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Evaluating The Influence Of Perfluorooctane Sulfonic Acid Exposure On Blood Glucose Levels: A Comprehensive Multiple Regression Analysis Considering Confounding Factors, Henry Mensah

Theses and Dissertations

Perfluorooctane sulfonate (PFOS) are widely used for industrial and commercial purposes and have received increasing attention due to their adverse effects on health. This thesis investigates the relationship between PFOS exposure and blood glucose levels, considering potential confounding factors. Regression analysis was conducted on a dataset comprising demographic, lifestyle, and biomarker data from a diverse population sample. Sex exhibited a significant role, with females demonstrating an 11.77% increase in blood glucose levels in response to PFOS exposure compared to males, supported by a p-value of 1.04 × 109. Body mass index (BMI) also played a pivotal role, revealing a 2.17% …

Senggani Fruit (Melastoma Malabathricum Linn.) Extract As A Natural Indicator In Ph-Responsive Pva-Taro Starch Plastic Packaging, Rika Risma Dewi, Intan Syahbanu, Winda Rahmalia

Turkish Journal of Chemistry

Polyvinyl alcohol (PVA)-starch-based bioplastics are widely used in many applications. pH-responsive plastic packaging was produced through the incorporation of senggani (Melastoma malabathricum Linn.) fruit extract into PVA-taro starch-based plastic packaging. The objective of this research was to examine the characteristics of senggani fruit extract under different pH conditions and explore its application as a pH indicator in intelligent packaging. The senggani fruit was extracted through the maceration method using a solvent comprising 96% ethanol and 3% citric acid, with a ratio of 85:15 (v/v). The senggani fruit extract solution underwent color changes, appearing pink at pH levels below 6, pale …

Rapid Synthesis Of Azoindolizine Derivatives Via Aryldiazonium Salts, Ferruh Lafzi̇

Turkish Journal of Chemistry

A practical, rapid, and efficient method for the synthesis of azoindolizine derivatives via aryldiazonium salts with excellent yields was reported. Firstly, the corresponding aniline derivatives were synthesized via a simple and rapid method. Then, the optimal reaction conditions were investigated using a variety of protic and aprotic solvents that demonstrating the robustness of the approach. Finally, the applicability of this method to various sources of indolizine and phenyldiazonium tetrafluoroborate salts was expanded.

Antiviral And Cytotoxic Activities And Chemical Profiles Of Two Species Of Abies Nordmanniana From Türkiye, Nazli Sarikahya, Gaye Sümer Okkali, Furkan Ozan Çöven, Sevda Zeinali̇, Gülce Gucur, Ayşe Di̇la Çağlar, Ece Uyar, Ahmet Ceyhan Gören, Ayşe Nalbantsoy

Turkish Journal of Chemistry

Abies is an important genus of the family Pinaceae, with about 50 species found in the highlands of Asia, Europe, North Africa, and North and Central America. The principal aim of the present work was to investigate the chemical content and biological potential of the resin and cone from Abies nordmanniana subsp. bornmulleriana and Abies nordmanniana subsp. equi-trojani, respectively. The flavonoid and phenolic contents of the resin and cones were evaluated using liquid chromatography-high resolution mass spectrometry (LC-HRMS). Additionally, the essential oil and fatty acid compositions were analyzed using gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detector (GC-FID).. Cytotoxicity …

Effect Of Quince Seed Gum (Qsg) On The Performance Of Injectable Hyaluronic Acid Hydrogels In Terms Of The Rheological, Morphological, And Mechanical Aspect, Serdar Kolay, Ni̇lhan Kayaman Apohan, Erdi̇nç Babuç, Gökay Gün

Turkish Journal of Chemistry

Injectable hydrogels play an important role in tissue engineering as a filling and repairing material. This study aimed to develop a new injectable hydrogel based on hyaluronic acid (HA) and quince seed gum (QSG) and investigate the effect of QSG on hydrogel performance. The amount of unreacted 1,4-Butanediol diglycidyl ether (BDDE) is maintained at an undetectable level for HA-QSG hydrogels. Amino acid analysis showed that the HA-QSG hydrogel had rich amino acid concentrations of leucine, arginine, and valine. After thermal sterilization, the elastic modulus of HA-QSG gels for dermal and intra-articular filler applications is 63 Pa and 92 Pa respectively. …

Dft Modeling Of Water-Assisted Hydrogen Peroxide Formation From A C(4a)-(Hydro)Peroxyflavin, Yilmaz Özkiliç

Turkish Journal of Chemistry

The cofactor of a class A monooxygenase is reduced at an external location of the enzyme and is subsequently pulled back into the active site after the reduction. This observation brings the question; is there any defense mechanism of the active site of a monooxygenase against the formation of the harmful hydrogen peroxide from the reactive C(4a)-(hydro)peroxide intermediate? In this study, the barrier energies of one to three water molecule-mediated uncoupling reaction mechanisms in water exposed reaction conditions were determined. These were found to be facile barriers. Secondly, uncoupling was modeled in the active site of kynurenine 3-monooxygenase complex which …

Design And Characterization Of Phosphonic Acid-Functionalized Grafted Sepiolite Nanohybrids And Their Adsorption Studies For Removal Of Copper Ions From Aqueous Solution, Mehwish Tahir, Asif Raza, Amara Nasir, Tariq Yasin, Shamila Imtiaz

Turkish Journal of Chemistry

In this study, we synthesized novel, economically efficient phosphonic acid-functionalized grafted sepiolite nanohybrids for selective elimination of copper ions from water. These nanohybrids were prepared by graft polymerization of glycidyl methacrylate onto sepiolite. We utilized free radical graft polymerization to graft glycidyl methacrylate (GMA) onto silanized sepiolite. The nanohybrids obtained exhibited a grafting percentage of 479% at 0.3 g of KPS initiator, 15% GMA monomer, and after 4 h of reaction. In pursuit of selectively removing metal ions from water, the nanohybrid with the highest grafting (PGE3) was chemically treated with phosphoric acid to introduce phosphonic acid groups on it. …

The Institutional Challenges Of A Quantified Self Study: An Attempt To Ascertain How Data Collected From A Mobile Device Can Be An Indicator Of Personal Mental Health Over Time, Julian Lazaras

University Honors Theses

The adoption of an application of new technology always comes with a bias, this is never more true for the case of human behavioral analytics within higher education. While movements such as the quantified self movement make strides to reinterpret the realm of data analytics, psychology, and computer science, there are inevitably limitations to the adoption and application of such approaches within the standard realm of research. Herein is presented a case where an effort to evaluate the prospect of use of mobile phone data as secondary indicators of personal mental health through the lens of data analysis was put …

Heterogeneous Resources In Infrastructures Of The Edge Network Paradigm: A Comprehensive Review, Qusay S. Alsaffar, Leila Ben Ayed

Karbala International Journal of Modern Science

The late 1990s saw the rise of the edge computing network paradigm, as well as an increase in the number of IoT de-vices. This concept is viewed as a link between cloud servers and end-devices, bringing processing and storage re-sources closer to clients. As a result of its low latency and high performance, researchers and developers have expressed interest in it. However, this paradigm confronts a number of obstacles and restrictions, including restricted and hetero-geneous resources at network edges. In this paper, we provide a detailed review of heterogeneous resources in edge network infrastructures using a three-dimensional method. These three …

Integrated Computational Approaches: Elucidating Molecular Mechanisms Of Pathogenic Proteins And Designing Novel Inhibitors Against Mycobacterium Tuberculosis And Sars-Cov-2, Justin David Carbone

Theses and Dissertations

Chapter 1 introduces computational strategies in computer aided drug design (CADD), focusing on physics-based methodologies to enhance drug discovery. This chapter also discusses the theoretical foundations and practical applications of molecular dynamics (MD) simulations including free energy and stochastic kinetic analysis. In Chapter 2, CADD methods lead to development of inhibitors targeting the RNA Dependent RNA Polymerase (RdRP) of SARS-CoV-2. Inspired by the nucleotide inhibitor Molnupiravir, we aim to design a combinatorial library of 72 novel inhibitors capable of impeding a dual threat inhibition mechanism inducing lethal mutations along with stalling viral replication with specific selectivity to RdRp over Human …

Incorporating Oxygen Isotopes Of Oxidized Reactive Nitrogen In The Regional Atmospheric Chemistry Mechanism, Version 2 (Icoin-Racm2), Wendell W. Walter, Masayuki Takeuchi, Nga L. Ng, Meredith G. Hastings

Faculty Publications

The oxygen isotope anomaly (Δ¹⁷O = δ¹⁷O − 0.52 × δ¹⁸O > 0) has proven to be a robust tool for probing photochemical cycling and atmospheric formation pathways of oxidized reactive nitrogen (NO_y). Several studies have developed modeling techniques to implicitly model Δ¹⁷O of NO_y molecules based on numerous assumptions that may not always be valid. Thus, these models may be oversimplified and limit our ability to compare model Δ¹⁷O values of NO_y with observations. In this work, we introduce a novel method for explicitly tracking Δ …

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 …

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age- And Alzheimer’S Disease-Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. …

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age- And Alzheimer’S Disease-Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. …

Ensemble-Smote: Mitigating Class Imbalance In Graduate On Time Detection, Theng-Jia Law, Choo-Yee Ting, Hu Ng, Hui-Ngo Goh, Albert Quek

Journal of Informatics and Web Engineering

In education, detecting students graduating on time is difficult due to high data complexity. Researchers have employed various approaches in identifying on-time graduation with Machine Learning, but it remains a challenging task due to the class imbalance in the dataset. This study has aimed to (i) compare various class imbalance treatment methods with different sampling ratios, (ii) propose an ensemble class imbalance treatment method in mitigating the problem of class imbalance, and (iii) develop and evaluate predictive models in identifying the likelihood of students graduating on time during their studies in university. The dataset is collected from 4007 graduates of …

Temporal Climatic Shifts In Henan Province: A 16-Decades Perspective Through Regression, Sarima, And Nar Modeling, Lin Qing, Ang Ling Weay, Shao Yiyang, Sellappan Palaniappan

Journal of Informatics and Web Engineering

Global warming is having a significant impact on all aspects of human production and life. This study employs a cross-sectional analysis to investigate the temporal dynamics of average temperature changes in Henan Province, China, from 1851 to 2012. Utilizing the Berkeley Earth Surface Temperature Data and the Daily Meteorological Dataset of China National Surface Weather Station v3.0, we applied regression analysis, Seasonal Autoregressive Integrated Moving Average (SARIMA), and Nonlinear Autoregressive Network (NAR) models to predict temperature trends. Results indicate a significant warming trend over the 160-year period, with the models demonstrating strong predictive performance, albeit with some variability. The study …

Unveiling The Efficacy Of Ai-Based Algorithms In Phishing Attack Detection, Tajamul Shahzad, Kashif Aman

Journal of Informatics and Web Engineering

Phishing poses a significant challenge in an ever-evolving world. The increased usage of the Internet has resulted in the emergence of a different kind of theft referred to as cybercrime. The term cybercrime describes the act of invading privacy and illegitimately obtaining personal information using digital platform. Primarily an approach named phishing is employed, which involves the use of spoof emails or bogus websites by the attackers to get the victim's personal information like their account credentials, debit, or credit card’s number, etc. To give the brief knowledge of phishing attacks and their types of the objective of this work …

Streamlining Dental Clinic Management For Effective Digitisation Productivity And Usability, Sin-Ban Ho, En-Yu Chew, Chuie-Hong Tan

Journal of Informatics and Web Engineering

Oral health is an integral part of overall health, and poor oral hygiene can lead to a variety of health problems. Modern oral care has greatly improved our quality of life, but the increasing demand for routine dental checkups and treatments calls for improved systems for managing patient records and appointments. While technology has significantly enhanced the efficacy and experience of dental care, many dental clinics still rely on paper records to record the patient’s oral condition, but these are not easily accessible to the patients for viewing. This study aims to address the issue by developing a Dental Clinic …

Development And Validation Of Autotronic Training Module For Automobile Technology Students In Polytechnics In Southern Nigeria, Saue, Baritule Prince, Chukuigwe, Ogbondah Nndameka, Bassey, Imaobong Sunday

Journal of Informatics and Web Engineering

A research was carried out to create and verify an autotronic training module for students studying vehicle technology at polytechnics located in Southern Nigeria. The design used for the project was Research and Development (R&D). An observation has been made that the curriculum of polytechnics in Nigeria lacks sufficient substance on autotronics technology. As a result, lecturers have challenges in fully imparting the abilities that are essential for the professional world. Undoubtedly, there is now a disparity between the training that craftsmen receive and the skills that are demanded by industries. The research was carried out in the southern region …

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 …

Feasibility Of Oil Palm Agroforestry System: Evaluating The Application Of Oil Palm Ash For Enhancing Cherry Tomato (Solanum Lycopersicum. Var. Nancy Rz) Production Using Brackish Water., Ime Joseph Bassey

Theses and Dissertations

Monoculture systems of oil palm production are ravaging the world’s tropical forests, causing deforestation and biodiversity loss, which contribute to climate change at an uncontrollable pace. Oil palm agroforestry systems (AFSs), one of the strategies of regenerative agriculture, have proven to reverse the unfavorable effects of the oil palm monoculture systems. A sustainable means of soil fertilization and irrigation must be explored to improve the feasibility of oil palm AFSs. This study evaluates the impact of the application of oil palm ash and brackish irrigation on cherry tomato production. The experiment was conducted in a hydroponic system using a 2*4 …

Zinc Oxide Nanostructures Synthesized By Hot Water Treatment For The Photocatalytic Degradation Of Organic Pollutants In Water, Ranjitha Kumarapuram Hariharalakshmanan

Theses and Dissertations

Photocatalysis using nanostructured semiconductors for the degradation of organic pollutants has received significant attention as an advanced water treatment method. A photocatalyst absorbs light with energy greater than or equal to its band gap and generates electron-hole pairs. These electrons and holes take part in redox reactions in water to generate reactive oxygen species, such as hydroxyl radicals and superoxide anions, which can break down organic contaminants. However, this method has some challenges, such as electron-hole recombination, which reduces the efficiency, high cost of nanostructure synthesis, and reduced durability of nanostructured photocatalysts in suspension form. The immobilization of photocatalyst nanostructures …

Hidden Scientists/Hidden Creatives, Con Kennedy

Conference Presentations

This presentation discussed how the UN Sustainable Development Goals (SDGs) were integrated into an existing graphic design module delivered on the BA in Visual Communication Design in a joint project with the TU Dublin School of Art and Design, School of Biological, Health and Sports Sciences
 Sustainability and Research Hub
Research, the Ethics and Integrity Office. The project explored underrepresented women in science and graphic design.

The Mrnacalc Webserver Accounts For The N1-Methylpseudouridine Hypochromicity To Enable Precise Nucleoside-Modified Mrna Quantification, Sarah E. Krul, Sean J. Hoehn, Carlos E. Crespo-Hernández

Faculty Scholarship

Nucleoside-modified messenger RNA (mRNA) technologies necessarily incorporate N1-methylpseudouridine into the mRNA molecules to prevent the over-stimulation of cytoplasmic RNA sensors. Despite this modification, mRNA concentrations remain mostly determined through the measurement of UV absorbance at 260 nm wavelength (A260). Herein, we report that the N1-methylpseudouridine absorbs approximately 40% less UV light at 260 nm than uridine, and its incorporation into mRNAs leads to the under-estimation of nucleoside-modified mRNA concentrations, with 5%–15% error, in an mRNA-sequence-dependent manner. We therefore examined the RNA quantification methods and developed the mRNACalc webserver. It accounts for the molar absorption coefficient of modified nucleotides at 260 …

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 …

Leveraging Biological Mechanisms In Machine Learning, Kyle J. Rogers

Theses and Dissertations

This thesis integrates biologically-inspired mechanisms into machine learning to develop novel tuning algorithms, gradient abstractions for depth-wise parallelism, and an original bias neuron design. We introduce neuromodulatory tuning, which uses neurotransmitter-inspired bias adjustments to enhance transfer learning in spiking and non-spiking neural networks, significantly reducing parameter usage while maintaining performance. Additionally, we propose a novel approach that decouples the backward pass of backpropagation using layer abstractions, inspired by feedback loops in biological systems, enabling depth-wise training parallelization. We further extend neuromodulatory tuning by designing spiking bias neurons that mimic dopamine neuron mechanisms, leading to the development of volumetric tuning. This …

Production Of The Siderophore Lysochelin In Rich Media Through Maltose-Promoted High-Density Growth Of Lysobacter Sp. 3655, Fang Zhang, Jia Liu, Lin Jiang, Yongbiao Zheng, Lingjun Yu, Liangcheng Du

Department of Chemistry: Faculty Publications

Siderophores are produced by bacteria in iron-restricted conditions. However, we found maltose could induce the biosynthesis of the siderophore lysochelin in Lysobacter sp. 3655 in rich media that are not compatible with siderophore production. Maltose markedly promoted cell growth, with over 300% increase in cell density (OD₆₀₀) when LB medium was added with maltose (LBM). While lysochelin was not detectable when OD₆₀₀ in LBM was below 5.0, the siderophore was clearly produced when OD₆₀₀ reached 7.5 and dramatically increased when OD₆₀₀ was 15.0. Coincidently, the transcription of lysochelin biosynthesis genes was remarkably enhanced following the …

Case Studies For Energy Efficient Machine Learning Inference Acceleration, Recep Erol

Theses and Dissertations

The advancements in machine learning, deep learning and AI have yielded remarkable tools and innovations, but certain groups face barriers preventing their utilization of these technologies. This research identifies and categorizes these barriers, focusing on three distinct groups: those lacking computational power, seeking to deploy models across multiple devices, and struggling with optimization challenges in high-performance computing centers. The study highlights the disconnect between academia's proposed solutions and their practical integration within industries and research centers, emphasizing the lack of convenience and integration among existing tools. To bridge this gap, this research offers a multifaceted approach. Firstly, it introduces publicly …

An Investigation Of The Mindset Context And Its Downstream Effects On Marginalized Student Outcomes In College Stem Courses, Ronia Naim Kattoum

Theses and Dissertations

Multiple national calls centered on critical thinking and social justice have been made to improve and reform higher education in science, technology, engineering, and mathematics (STEM) courses to increase the representation of students from marginalized groups in the STEM workforce and equip all students for success. To help answer this call, our project has two overarching goals: 1) Identify pathways to increase student success in STEM courses at a moderately selective metropolitan institution with a diverse population that can be generalized to similar institutions, and 2) determine how instructional practices influence perceptions of the learning environment, especially for marginalized students. …