Digital Commons Network^™

High-Performance Computing In Next-Generation Sequencing Read Alignment, Minh H. Pham

USF Tampa Graduate Theses and Dissertations

Advancements in Next-Generation Sequencing (NGS) have dramatically reduced the cost and increased the speed of DNA sequencing. However, this rapid influx of data necessitates efficient and robust analysis tools, particularly for the complex task of aligning short NGS reads to reference genomes such as the human genome. We explore groundbreaking computational strategies and hardware acceleration to optimize this critical alignment process. This dissertation is structured around three innovative studies. First, we introduce a novel approach to dynamic memory allocation tailored for massively parallel systems, particularly Graphical Processing Units (GPUs), to support NGS alignment and other applications. Unlike traditional memory allocators …

Quantification And Diversity Of A Ubiquitous Ssdna Phage Group (Gokushovirinae) In The Red Sea Through The Polony Technique, Natalie A. Sawaya

USF Tampa Graduate Theses and Dissertations

With average concentrations of 107 virus-like particles per milliliter of seawater, viruses comprise the second largest biomass in the ocean, where they are a driving force of microbial evolution and constitute important roles in Earth’s biogeochemical cycles. Bacteriophage (phage), viruses that infect bacteria, are of particular importance in the marine ecosystem as they impact the efficiency of the microbial loop, which recycles carbon in surface waters, counteracting vertical export through the biological pump. Although double-stranded DNA phage have been researched extensively, single-stranded DNA (ssDNA) phage remain understudied, mostly due to methodological limitations.

The incorporation of rolling circle amplification (RCA) into …

Sars-Cov-2 Neurotropism: Understanding Effects At The Blood-Brain Barrier And Hematogenous Neuroinvasiveness, Taylor E. Martinez

USF Tampa Graduate Theses and Dissertations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has provisional counts of over 110 million documented cases and 1.218 million deaths (as of February 2024) in the United States since January 2020. SARS-CoV-2 is an airborne respiratory virus that primarily infects the lungs via the ACE2 receptor but has well-documented secondary target organs including the kidneys, the gastrointestinal tract, the heart, and the skin. SARS-CoV-2 also infects the brain, but the hematogenous route of viral entry to brain is still not fully characterized. Understanding how SARS-CoV-2 traverses the blood-brain barrier (BBB) as well as how it …

The Polyaneuploid Cancer Cell State And Therapeutic Resistance: Eco-Evolutionary Dynamics In Structured Populations, Anuraag Bukkuri

USF Tampa Graduate Theses and Dissertations

In this dissertation, I develop and apply eco-evolutionary modeling techniques to understand how the polyaneuploid cancer cell (PACC) state, entered when aneuploid cells exit the cell cycle after S phase and undergo a whole genome duplication, contributes to therapeutic resistance. Since resistance remains one of the primary causes of treatment failure in cancer patients, it is critical to understand how such demographic state transitions allow for acclimatization of cancer cells to therapeutic stressors and how they interact with evolutionary processes to promote irreversible resistance.

In Chapters Two and Three, I lay the foundation for this work. In Chapter Two, I …

Emergent Magnetism And Hyperthermia In Phase- And Size-Tunable Iron Oxide Nanostructures, K Mudiyanselage Tharindu Supun Bandara Attanayake

USF Tampa Graduate Theses and Dissertations

Iron oxide nanoparticles (IONPs) hold immense potential across diverse fields, from spintronics, magnetic hyperthermia to drug delivery, biodetection, and magnetic resonance imaging. Unlocking these applications hinges on our ability to tailor the magnetic properties of IONPs, and this dissertation presents novel and powerful approaches for enhancing magnetic and hyperthermic responses of multiphase iron oxide nanostructures. This is achieved by manipulating their phase volume fraction, size, and shape with a focus on the magnetic tunability of nanostructures via strategic control over structural and environmental parameters. The aforementioned has been achieved by the following three key approaches: (i) phase-tunability of iron oxide …

Predicting Ph At In-Situ Temperature For Aquatic Environments, Sarah E. Bartoloni

USF Tampa Graduate Theses and Dissertations

pH is typically measured at a constant temperature and, as needed, converted to in-situ temperature using a system of thermodynamic equations. Using this equilibrium approach, adjustment of pH to in situ conditions requires two measured CO2 system parameters (pH, total alkalinity, dissolved inorganic carbon, or CO2 fugacity). Currently, when pH is the only measured CO2 system parameter, linear models are used to adjust the pH to in-situ temperature. Although many studies have attempted to optimize CO2 equilibrium constants (K1 and K2) for the CO2 system over a range of conditions, very little prior work has experimentally examined which CO2 system …

Macrophage-Driven Car T Cell Resistance In B Cell Lymphoma, Sae Bom Lee

USF Tampa Graduate Theses and Dissertations

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment of patients with relapsed/ refractory large B cell lymphoma (LBCL). Despite its promising efficacy, a subset of patients experiences primary resistance or relapse. In Chapter 2, we explore the tumor microenvironment (TME)-induced resistance mechanisms in patients with LBCL. Analysis of the intratumoral immune infiltrates in pre-infusion tumor biopsies revealed that the levels of immunoregulatory macrophages were elevated in patients who responded poorly to axicabtagene ciloleucel (axi-cel). Using preclinical mouse B cell tumor models, we found that the CAR T-cell-produced interferon-gamma (IFN-γ) enhanced the expression of inducible nitric oxide synthase (iNOS, …

Arthropod Associates Of The Gray Catbird On Vaca Key, Lawrence J. Hribar, Aline D. Tassi

Florida Field Naturalist

No abstract provided.

Lice And Mites From A Fall Warbler On Vaca Key, Lawrence J. Hribar

Florida Field Naturalist

No abstract provided.

Florida Scrub-Jay (Aphelocoma Coerulescens) Pair Constructs Highest Nest On Record, Meredith Heather, Tori D. Bakley, Sahas Barve

Florida Field Naturalist

No abstract provided.

Activities And Habitat Use By Feral Mallards In An Urban Ecosystem, Zachary J. Smith, Joni Downs, Mahnoor Kamal, Jonathan D. Major

Florida Field Naturalist

No abstract provided.

Interactions Between Sympatric Florida Scrub-Jays And Southeastern American Kestrels, Karl E. Miller, Benjamin Ewing

Florida Field Naturalist

No abstract provided.

Winter Return Rates, Patch Fidelity, And Response To Prescribed Fire For Grasshopper And Savannah Sparrows In Southwestern Florida, Bob Altman, Kathleen N. Smith, Joseph Bozzo, Robert T. Meyer

Florida Field Naturalist

No abstract provided.

Arthropods Taken From Birds On Vaca Key, Monroe County (Columbiformes: Columbidae; Passeriformes: Parulidae, Sturnidae, Turdidae), Lawrence J. Hribar

Florida Field Naturalist

No abstract provided.

Black Spiny-Tailed Iguana (Ctenosaura Similis) Use Of Gopher Tortoise (Gopherus Polyphemus) Burrows In Buckingham, Florida, Josie Rivero, Andrew M. Durso

Florida Field Naturalist

No abstract provided.

Current Distribution Of Black Rails In Florida, Amy C. Schwarzer, Gina Kent, Bryan D. Watts, Ken Meyer, Amanda Powell, Brittany Bankovich, W. Andrew Cox

Florida Field Naturalist

No abstract provided.

Habitat Associations For Eastern Black Rail (Laterallus Jamaicensis Jamaicensis) In South Florida, Chance Hines, Laura Duval, Bryan Watts

Florida Field Naturalist

No abstract provided.

Comparing The Frequency Of Incest Between Siblings In Two Populations Of Florida Scrub-Jays (Aphelocoma Coerulescens), Kelly A. Roberts, Abigail Valine, Angela Tringali, Michelle Dent, Reed Bowman

Florida Field Naturalist

No abstract provided.

Review: An Atlas Of Speciation In African Passerine Birds By Bp Hall And Re Moreau, Donald S. Heintzelman

Eastern Bird Banding Association News

No abstract provided.

Call For Papers For Joint Ebba-Nebba Annual Meeting Chevy Chase Md 1976, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.

Population Estimate For The American Kestrel In The Great Valley Section Of Pennsylvania, G. Robert Ganis

Eastern Bird Banding Association News

No abstract provided.

Corrigendum, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.

Weight, Wing Length, And Fat Class Measurements Of Living Tree Sparrows (Spizella Arborea), Kenneth W. Prescott

Eastern Bird Banding Association News

No abstract provided.

Banders' Marketplace, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.

The Role Of Banding Studies In Evaluating The Accumulation And Cycling Of Radionuclides And Other Environmental Contaminants In Free-Living Birds, Lehr Birsbin Jr., Jeff Swinebroad

Eastern Bird Banding Association News

No abstract provided.

On The Netting Of Certain Finches, Curtis S. Adkisson

Eastern Bird Banding Association News

No abstract provided.

Attracting Birds With Taped Calls In The Ramapos, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.

News From The Banding Lab, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.

American Banding Directory Ii L-Z, Kenneth W. Prescott

Eastern Bird Banding Association News

No abstract provided.

Popular Trap Designs, Frederick S. Schaeffer

Eastern Bird Banding Association News

No abstract provided.