Digital Commons Network^™

Draft Genome Assemblies Of Three Klebsiella Grimontii Strains Isolated From Catheterized Urine Samples From The Same Male Participant Over The Course Of 6 Months, Helen Appleberry, Warwick Price, Lorenzo Roque, Evelyn Umana, Alan J. Wolfe, Catherine Putonti, Alex Kula

Biology: Faculty Publications and Other Works

Klebsiella grimontii is a newly identified species within the Klebsiella oxytoca complex. Here, we present the draft genome sequence of three K. grimontii strains that were isolated from catheterized urine samples collected from a participant in a longitudinal study over ~6 months.

Deep Sequence-Coupled Biopanning And Vaccine Development, Julianne Peabody

Biomedical Sciences ETDs

Virus-like particles (VLPs) are nanoparticles comprised of viral structural proteins. They physically resemble the virus from which they are derived but lack genomic material. They are non-infectious, non-replicating, and have a favorable safety profile. VLPs are highly immunogenic with a dense, repetitive structure that is strongly activating for B cells. VLPs can be utilized to develop vaccines and can be used either as direct immunogens or platforms for the display of heterologous antigens. The display of foreign peptides on VLPs can be used to elicit high-titer antibodies against the displayed peptide. A virus-like particle based on the RNA bacteriophage MS2 …

Identification And Characterization Of Intrinsically Disordered Protein Regions, Guy Wayne Dayhoff Ii

USF Tampa Graduate Theses and Dissertations

This dissertation investigates protein intrinsic disorder and intrinsically disordered protein regions (IDPRs) through the development and application of advanced computational and experimental techniques. Chapter 1 provides an introduction to protein intrinsic disorder, outlining the historical context and fundamental concepts that highlight the importance of intrinsically disordered proteins (IDPs) and IDPRs in various biological processes. Chapter 2 focuses on the rapid prediction and analysis of protein intrinsic disorder. We introduce RIDAO (Rapid Intrinsic Disorder Analysis Online), a high-efficiency web-based tool that integrates multiple disorder predictors. RIDAO significantly outperforms existing predictors in computational efficiency, making it suitable for large-scale proteomic studies. We …

Spinal Movement Disorders In Nmosd, Mogad, And Idiopathic Transverse Myelitis: A Prospective Observational Study, Hesham Abboud, Rongyi Sun, Nikhil Modak, Mohamed Elkasaby, Alexander Wang

Faculty Scholarship

Background: Retrospective studies suggest that spinal movement disorders, especially tonic spasms, are prevalent in NMOSD. However, there have been no prospective studies evaluating spinal movement disorders in NMOSD, MOGAD, and idiopathic transverse myelitis (ITM). Methods: Patients referred to a tertiary neuroimmunology clinic for spinal cord demyelination (excluding MS) were evaluated. All patients answered a movement disorders survey and underwent a movement disorder-focused exam. Movement disorders were compared among patients with NMOSD with and without AQP4-IgG, MOGAD, and ITM. Patients with and without involuntary movements were also compared to identify predictors of spinal movement disorders. Results: Sixty-three patients were evaluated from …

Contributions Of Brain Microstructures And Metabolism To Visual Field Loss Patterns In Glaucoma Using Archetypal And Information Gain Analyses, Yueyin Pang, Ji Won Bang, Anisha Kasi, Jeremy Li, Carlos Parra, Els Fieremans, Gadi Wollstein, Joel S. Schuman, Mengyu Wang, Kevin C Chan

Wills Eye Hospital Papers

PURPOSE: To investigate the contributions of the microstructural and metabolic brain environment to glaucoma and their association with visual field (VF) loss patterns by using advanced diffusion magnetic resonance imaging (dMRI), proton magnetic resonance spectroscopy (MRS), and clinical ophthalmic measures.

METHODS: Sixty-nine glaucoma and healthy subjects underwent dMRI and/or MRS at 3 Tesla. Ophthalmic data were collected from VF perimetry and optical coherence tomography. dMRI parameters of microstructural integrity in the optic radiation and MRS-derived neurochemical levels in the visual cortex were compared among early glaucoma, advanced glaucoma, and healthy controls. Multivariate regression was used to correlate neuroimaging metrics with …

Hormonal Differences In Perpetrators Of Intimate Partner Violence, Arturo L. Cantos, Gabriela Ontiveros, Robert K. Dearth, K. Daniel O'Leary

Psychological Science Faculty Publications

Objective: In order to gain a better understanding of the individual and joint impact of testosterone and cortisol on behavior, the present study was developed to test the differences in each hormone alone and conjointly between perpetrators of IPV and non-violent controls.

Method: Perpetrators of IPV on probation were compared to a control group of non-aggressive males from Hidalgo County in the Rio Grande Valley on baseline testosterone and cortisol, as well as several relevant questionnaires measuring aggression and trait anger. Differences in cortisol following exposure to a stressful event were also examined. Procedures included two laboratory visits consisting of …

Rna 2′-O-Methylation Promotes Persistent R-Loop Formation And Aid-Mediated Igh Class Switch Recombination, Muzaffer Ahmad Kassab, Yibin Chen, Xin Wang, Bo He, Eric J Brown, Xiaochun Yu

Faculty, Staff and Student Publications

BACKGROUND: RNA-DNA hybrids or R-loops are associated with deleterious genomic instability and protective immunoglobulin class switch recombination (CSR). However, the underlying phenomenon regulating the two contrasting functions of R-loops is unknown. Notably, the underlying mechanism that protects R-loops from classic RNase H-mediated digestion thereby promoting persistence of CSR-associated R-loops during CSR remains elusive.

RESULTS: Here, we report that during CSR, R-loops formed at the immunoglobulin heavy (IgH) chain are modified by ribose 2'-O-methylation (2'-OMe). Moreover, we find that 2'-O-methyltransferase fibrillarin (FBL) interacts with activation-induced cytidine deaminase (AID) associated snoRNA aSNORD1C to facilitate the 2'-OMe. Moreover, deleting AID C-terminal tail impairs …

Examining Psycho-Social Factors Of Foster Parents Who Engage In Contact Sexual Abuse, Heather Lee Manning

Walden Dissertations and Doctoral Studies

Previous work has been done to identify psych-social factors of criminals, although no work currently exists to identify the specific type of sexual offender identified within this study- foster parents who sexually offend foster children. This qualitative study focused on pre-determined psycho-social factors of both male and female offenders. The study reviewed nine cases which met the inclusion criteria and where sufficient data was able to be collected. Results of the study revealed that most offenders were male, most were married or in an otherwise committed relationship with a consenting adult during the time of their offending behaviors. These finding …

Impact Of Parental Attachment On Family Communication Patterns About Sex And Intimacy, Trish Mook

Walden Dissertations and Doctoral Studies

Risky sexual behaviors in adolescence continue to be a social problem that impacts individuals, families, and communities across the United States. Previous research showed that parents who actively talk with their adolescents about sex and intimacy topics reduce their likelihood of engaging in these behaviors. Still, less is known about what motivates a parent to engage in these discussions. This correlational quantitative research study aimed to apply Bowlby’s attachment theory and McLeod and Chaffee’s family communication patterns theory to identify if a relationship exists between parental attachment style and the family communication patterns that a parent employs when discussing sex …

Self-Explainable Graph Neural Network For Alzheimer Disease And Related Dementias Risk Prediction: Algorithm Development And Validation Study, Xinyue Hu, Zenan Sun, Yi Nian, Yichen Wang, Yifang Dang, Fang Li, Jingna Feng, Evan Yu, Cui Tao

Faculty, Staff and Student Publications

Background: Alzheimer disease and related dementias (ADRD) rank as the sixth leading cause of death in the United States, underlining the importance of accurate ADRD risk prediction. While recent advancements in ADRD risk prediction have primarily relied on imaging analysis, not all patients undergo medical imaging before an ADRD diagnosis. Merging machine learning with claims data can reveal additional risk factors and uncover interconnections among diverse medical codes.

Objective: The study aims to use graph neural networks (GNNs) with claim data for ADRD risk prediction. Addressing the lack of human-interpretable reasons behind these predictions, we introduce an innovative, self-explainable method …

The Role Of Placental Kisspeptin In Trophoblast Invasion And Migration: An Assessment In Kiss1r Knockout Mice, Bewo Cell Lines And Human Term Placenta, E. N. Panting, J. H. Weight, J. A. Sartori, D. A. Coall, J. T. Smith

Research outputs 2022 to 2026

Context: There is mounting evidence implicating kisspeptin signalling in placental development and function. Aims: This study aimed to elucidate kisspeptin's role in trophoblast invasion and migration using three experimental models. Methods: First, we examined the mouse fetus and placenta in a kisspeptin receptor (Kiss1r) knockout (KO) model. Fetal/placental weights and gene expression (quantitative polymerase chain reaction) were assessed. Second, we determined kisspeptin effects on a human trophoblast (BeWo) cell line in vitro. Third, we examined KISS1 and KISS1R gene expression in human placenta from term and pre-Term pregnancies. Key results: No difference was found in fetal or placental weight between …

Intratumoral Immune Triads Are Required For Immunotherapy-Mediated Elimination Of Solid Tumors, Gabriel Espinosa-Carrasco, Edison Chiu, Aurora Scrivo, Paul Zumbo, Asim Dave, Doron Betel, Sung Wook Kang, Hee-Jin Jang, Matthew D Hellmann, Bryan M Burt, Hyun-Sung Lee, Andrea Schietinger

Faculty, Staff and Students Publications

Tumor-specific CD8+ T cells are frequently dysfunctional and unable to halt tumor growth. We investigated whether tumor-specific CD4+ T cells can be enlisted to overcome CD8+ T cell dysfunction within tumors. We find that the spatial positioning and interactions of CD8+ and CD4+ T cells, but not their numbers, dictate anti-tumor responses in the context of adoptive T cell therapy as well as immune checkpoint blockade (ICB): CD4+ T cells must engage with CD8+ T cells on the same dendritic cell during the effector phase, forming a three-cell-type cluster (triad) to license CD8+ T cell cytotoxicity and cancer cell elimination. …

Authenticated Diagnosing Of Covid-19 Using Deep Learning-Based Ct Image Encryption Approach, Mohamed Attia Abdelgwad, Amira Hassan Abed, Mahmoud Bahloul

Future Computing and Informatics Journal

Researchers are motivated to use artificial intelligence in biometrics, medical imaging encryption, as well as cybersecurity due to its rapid progress. An encryption method for CT scans—which are used to diagnose COVID-19 disease—is proposed in this study. The suggested encryption method creates a connection among an individual's face picture and CT image to increase confidentiality. The simple CT picture is first enhanced with a host image. An encryption key is multiplied by the final result. This key is produced by applying a Convolutional Neural Network (CNN) to recognize characteristics from people's face photographs. Additionally, a straightforward CNN with three convolutional …

Segmentation And Classification Of Left Ventricular Abnormalities In Cardiac Mri Using Initial Point Prediction Based Deformable Model, Md. Asadur Rahman, Md. Al Noman, A. B. M. Aowlad Hossain

Future Computing and Informatics Journal

The shape of the left ventricle (LV) of a cardiac magnetic resonance image (CMRI) helps physicians to diagnose different cardiac abnormalities. The similarity of pixel intensity and shape of LV with neighbor tissues, the imprecision of boundaries, and the presence of noise are the challenges to accurate segmentation of LV. This paper contributes to the successful implementation of an automatic edge contouring method to segment LV area from CMRI and detect whether the ventricle belongs to abnormalities. This method proposes the regression-based artificial neural network to predict the possible initial position of the deformable edge-based active contour model for precise …

Defensive Publication: Multi-Modal Modular Neural Network For Game Ai, Renee Gagnon

Defensive Publications Series

This publication describes a DQN-based Modular Neural Network architecture designed for Game AI applications. The system combines a Deep Q-Network (DQN) with a Convolutional Neural Network (CNN), Long Short-Term Memory Network (LSTM), and Spiking Neural Network (SNN) in a modular, sequential structure to process game state information, learn optimal strategies, and make decisions.

Evaluation Of Land Resilience Against Natural Disasters Using Ecosystem Services Approach In Kendari City, Southeast Sulawesi, Indonesia, La Ode Restele, Fitra Saleh, L. M. Iradat, Jufri Karim, Noor Husna Khairisa

Jurnal Pendidikan Geografi: Kajian, Teori, dan Praktek dalam Bidang Pendidikan dan Ilmu Geografi

Kendari City has multiple disasters hazard, especially floods and landslides. Consequently, the city requires systematic preventive efforts to minimize the potential disaster risk. This study aims to create a spatial model to determine the resilience of the land against floods and landslides with an ecosystem services approach. We used Sentinel-2 and DEMNAS (National Digital Elevation Model of Indonesia) as our primary data collection tools. Sentinel-2 was used to compile land use maps, and DEMNAS was the basis for compiling landform maps. The integration of the two was carried out by the analytic hierarchy process (AHP). The results showed that 8,259.98 …

Automatic Geographic Information System Algorithm For Temporal Mangrove Observation: A Case Study In Gopek Beach, North Banten, Della Ayu Lestari, Willdan Aprizal Arifin, Novi Sofia Fitriasari, Taufiq Ejaz Ahmad, Amien Rais, Dhea Rahma Azhari

Jurnal Pendidikan Geografi: Kajian, Teori, dan Praktek dalam Bidang Pendidikan dan Ilmu Geografi

Temporal observation is a series of processes started by collecting the necessary data, which is then processed, so that valid information is obtained to support the right decision. To increase the ease of data collection, an automatic algorithm is needed to increase efficiency, shorten the time, and reduce the required resources. The automatic algorithm based on the geographic information system developed in this study was applied to monitoring mangrove forests in Gopek Beach, located on the north coast of Serang, Banten. Using the cloud computing process from an automatic algorithm, the results of vegetation monitoring showed increased efficiency in time …

Effects Of Service-Learning With One Movement For A Nature Program On Senior High School Students Pro-Environmental Behaviors, Fathul Bari, Sumarmi Sumarmi, I Komang Astina

Jurnal Pendidikan Geografi: Kajian, Teori, dan Praktek dalam Bidang Pendidikan dan Ilmu Geografi

This study aims to determine the effect of the service-learning model using one movement for nature activities on students' pro-environmental attitudes. The design used in this study was quasi-experimental. This research was carried out at State Senior High School 1 Tanjung Bumi Madura in class XI IPS 2 as a control class and XI IPS 3 as an experimental class. Data analysis was performed using the SPSS 24.0 application. The results of the normality test suggested that the data were not normally distributed, therefore, the calculation was carried out using the Wilcoxon Signed-Rank test. Based on the results of the …

Crossover Of Supervisors' Perceptions Of Co-Worker Support To Employees' Well-Being, Shalene Joyce Allen

Dissertations and Theses

This study expands scholarly understanding of the positive impact of supervisors' perceptions of support on employee work-family and well-being experiences. Specifically, this study examines the role of resource-based positive crossover from supervisors' perceptions of co-worker support behavior to their employees. The current research draws on Systems Theory to understand the context, Conservation of Resources Theory to understand the type of resource purported to position individual resource gains, and crossover-spillover theory to understand the process through which resources crossover from supervisor to employee. Based on prior theory, this dissertation investigates a positive crossover effect of supervisors' perceptions of co-worker support at …

From Viral Rumors To Fact-Checked Information: The Influence Of Social Media Platforms And Fact-Checking Organizations On Public Trust During The Covid-19 Crisis, Chinyere Linda Agbasiere

Theses and Dissertations

The COVID-19 pandemic not only disseminated a viral health threat worldwide but highlighted the rapid spread of misinformation, commonly called an "infodemic." This study investigates the influence of social media and fact-checking organizations in shaping public trust and information consumption during the pandemic. Utilizing a mixed-method approach of surveys and interviews, I analyzed 9 interviews. The interviews were analyzed using thematic analysis (Braun & Clarke, 2006) and Owen's (1984) principles of recurrence, repetition, and forcefulness, and three main themes were developed inductively. The findings reveal that while social media was a primary source of information, it also served as a …

Editorial: Interaction And Dynamics Of Biological Molecules, Mohana Priya Arumugam, Umashankar Vetrivel, Jeyakanthan Jeyaraman, Subhash Chauhan, Jayakanthan Mannu

School of Medicine Publications

No abstract provided.

Unveiling Novel Genetic Variants In 370 Challenging Medically Relevant Genes Using The Long Read Sequencing Data Of 41 Samples From 19 Global Populations, Yanfeng Ji, Junfan Zhao, Jiao Gong, Fritz J Sedlazeck, Shaohua Fan

Faculty, Staff and Students Publications

Background: A large number of challenging medically relevant genes (CMRGs) are situated in complex or highly repetitive regions of the human genome, hindering comprehensive characterization of genetic variants using next-generation sequencing technologies. In this study, we employed long-read sequencing technology, extensively utilized in studying complex genomic regions, to characterize genetic alterations, including short variants (single nucleotide variants and short insertions and deletions) and copy number variations, in 370 CMRGs across 41 individuals from 19 global populations.

Results: Our analysis revealed high levels of genetic variants in CMRGs, with 68.73% exhibiting copy number variations and 65.20% containing short variants that may …

Broadcasters, Receivers, Functional Groups Of Metabolites, And The Link To Heart Failure By Revealing Metabolomic Network Connectivity, Azam Yazdani, Raul Mendez-Giraldez, Akram Yazdani, Rui-Sheng Wang, Daniel J Schaid, Sek Won Kong, M Reza Hadi, Ahmad Samiei, Esmat Samiei, Clemens Wittenbecher, Jessica Lasky-Su, Clary B Clish, Jochen D Muehlschlegel, Francesco Marotta, Joseph Loscalzo, Samia Mora, Daniel I Chasman, Martin G Larson, Sarah H Elsea

Faculty, Staff and Students Publications

Background and objective: Blood-based small molecule metabolites offer easy accessibility and hold significant potential for insights into health processes, the impact of lifestyle, and genetic variation on disease, enabling precise risk prevention. In a prospective study with records of heart failure (HF) incidence, we present metabolite profiling data from individuals without HF at baseline.

Methods: We uncovered the interconnectivity of metabolites using data-driven and causal networks augmented with polygenic factors. Exploring the networks, we identified metabolite broadcasters, receivers, mediators, and subnetworks corresponding to functional classes of metabolites, and provided insights into the link between metabolomic architecture and regulation in health. …

Inactivation Of Bacterial And Viral Indicators In The Secondary Effluent Of Al-Khober Wastewater Treatment Plant With Ozone, Uv-Radiation And Electrochemical Process: A Comparative Study, Muhammad Saleem Dr.

Journal of Engineering Research

Increased use of available water resources necessitates the reuse of treated wastewater at least for irrigation purposes. Generally, pathogenic microorganisms are present in treated wastewater; these pathogens are responsible for spread of many infectious diseases. Disinfection stands out as the pivotal stage in the treatment of effluents during wastewater reuse, crucial for averting the transmission of infectious diseases However, disinfection of wastewater with chlorine may form toxic by-products, a number of which are mutagenic and/or carcinogenic. The aim of present study was to examine the possibility of using three processes, namely; ozonation, UV-radiation, and electrochemical process for disinfection of secondary …

3d Printing Technology: Challenges, And Potentials In Achieving Sustainable Buildings, Sahar Mohamed Abd El Rahman, Sobhy Ibrahim Esmail

Journal of Engineering Research

The utilization of 3D printing technology in building construction has emerged as a promising approach with the potential to revolutionize the industry and significantly impact sustainability. This paper examines the role of 3D printing in building construction and explores its implications for sustainability. Through the ability to fabricate complex designs with precision and efficiency, 3D printing offers advantages such as reduced material waste, lower energy consumption, and decreased carbon emissions. Additionally, the use of locally sourced, recyclable materials combined with the customization capabilities of 3D printing enhances resource efficiency and minimizes environmental impact. Furthermore, the construction process is streamlined, leading …

Securing Body Area Networks With Fingerprint Cryptography And Authentication In Manet, Alaa M. Elbanaa, Roayat Ismail Abdelfatah, Mohamed E. Nasr

Journal of Engineering Research

Standard MANETs face issues like incorrect transmission and vulnerability to unauthorized node access, posing significant security concerns, especially regarding authentication procedures. To address these challenges, researchers are exploring innovative approaches to enhance authentication mechanisms within MANETs. In this paper, we present a novel solution integrating a Body Area Network (BAN) scheme to capture biomedical data from sensors such as ECG and EEG, facilitating data transmission across MANETs. Furthermore, we employ a hybrid Elgamal algorithm for encrypting biomedical data, bolstered by fingerprint biometrics to fortify the cryptographic process, enhancing network security. Additionally, we conduct comparative analyses, exploring different key sizes and …

Prediction Of Noise From A Construction Site, Amira Mostafa Ibrahim Miss, Nashwa Mohamed Yossef Prof, Adel Ibrahim Eldosouky Emeritus Professor

Journal of Engineering Research

Construction activities significantly contribute to environmental noise pollution, affecting workers' health and the surrounding community, posing significant challenges to human well-being and productivity. This paper presents a prediction method and a modelling technique used to assess construction site noise. Various factors influencing noise generation and propagation, such as equipment types, operational conditions, site characteristics, and environmental factors, are discussed. This paper explores the application of Monte Carlo technique as an effective method for predicting construction site noise and planning noise mitigation strategies.

Performance Evaluation Of Electrocoagulation System For Wastewater Treatment, Mohamed Ahmed Reda Hamed Dr

Journal of Engineering Research

ABSTRACT

This study aimed to evaluate the performance of an electrocoagulation reactor (EC) and investigate its efficiency in heavy-polluted industrial wastewater treatment. The electrocoagulation (EC) reactor has been experimentally evaluated using aluminium (Al) electrodes and connected to a direct current power at various applied voltage levels at room temperature in a relatively limited reaction time.

The treatment performance efficiency of the selected dominant EC operating parameter groups: pH, reaction time, inter-electrode distance, and applied voltage was investigated. The results demonstrate that the applied voltage to the electrocoagulation reactor was the most significant factor in pollutant removal. The maximum total suspended …

Survey And Analysis Of Safety Components And Costs In Construction Projects In Egypt, Emad E. Etman Prof., Haytham Sanad Prof., Asmaa Ibrahim Khater

Journal of Engineering Research

The difficulty of determining the factors that achieve safety on Egyptian construction sites as a result of multiple and different criteria and different relative weights of the criteria represents a challenge to achieve safety and a secure environment on construction sites. This issue has been of interest for many decades and continues to be a topic of discussion today because of construction project management is rapidly modernizing. The paper aims to identify the safety standards most commonly used on construction sites, and determine their relative weights as seen by the target audience and also estimate the cost of safety measures …

Spatial Environmental Suitability For The Localization Of Sanitary Waste Landfills In Egypt Using Environmental Information Systems: Applying To Safaga Qism, Wessam Mostafa Emam, Dalia Mahmoud Hassan

Journal of Engineering Research

This research focuses on the application of an environmental information system to help achieve balance and interrelation between the various environmental standards affecting the selection of the site to the sanitary landfill in the touristic Safaga qism of the Red Sea. According to the sustainable development strategy of Egypt’s Vision 2030, the issue of solid waste is one of the most important environmental challenge that faced sustainable development in Egypt. In light of the increasing number of unauthorized dumps of waste that pollute the environment, the Ministry of Environment adopted a national project to establish a network of sanitary landfills, …