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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 …

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 …

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 …

Trends And Patterns Of Plant Conservation Research In Borneo: A Review, Rizmoon Nurul Zulkarnaen, Sabri Mohd. Ali, Daniele Cicuzza

ASEAN Journal on Science and Technology for Development

Borneo hosts exceptional plant diversity, including numerous endemic species, but faces significant threats from rapid habitat loss driven by deforestation and land-use changes. This study aimed to analyze research trends and forecast future directions through a bibliometric analysis of Scopus data spanning from 1914 to 2023. The bibliometric analysis included publication outputs, citation patterns, thematic mapping, and keyword co-occurrence. We used VOSviewer to visualize bibliometric networks and the Bibliometrix package in R to perform advanced bibliometric analysis and interactive data exploration. The analysis revealed a continuous rise in publications (998 documents), with the Journal of Ecology identified as the most …

Moose Abundance And Calf:Cow Ratios On The Blackfeet Indian Reservation And Glacier National Park, Landon Joel Magee

Graduate Student Theses, Dissertations, & Professional Papers

Many moose (Alces alces; Sikihtsisoo) populations across North America, especially along their southern range, are declining due to factors such as climate change, parasites and disease, predation, habitat loss and degradation, and overharvest. These declines highlight broader ecological concerns, as moose play a critical role as prey within their ecosystems. Despite their importance, data on crucial demographic parameters like abundance and age ratios are sparse for moose, complicating management efforts. Conventional monitoring methods, including radio-collaring, harvest data, public surveys, and aerial surveys, face significant logistical and financial challenges, and often fail to provide a comprehensive understanding of …

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 …

New Treatment Modality For Metastatic Cancer By Targeting The Endothelin Type A Receptor (Etar), Elbara Fathelrahman Abdelmoula

Theses

Ambrisentan, an FDA-approved selective antagonist of the Endothelin Type A Receptor (ETAR) for pulmonary arterial hypertension, has shown potential in limiting cancer growth and metastasis. While effective treatment options for melanoma remain elusive, this study investigates the effects of Ambrisentan on invasive, metastatic B16F10 melanoma using a syngeneic mouse model, aiming to assess Ambrisentan’s impact on tumor growth, metastasis, and overall host survival in B16F10 melanoma, along with gaining mechanistic insights into ETAR antagonism. C57Bl/6 mice were divided into two groups, receiving either dH2O or Ambrisentan orally. Treatments commenced prior to tumor implantation and continued post-implantation. Luciferase-expressing B16F10 cells facilitated …

Natural Selection On Feralization Genes Contributed To The Invasive Spread Of Wild Pigs Throughout The United States, Niek W. G. Barmentlo, Patrick G. Meirmans, William H. Stiver, Joseph G. Yarkovich, Blake E. Mccann, Antoinette J. Piaggio, Dominic Wright, Timothy J. Smyser, Mirte Bosse

United States Department of Agriculture Wildlife Services: Staff Publications

Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive …

Binding Affinity, Selectivity, And Pharmacokinetics Of The Oxytocin Receptor Antagonist L-368,899 In The Coyote (Canis Latrans), Sara M. Freeman, J. Leon Catrow, James Eric Cox, Alexandra Turano, Mckenna A. Rich, Hillary P. Ihrig, Naveena Poudyal, Cheng-Wei Tom Chang, Eric M. Gese, Julie K. Young, Aaron L. Olsen

United States Department of Agriculture Wildlife Services: Staff Publications

L-368,899 is a selective small-molecule oxytocin receptor (OXTR) antagonist originally developed in the 1990s to prevent preterm labor. Although its utility for that purpose was limited, L-368,899 is now one of the most commonly used drugs in animal research for the selective blockade of neural OXTR after peripheral delivery. A growing number of rodent and primate studies have used L-368,899 to evaluate whether certain behaviors are oxytocin dependent. These studies have improved our understanding of oxytocin’s function in the brains of rodents and monkeys, but very little work has been done in other mammals, and only a single paper in …

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 …