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Identifying Nutrient Dynamics And Relative Groundwater Contribution In Wetlands At Fish Lake Environmental Center, Lapeer Mi, Rose Allen

Senior Honors Theses and Projects

Wetlands are complex ecosystems that are dependent on hydrologic processes and water chemistry. Understanding the role that water chemistry and nutrients play in wetland ecosystems is crucial to wetland management and restoration. The Fish Lake Environmental Education Center near Lapeer Michigan, is glacially influenced, and contains a large bog. Between the bog and lake there are multiple kettles that contain ephemeral wetlands in the spring. Bogs are primarily precipitation sourced, whereas the kettle wetlands may be a combination of precipitation and groundwater sourced. Previous studies indicated that groundwater flow direction is towards Fish Lake, but it was unclear to what …

Patterns Of Epiphytic Bacterial Growth On Flower Surfaces: Relationships With Flower Longevity And Environmental Factors, Rita Nkem Afagwu

Graduate Theses/Dissertations

Flowers host diverse communities of epiphytic bacteria, which can impact floral functions, pollinator interactions, and overall plant fitness. However, little is known about how the abundance of these bacteria change as flowers age, and how these shifts may correlate with floral longevity. In this study I investigate the change in bacterial abundance across the lifespan of a flower from anthesis (opening of bud to flower) to senescence (wilting of flower) and to explore the potential implications for floral longevity. We tracked the age of the flowers by determining the average age to senescence in flowers of 8 plant species over …

Developmental Patterns Underlying Variation In Form And Function Exhibited By House Gecko Toe Pads, Aaron H. Griffing, Tony Gamble, Ashmika Behere, Timothy E. Higham, Greta M. Keller, John Resener, Thomas J. Sanger

Biological Sciences Faculty Research and Publications

Adhesive toe pads have evolved numerous times over lizard evolutionary history, most notably in geckos. Despite significant variation in adult toe pad morphology across independent origins of toe pads, early developmental patterns of toe pad morphogenesis are similar among distantly related species. In these distant phylogenetic comparisons, toe pad variation is achieved during the later stages of development. We aimed to understand how toe pad variation is generated among species sharing a single evolutionary origin of toe pads (house geckos—Hemidactylus). We investigated toe pad functional variation and developmental patterns in three species of Hemidactylus, ranging from highly …

Bacillus Subtilis-Derived Peptides Disrupt Quorum Sensing And Biofilm Assembly In Multidrug-Resistant Staphylococcus Aureus, Kyle R. Leistikow, Daniel S. May, Won Se Suh, Gabriel Vargas Asensio, Adam J. Schaenzer, Cameron R. Currie, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Multidrug-resistant Staphylococcus aureus is one of the most clinically important pathogens in the world, with infections leading to high rates of morbidity and mortality in both humans and animals. The ability of S. aureus to form biofilms protects cells from antibiotics and promotes the transfer of antibiotic resistance genes; therefore, new strategies aimed at inhibiting biofilm growth are urgently needed. Probiotic species, including Bacillus subtilis, are gaining interest as potential therapies against S. aureus for their ability to reduce S. aureus colonization and virulence. Here, we search for strains and microbially derived compounds with strong antibiofilm activity against multidrug-resistant S. …

Advanced Mathematical Graph-Based Machine Learning And Deep Learning Models For Drug Design, Farjana Tasnim Mukta

Theses and Dissertations--Mathematics

Drug discovery is a highly complicated and time-consuming process. One of the main challenges in drug development is predicting whether a drug-like molecule will interact with a specific target protein. This prediction accelerates target validation and drug development. Recent research in biomolecular sciences has shown significant interest in algebraic graph-based models for representing molecular complexes and predicting drug-target binding affinity. In this thesis, we present algebraic graph-based molecular representations to create data-driven scoring functions (SF) using extended atom types to capture wide-range interactions between targets and drug candidates. Our model employs multiscale weighted colored subgraphs for the protein-ligand complex, colored …

Geographical Variation In Songs Of Bachman’S Sparrow (Peucaea Aestivalis), L. Nguyen, K. Doñas, J. Jackson, R. Kannan

Journal of the Arkansas Academy of Science

We present an analysis of geographic variation in primary song components of the Near Threatened North American endemic, Bachman’s Sparrow (Peucaea aestivalis). These songs have 2 distinct portions: an introductory tweet we call the "whistle" and a more complex second portion that we call the "trill". We analyzed 327 songs from 111 recordings downloaded from eBird.org from the entire current range of the species. We grouped the recordings into 3 distinct geographic clusters, East, Central, and West. The data measured from spectrograms suggest a significant statistical difference among groups for 3 measured characteristics: frequency range of trill, number of horizontal …

A Class Of Game-Theoretic And Fokker-Planck Optimal Control Frameworks In Colon And Esophageal Cancer, Mesfer Alajmi Phd

Mathematics Dissertations - Archive

In this dissertation, we first present a new stochastic framework for parameter estimation and uncertainty quantification in colon cancer-induced immune responses. A stochastic process that captures the system's inherent randomness determines the dynamics of colon cancer. The stochastic framework is based on the Fokker-Planck equation, which represents the evolution of the probability density function corresponding to the stochastic process. We formulate an optimization problem that takes individual patient data with randomness present and solves it to obtain the unknown parameters corresponding to the individual tumor characteristics. Furthermore, we perform a sensitivity analysis of the optimal parameter set to identify the …

Nanotube Spectral Fingerprinting And Machine Learning For Optimized Bioimaging/Sensing Applications, Aceer Nadeem

Open Access Dissertations

This thesis presents a multifaceted exploration of the optimization and application of single-walled carbon nanotubes (SWCNTs) in biomedical contexts, with a specific focus on enhancing their stability, functionality, and use as optical biosensors. The research spans several key areas, including the development of innovative techniques that couple machine learning with spectral fingerprinting for advanced diagnostics, the investigation of SWCNT chirality and its implications for cellular interactions, and the optimization of lyophilization processes to improve long-term stability and reproducibility.

The first section of the thesis delves into the fundamental properties of SWCNTs, emphasizing their unique electronic and optical characteristics. These properties, …

Occurrence And Fate Of Per- And Polyfluoroalkyl Substances (Pfas) In Atmospheric Deposition, Surface Waters, And Sediments Discharging To The Great Bay Estuary, New Hampshire, Katherine Alexina Wieck

Master's Theses and Capstones

Per- and polyfluoroalkyl substances (PFAS) are a class of several thousand synthetic organic compounds commonly utilized in the manufacturing of consumer products and in industrial processes since their initial development in the 1940s. Although the widespread presence of PFAS in environmental matrices derives from many different industrial and domestic sources, recent studies characterizing their fate in aqueous systems have primarily focused on point source discharge, such as those from wastewater treatment facilities, airports, and industrial complexes. Focusing on point sources neglects atmospheric deposition, an important diffuse background source of PFAS into surface waters and sediments. Furthermore, atmospheric deposition is likely …

Icvd Polymer Thin Film Bio-Interface-Performance For Fibroblasts, Cancer-Cells, And Viruses Connected To Their Functional Groups And In Silico Studies, Asmaa Taha

Nanotechnology Research Centre

Thin polymer coatings are used to improve the interface between biological species and functional materials. Their interaction is significantly influenced by the functional groups and roughness of the polymer film and prediction of the interaction is thus of great interest. However, for conventional polymer films, this cannot be examined independently because of the interplay of defects, residual solvent molecules, roughness, and functional groups. Solvent-free polymer films prepared by initiated chemical vapor deposition (iCVD) exhibit conformal, defect-free characteristics and enable precise tailoring of the functional groups. This facilitates to isolate the contribution of functional groups on the bio-interface performance. Consequently, in …

Stress Physiology Of Bats: Methodological And Biological Studies Using Hair Cortisol, Marcus Jorgensen

All-Inclusive List of Electronic Theses and Dissertations

Stress physiology in bats can be studied through various non-invasive methods, with hair cortisol levels being a particularly valuable measure. Hair cortisol analysis provides insights into the long-term stress levels and physiological states of bats, as it captures cortisol accumulation over time. This method helps researchers understand how different stressors and environmental factors impact bat populations. In mydissertation, I focused on assessing the validity and reliability of hair cortisol measurements in bats and explored the implications of these measurements for understanding bat stress physiology. In the first chapter, I evaluated the use of commercial enzyme immunoassay kits to measure cortisol …

Optimizing Large Language Models And Multimodal Approaches For Biomedical Publication And Satellite Imagery, Youngsun Jang

Electronic Theses and Dissertations

This dissertation comprises two main sections: the first focuses on natural language processing (NLP) for extracting key information from scientific literature using large language models (LLMs), and the second addresses remote sensing for detecting natural disasters, such as floods, from satellite imagery using a multimodal approach. The first section investigates methods to enhance Transformer-based models in classifying and extracting information from biomedical scientific publications. Key contributions include the development of a custom dataset for classification and Question and Answering (Q&A) tasks, fine-tuning Transformer models like the Bidirectional Encoder Representations from Transformers (BERT) and addressing multi-span answer issues with the TAg-based …

Human Olfactory Assessment Of Scented Volatile Chemical Product Emissions, Jordan Cross, Brian Magnuson, Zachary Limaye, Rashmika Manipati, Chunxu Huang, Jianghui Liu, Brandon Boor, Nusrat Jung

International High Performance Buildings Conference

No abstract provided.

Functionalized 1,4-Naphthoquinone-Annulated N-Heterocyclic Carbenes For Biomedical Applications, Dilsha Samanali Wickramasinghe

Browse all Theses and Dissertations

Gold has long been recognized for its medicinal applications, dating back centuries. The use of N-heterocyclic carbenes (NHCs), stable, tunable ligands, has revolutionized the development of metal complexes, particularly those involving gold. Among these, Au-NHC complexes have shown significant promise in treating various diseases, especially arthritis and cancer. More recently, our research has focused on synthesizing dual-targeting naphthoquinone-annulated NHC-based gold(I) complexes, which have demonstrated impressive therapeutic potential in cancer treatment. This emphasizes the growing importance of gold-based complexes in developing more selective and effective cancer therapies. By strategically tuning the electronic and steric properties of these complexes, we have explored …

Associations Between Urine Specific Gravity And Race/Ethnicity At The Population Level: Implications For Hydration Status Categorization, Ian P. Winter, Brain K. Ferguson, Patrick B. Wilson

Exercise Science Faculty Publications

Objective

We aimed to evaluate how urine specific gravity (USG) and rates of supposed hypohydration vary by race/ethnicity, and to examine how adjustment for several important factors impacts estimated USG.

Methods

Using the National Health and Nutrition Examination Survey, this cross‐sectional study evaluated a total of 4195 (2098 female, 2097 male) Americans and categorized them as supposedly hypohydrated (USG≥1.020) or not using spot urine samples. USG and prevalence of supposed hypohydration were compared across racial/ethnic groups, separately by gender. The analyses considered the impact of urine creatinine, body composition, age, dietary nutrients, and physical activity.

Results

Differences in supposed hypohydration …

Advanced Techniques In Time Series Forecasting: From Deterministic Models To Deep Learning, Xue Bai

Graduate Theses, Dissertations, and Problem Reports (ETD)

This dissertation discusses three instances of temporal prediction, applied to population dynamics and deep learning.

In population modeling, dynamic processes are frequently represented by systems of differential equations, allowing for the analysis of various phenomena. The first application explores modeling cloned hematopoiesis in chronic myeloid leukemia (CML) via a nonlinear system of differential equations. By tracking the evolution of different cell compartments, including cycling and quiescent stem cells, progenitor cells, differentiated cells, and terminally differentiated cells, the model captures the transition from normal hematopoiesis to the chronic and accelerated-acute phases of CML. Three distinct non-zero steady states are identified, representing …

Conformational Investigation Of Biopolymers Through Molecular Dynamics (Md) Simulations And In-Droplet Hdx-Ms Utilizing Cvssi, Samira Hajian Foroushani

Graduate Theses, Dissertations, and Problem Reports (ETD)

Over the last two decades, mass spectrometry (MS) has received significant interest in biological study platforms, especially in the areas of proteomics and metabolomics. With the development of soft ionization methods like electrospray ionization (ESI), mass spectrometry has emerged as a potent method for directly characterizing proteins in their native state. The recent invention of capillary vibrating sharp-edge spray ionization has opened new avenues for the study of biopolymer native structure including the usage of droplet charge tuning and in-droplet hydrogen-deuterium exchange (HDX) labeling. With this new technique comes the opportunity to study biopolymer ion structure preservation with molecular dynamics …

Investigating The Protein Interactome Of Escherichia Coli To Understand Metabolic Regulation When Proteins Bind: A Systems Biology Study., Shomeek Chowdhury

Theses and Dissertations

Proteins bind other proteins and work together as machines to perform many biological functions. Metabolic enzymes governing the life-sustaining metabolic reactions and therefore, metabolism are proteins which also binds other proteins. In this dissertation work, I have explored proteins when they interact with metabolic enzymes, play any role in regulating the cell’s metabolism. I study this phenomenon in Escherichia coli whose protein-protein interaction data is readily available in public databases with proper reference to the experimental study. Another good reason is the predictions we make in this computational study can be tested and validated in E. coli as it is …

Computational Characterization Of Extracellular Electro-Osmotic Flow During Tissue Repair, Ashley Jorgensen-Blocker

Electronic Theses and Dissertations

Electrical stimulation (ES) therapy promotes the healing of chronic epidermal wounds and suppresses the degeneration of articular cartilage. Despite the success of ES therapy, the underlying mechanisms by which ES promotes tissue repair are largely unknown, preventing the standardization and optimization of treatments. One proposed mechanism involves electro-osmotic flow (EOF), electrically driven water flow generated within close proximity to the cell surface. EOF induces the transport of macromolecules and removes metabolic wastes and inflammatory molecules from these dense tissues through interstitial flow. This dissertation investigates the application of weak electric fields (EFs) to non-excitable cells and the generation of EOF …

Fda Modernization Act 2.0: The Beginning Of The End For Animal Testing In Drug Development, Julia Williams

Animal Law Review

Historical drug testing protocols utilized animal testing to determine whether drugs were safe and effective for use in humans. However, recognizing that testing drugs on other species is potentially dangerous for humans, troubled by failures, unnecessarily expensive, and time consuming, the FDA Modernization Act 2.0, passed in December 2022, removed animal testing as a requirement for new drug applications. While this was an important step forward, a notable failure of that Act is that it did not go far enough to end animal testing. Accordingly, this Article proposes an FDA Modernization Act 3.0.

The FDA Modernization Act 3.0 would ensure …

Enhancing Identification Of Meteorological And Biological Targets Using The Depolarization Ratio For Weather Radar: A Case Study Of Faw Outbreak In Rwanda, Fidele Maniraguha, Anthony Vodacek, Kwang Soo Kim, Emmanuel Ndashimye, Gerard Rushingabigwi

All Rsif Scholars' Publications

Leveraging weather radar technology for environmental monitoring, particularly the detection of biometeors like birds, bats, and insects, presents a significant challenge due to the dynamic nature of their behavior. Unlike hydrometeor targets, biometeor targets exhibit arbitrary changes in direction and position, which significantly alter radar wave polarization upon scattering. This study addresses this challenge by introducing a novel methodology utilizing Rwanda’s C-Band Polarization Radar. Our approach exploits the capabilities of dual-polarization radar by analyzing parameters such as differential reflectivity (ZDR) and correlation coefficient (RHOHV) to derive the Depolarization Ratio (DR). While existing radar metrics offer valuable insights, they have limitations …

An Ontology Based System For Cancer Diseases Knowledge Mining, Shinead Casey

Theses

National cancer registries play an important role in understanding the patterns and trends of cancer diseases, prevention methods, and treatment management. However, issues arising from data silos and an inability to link heterogeneous data sources have led to problems within the healthcare industry. This became apparent in Ireland in 2018 when Dr Scally’s scoping inquiry into the CervicalCheck controversy highlighted patient safety issues relating to disjointed data and an inability to link datasets.

Worldwide, semantic technologies are being utilised for their ability to link diverse data and enhance analytical capabilities. Therefore, this thesis will examine the use of a knowledge …

Large T Antigen Mediated Target Gene Replication Improves Site-Specific Recombination Efficiency, Zening Wang, Chuan Chen, Xin Ge

Faculty, Staff and Student Publications

With advantages of high-fidelity, monoclonality and large cargo capacity, site-specific recombination (SSR) holds great promises for precise genomic modifications. However, broad applications of SSR have been hurdled by low integration efficiency, and the amount of donor DNA available in nucleus for SSR presents as a limiting factor. Inspired by the DNA replication mechanisms observed in double-stranded DNA virus SV40, we hypothesized that expression of SV40 large T antigen (TAg) can increase the copy number of the donor plasmid bearing an SV40 origin, and in consequence promote recombination events. This hypothesis was tested with dual recombinase-mediated cassette exchange (RMCE) in suspension …

Monte-Carlo Method For Identifying Aberrantly Expressed Genes In Cancer, Matthew M. Beltran

Theses and Dissertations

Gene expression provides insight into the functional variations on the cellular level that shape biological phenomena. Several recent sequencing technologies have produced an abundance of expression profiles spurring entirely new disciplines of biological study. With this myriad of data, the new task is deciding how to assess and extract meaningful insights. Identifying genes with expression changes in disease conditions is often the first step in finding potential biomarkers for diagnosis, and targets for pharmaceutical treatments. Parametric statistical tests at the individual gene level have been the conventional approach for finding differentially expressed genes. These tests exhibit high statistical power but …

Elaboration Of Diquinanes To Access Trifunctional Angular Triquinanes And Designed Dna Polymerase Α Inhibitors, Spencer M. Webber

University of the Pacific Theses and Dissertations

Natural products are of great significance to the pharmaceutical industry in the development of new drugs. Diquinane or bicyclo[3.3.0]octane is a conspicuous structural unit existing in the carbo-frameworks of a wide range of natural products such as alkaloids and terpenoids. These diquinane-containing molecules not only exhibit intriguing architectures, but also showcase a broad spectrum of significant bioactivities, which draw widespread attention from the global synthetic community. A more specific group of compounds containing a diquinane moiety with one extra 5-membered ring are called the angular triquinanes.In this work, we have developed a general synthetic scheme to the angular triquinanes. We …

The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. To monitor and tune the performance of various loss functions for the secondary structure detection problem, we investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1,355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function …

Beyond Implicit Bias, Thomas Albright, William A. Darity Jr., Diana Dunn Dunn, Rayid Ghani, Deena Hayes-Greene, Tanya K. Hernandez, Sheryl Heron

Faculty Scholarship

In their introduction to this edition of Dædalus, Goodwin Liu and Camara Phyllis Jones write that “it is unlikely that implicit bias can be effectively addressed by cognitive interventions alone, without broader institutional, legal, and structural reforms.” They note that the genesis for the volume was a March 2021 workshop on the science of implicit bias convened by the Committee on Science, Technology, and Law of the National Academies of Sciences, Engineering, and Medicine. That workshop provided an opportunity to demonstrate that implicit bias is a common form of cognitive processing that develops in response to social, cultural, and …

State Barrier Fence - Esperance Extension Project Overview 2024, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity published reports

Western Australia’s State Barrier Fence plays an important role in protecting landholders inside the fence by preventing the movement of animal pests, including wild dogs and emus, from pastoral areas into the agricultural regions. It is a state asset which is managed by the Department of Primary Industries and Regional Development.

The original fences (numbers 1, 2 and 3) were constructed between 1902 and 1907. Originally known as the Rabbit Proof Fences, it has also been known as the State Vermin Fence, the Emu Fence and now the State Barrier Fence. Since 2010, the fence has been upgraded to wild …

Investigation Of The Essential Oil Constituents Of Pimenta Racemosa Aerial Parts And Evaluation Of Its Antiviral Activity Against Hsv 1 And 2, Fathia S. Elshaarawy, Mohamed I. S. Abdelhady, Wafaa Hamdy, Haitham A. Ibrahim

Trends in advanced sciences and technology

Pimenta racemosa is a well-known plant used in traditional medicine to treat several ailments. Current pharmaceutical industries rely heavily on the discovery of secondary metabolites found in plants to aid in the development of novel drugs with potential biological activity. This study aimed to investigate the essential oil constituents of Pimenta racemose (Mill.) J. W. Moore aerial parts (leaves and small branches) and evaluate its antiviral activity. The essential oil was prepared by conventional hydro distillation method. The prepared oil was analyzed by GC/MS. Identification of the essential oil constituents was achieved by comparing retention indices (RI) relative to standard …

Evaluating The Use Of Baited Remote Underwater Video (Bruv) In Assessing Shark And Fish Populations In A Low Visibility Estuarine System, The Tolomato River, Fl, Usa, Sarah Worthington

UNF Graduate Theses and Dissertations

Recently, there has been increasing use of baited remote underwater video (BRUV) surveys for assessing shark and fish populations in marine ecosystems. This approach can be useful because it may provide a non-destructive, non-extractive, and cost-effective alternative to traditional fishing-based methods. However, to date, most studies using BRUVs have focused on their use in high-visibility ecosystems, such as tropical reefs. Furthermore, few studies have compared results from BRUV surveys with those obtained using traditional methods to evaluate the efficacy of this approach. Therefore, the goal of this study was to evaluate the effectiveness of using BRUV surveys to assess shark …