates on GW data from a network of detectors and enhances the detection probability while reducing the false …

Green Synthesis Of Spiro Compounds And The Phytochemical Investigation Of Diethyl Ether Fraction Of Camu-Camu (Myrciaria Dubia) Leaves, Judith Anane

Theses and Dissertations

There are a lot of lucrative plant species found in the Amazon and camu-camu (Myrciaria dubia (H.B.K.) Mc Vaugh) is distinct among them. This is due to its exceptional Vitamin C content which varies from 1600 to 6112 mg/100g of pulp. Besides the fruits which is popularly used, different parts of camu-camu plants including the stems, leaves, seeds, barks, and roots are also traditionally used in folklore practices for treating various ailments and diseases and research has showed the presence of antioxidant, antimicrobial, anticancer, anti-inflammatory agents present in these parts. In this study, the characterization of a bioactive compound, …

Glitch Estimation And Removal Using Adaptive Spline Fitting And Wavelet Shrinkage On The Gravitational Wave Data, Mohammad Abu Thaher Chowdhury

Theses and Dissertations

The false alarm rate and reduced sensitivity of searches for astrophysical signals are caused by transient signals of earthly origin, or "glitches," in gravitational wave strain data from groundbased detectors. The greater number of observable astrophysical signals will increase the likelihood of glitch overlaps and exacerbate their negative impact for future detectors with higher sensitivities. The wide morphological diversity and unpredictable waveforms of glitches, and with the vast majority of cases lacking supplemental data present the main obstacles to their mitigation. Thus, nonparametric glitch mitigation techniques are required, which should operate for a wide range of glitches and, in the …