Digital Commons Network^™

Identification Of Conditionally Essential Genes Required For Salmonella Enterica Serovar Typhimurium Adaptation To The Chicken Cecal Extract Through Ex Vivo Modeling And Transposon Insertion Sequencing, Deborah Bukola Olubanjo

Graduate Theses and Dissertations

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains a major foodborne pathogen associated with chicken, where it can persist in the intestinal tract without overt disease and contribute to zoonotic transmission. The chicken cecum represents a complex ecological niche shaped by microbial competition, host-derived substrates, short-chain fatty acids, oxygen limitation, extracellular components, and diverse metabolic gradients. Although transposon insertion sequencing (Tn-seq) has been widely used to define bacterial fitness determinants, limited work has examined genome-wide adaptation of S. Typhimurium in chicken ceca-derived ex vivo systems that preserve key features of the avian cecal environment. This dissertation investigated conditionally essential genes required …

Uti, Delirium, And Dementia: A Conceptual Bioinformatics Framework For Clinical Attribution, Rob E. Carpenter, Andrew Krouse

Human Resource Development Faculty Publications and Presentations

Urinary tract infection (UTI) is frequently invoked to explain delirium, confusion, and functional decline in persons with dementia. Yet urine positivity in this population often reflects asymptomatic bacteriuria, colonization, chronic pyuria, contamination, or sampling noise rather than clinically attributable infection. For biomedical informatics and computational diagnostics readers, this narrative review contributes an integrative conceptual bioinformatics framework for probabilistic clinical attribution of suspected UTI in dementia under uncertainty. We formalizes the attribution problem by distinguishing organism detection from a clinically plausible infection-related contribution to neurocognitive decline. The framework integrates clinical, laboratory, biological, and longitudinal data to clarify whether urinary findings are …

Nitrogen Use Efficiency Of Rice Expressing Arabidopsis Thaliana Dreb1a Gene, Yanis Anetha Vasquez Valdes

Graduate Theses and Dissertations

Rice is a globally consumed crop and feeds more than half of the world’s population. Nitrogen (N) fertilization is required for increasing rice crop production and yield, but producers often overuse N fertilizers, exceeding plant uptake capacity. Around 40% of the applied N is lost through volatilization and denitrification to the environment, causing algal bloom formation, greenhouse gas emissions, and water pollution. Therefore, improving nitrogen use efficiency (NUE) in rice has become a principal objective to achieve sustainable agriculture. NUE is a complex trait in rice that coordinates three processes: nitrogen uptake, transport and assimilation, which together support photosynthesis, biomass …

Evaluation Of Thresholds For Adult Tarnished Plant Bug, Lygus Lineolaris (Beauvois), In Thryvon® Cotton, William Anderson Fletcher

Graduate Theses and Dissertations

Tarnished plant bug (TPB) is the most economically damaging insect pest of Mid-South cotton. TPB reduces yield is reduced by damaging squares, terminal growth, and small bolls, resulting in reduced yield. Currently, cotton grown in the Mid-South averages 1-6 insecticide applications per year for control of TPB. The introduction of ThryvOn® cotton technology provides a new management strategy for TPB control. ThryvOn® technology produces the Bacillus thuringiensis (Bt) protein Mpp51Aa2, which has insecticidal activity on TPB. A field study was conducted at five locations in 2024 and seven locations in 2025 across the Mid-South to evaluate different threshold levels for …

Pearson Syndrome: Expanding The Clinical Spectrum Of A Mitochondrial Cytopathy-A Case Report, Alizah Faisal, Hooria Waqas, Hania Masood, Armeen Butt, Saad Rahman, Muhammad Sheraz Hameed, Syed Rafay Hussain Zaidi, Ali Iqbal, Muhammad Usama Naveed

Department of Medicine Faculty Papers

BACKGROUND: Pearson syndrome (PS) is a rare multisystem mitochondrial disorder characterized by single large-scale mitochondrial DNA deletions (SLSMDs). It typically presents in infancy with refractory sideroblastic anemia, exocrine pancreatic insufficiency, and failure to thrive. Due to its heterogeneous manifestations and resemblance to other hematological conditions, early diagnosis remains a clinical challenge.

CASE PRESENTATION: A south asian male infant presented with persistent pancytopenia, severe anemia unresponsive to intravenous and oral iron and multivitamin supplements, exocrine pancreatic insufficiency, failure to thrive, and metabolic acidosis. Born to consanguineous parents, the child had a significant family history of early infant deaths and hematological abnormalities. …

Mosaic Loss Of Y Chromosome Associates With Lung Function, Emphysema, And Epigenetic Aging, Woei Yuh Saw, Kangjin Kim, Yichen Huang, Jeong H. Yun, Xiaolong Ma, Jason Bacon, Yash Pershad, Daniel Levy, George T. O’Connor, John Blangero

Human Genetics Publications

Rationale: As the global population ages, identifying risk factors for age-related diseases, such as COPD, is crucial for public health. Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mosaicism event, but its relationship with pulmonary health remains undercharacterized. Objectives: To examine the association between mLOY and pulmonary outcomes in men. Methods: Leveraging mLOY assessment (cell fraction ≥ 5%) in over 12 000 men, including 5097 from the COPDGene Study and 7235 from six additional cohorts in the Trans-Omics for Precision Medicine program, we investigated mLOY associations with respiratory outcomes and epigenetic aging using multivariable cross-sectional, …

Cultivating Narratives: A Critical Discourse Analysis Of Higher Education Student-Led Farms And Gardens, Maximilan Sherard, Marc T. Sager

Publications

Despite extensive research on community agriculture, little attention has been paid to student-led farms or gardens (SFGs) in higher education contexts. SFGs represent a unique site for community agriculture due to their diverse stakeholders, academic affiliations, and the institutional policies they navigate. This study examines online promotional materials from 42 SFGs located on land-grant higher education campuses across the United States. Using critical discourse analysis, we (1) map these organizations’ practices and (2) identify competing discourses about community and agriculture within their promotional narratives. We identify and explain four core practices (membership, growing, distribution, and purpose) and connect these practices …

A Comparative Study Of Aging And Cortical Folding In Chimpanzees And Olive Baboons, William D. Hopkins, Angela M. Achorn, Michele M. Mulholland, Elizabeth R. Magden, Steven J. Schapiro, Courtney L, Fults, Jean‐Francois Mangin, Adrien Meguerditchian

Anthropology Faculty Publications

In light of the evidence that nonhuman primates naturally develop Alzheimer's disease neuropathologies, there is a renewed interest in research on the comparative biology of aging, including neurological changes across the age groups in species with diverse lifespans. In this paper, we examined age‐related differences in two measures of cortical folding, mean depth and fold opening, in a sample of chimpanzees (Pan troglodytes) and olive baboons (Papio anubis). We found significant species differences in the slope and pattern of age‐related changes in cortical folding. As predicted, chimpanzees showed negative linear associations between age and mean depth and …

Mechanistic And Spatio-Temporal Modelling Of Cassava Whitefly (Bemisia Tabaci) Risk Under Climate Change: Projections For Africa With Case Evidence From Malawi, Lumbani Benedicto Banda, Frank Thomas Ndjomatchoua, Ritter A. Guimapi, Komi Mensah Agboka, Abdelmutalab G.A. Azrag, Wezi G. Mhango, Trust Kasambala Donga, Chikondi Makwiza, Karl H. Thunes, Elfatih M. Abdel-Rahman

All Peer-Reviewed Publications

The cassava whitefly (Bemisia tabaci) greatly constrains cassava production across Africa due to its role as a vector of viral diseases that cause substantial yield losses. Effective management of this insect pest requires detailed knowledge of its spatio-temporal distribution, however long-term datasets are scarce. Mechanistic models circumvent these long-term data needs by modelling temperature-dependent processes that govern population dynamics. Nevertheless, their application to B. tabaci remains poorly explored. Here, we developed a mechanistic model to derive a risk index (RI) for B. tabaci across Africa, focusing on Malawi. The model integrates the effects of temperature on the life stages of …

Common Cybersecurity Attack Types And Zeek-Based Detection Strategies In Iot Networks, Christofer Piedra, Alain Edwards

Florida Atlantic Undergraduate Research Journal

As cybersecurity threats increase in scale and complexity, the ability to distinguish hostile traffic from benign network activity is essential. This research examines five prevalent cyberattack categories that impact IoT environments and outlines detection strategies utilizing the open-source Intrusion Detection System (IDS) Zeek. This study provides practical detection methods designed for scalable, real-time environments by classifying five commonly encountered attacks, namely: Reconnaissance, Denial of Service (DoS) and Distributed Denial of Service (DDoS), Brute Force, Man-in-the-Middle (MitM) and Spoofing, and Botnet and Malware Behavior. For each attack, we analyze the prevalence, operational impact, and associated indicators. We also present Zeekbased pseudocode …

An In-Silico Investigation Of Induced Target Neural Activity Through Simulation-Based Inference Informed Deep Brain Stimulation, James Lee, Ty Roachford

Florida Atlantic Undergraduate Research Journal

Deep Brain Stimulation (DBS) is clinically effective for various neurological disorders, yet its underlying neuronal mechanisms remain unknown. Building on previous studies, we used an in-silico Hodgkin-Huxley biophysical model to investigate hippocampal CA1 responses to DBS. Our simulations replicate key experimental findings, confirming robust somatic depolarization at 140 Hz and a more gradual ramp at 40 Hz, alongside distinct transient and sustained voltage profiles. Both frequencies modulated firing rates, supporting the notion that DBS disrupts pathological network activity. Beyond frequency-specific effects, we employed Simulation-Based Inference (SBI) to identify the DBS features needed to suppress spiking and match a quiescent target …

A Comprehensive Overview Of The Quantum Approximate Optimization Algorithm, Vincent Stafford

Florida Atlantic Undergraduate Research Journal

As quantum computing research advances, the Quantum Approximate Optimization Algorithm (QAOA) has emerged as a leading approach to harnessing current quantum hardware for solving complex combinatorial optimization problems. This pedagogical, expository paper outlines the mathematical foundations of QAOA, explains its step-by-step implementation from first principles in a manner accessible to advanced undergraduate students and non-specialists, and explores real-world applications such as protein folding and job scheduling. We also examine the algorithm’s performance challenges, including barren plateaus and circuit depth limitations.

Artist Statement, Zarina Mason

Florida Atlantic Undergraduate Research Journal

No abstract provided.

Soilless Substrates As A Critical Control Point For Mitigating Food Safety Risks Within Hydroponic Leaf Lettuce Production, Eric Nuertey Tetteh

Graduate Theses and Dissertations

The effect of hydroponic soilless substrates and microbial biocontrol agents on the persistence of foodborne pathogens in indoor lettuce production is variable depending on substrate type, pathogen species, and biocontrol formulation. This study addressed key gaps by first characterizing the ability of different substrates to support Salmonella and Listeria monocytogenes survival and then evaluating the ability of pine biochar and Bacillus subtilis to suppress pathogen persistence in selected substrates under controlled conditions. In the first experiment, the persistence of Salmonella and L. monocytogenes was evaluated in four soilless substrates: rockwool (RW), low density foam (LDF), peat moss (PM) and coco …

Genome-Wide Cline Analysis Identifies New Locus Contributing To A Barrier To Gene Flow Across An Antirrhinum Hybrid Zone, David L. Field, Sean Stankowski, Taylor Reiter, Jitka Polechova, Desmond Bradley, Daniel M. Richardson, Annabel Whibley, Arka Pal, Daria Shipilina, Louis Boell, Melinda Pickup, Yongbiao Xue, Enrico Coen, Nicholas Barton

Research outputs 2022 to 2026

Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal of evolutionary genetics. Much effort has focused on locating candidate genes and potential barrier loci by scanning genomes for regions of excess differentiation (FST). An alternative, and perhaps more robust approach, is to scan for genomic regions exhibiting steep clines in allele frequency across a hybrid zone. We develop a computationally efficient method for approximating cline parameters for large number of loci, and apply it to genomic data from across a hybrid zone between flower colour varieties of Antirrhinum majus (A. m. …

Antioxidant And Anti-Hemolytic Capacities Of Eucalyptus Camaldulensis Leaves, Achwaa Chbib, Malak Mezher, Mohamad Nasser, Akram Hijazi, Mahmoud I. Khalil

BAU Journal - Science and Technology

The effects of medicinal plants on the prevention of many diseases are due to their chemical composition. Eucalyptus camaldulensis (E. camaldulensis) is a native tree in Australia. Its extracts and essential oils (EOs) are applicable in the domains of pharmaceuticals and medicine. This work determined the anti-hemolytic and antioxidant capacities of the ethanolic (EE), methanolic (ME), and aqueous (AE) extracts from the leaves of Lebanese E. camaldulensis.  The leaves of E. camaldulensis were extracted with ethanol, methanol, and water solvent. Qualitative phytochemical analyses were applied to reveal the compounds of these extracts. The Folin-Ciocalteau and Aluminum chloride …

Afforestation Strategies In Semi-Arid Mediterranean Ecosystems: Experimental Evidence From Chmistar, Lebanon, Ahmad Saker, Mohammad Saleh, Wael Mostafa, Safaa Baydoun, Jamilah Borjac, Dalia El-Badan

BAU Journal - Science and Technology

The success rate of broadleaf tree growth in semi-arid Mediterranean environments is reduced in afforestation operations constrained by water scarcity, shallow soil depth, and intense competition from herbaceous vegetation. This study, conducted between 2022 and 2024 in Chmistar, East Lebanon, using a completely randomized block design, aimed to evaluate the impact of three planting broadleaf trees techniques (traditional digging pits , hoedad tools, and auger digging) and four effective vegetation control (herbicide application, mowing,  mulching, and no control) on the early growth of three native broadleaf tree species (Pistacia palaestina, Quercus calliprinos, and Quercus infectoria ).

The …

Urban-Rural Differences In The Association Between Physical Activity And Overweight/Obesity Among Indonesian Adolescents: A Cross-Sectional Study, Wahyu Wulandari, Mufti As Siddiq M. Irzal, Lady Farah Fatmawati

Jurnal Epidemiologi Kesehatan Indonesia

Adolescent overweight/obesity is an increasing public health concern and contributes to the risk of non-communicable diseases later in life. Physical activity plays an important role in weight regulation. However, its association with overweight/obesity may vary according to residential setting. This study aimed to examine the association between physical activity and overweight/obesity among adolescents living in rural and urban areas of Indonesia. A cross-sectional study was conducted using data from the 2023 Indonesian Health Survey. The study included 115,372 adolescents aged 10–18 years. Physical activity was classified based on total Metabolic Equivalent of Task (MET)-minutes per week (≥600 MET-minutes/week), while nutritional …

Analysis Of Priority Vaccine-Preventable Diseases Using The Paho-Adapted Hanlon Method In Bogor City In 2024, Sonia Annisa Br Ketaren, Tri Yunis Miko Wahyono, Bai Kusnadi

Jurnal Epidemiologi Kesehatan Indonesia

Vaccine-preventable diseases (VPDs) remain a major public health challenge despite substantial progress in immunization programs. In Indonesia, routine immunization coverage has shown a post-pandemic recovery trend; however, disparities in access to health services and surveillance quality persist across regions. This study aimed to determine priority VPD problems in Bogor City and identify factors contributing to the highest-ranked disease. A mixed-methods study was conducted in Bogor City from October 2024 to January 2025. Quantitative prioritization was performed using the Pan American Health Organization (PAHO)-adapted Hanlon method across eight VPDs. Qualitative data were collected through in-depth interviews with key informants and analyzed …

The Development Of An In Silico Vaccine Design-Based E-Module To Improve Students' Biological Literacy, Qairinasherin Qwine Ferendi, Rusdi Rusdi, Hanum Isfaeni

Jurnal Pendidikan Sains

Low levels of biological literacy among students, particularly in biotechnology, highlight the need for innovative digital learning media that facilitate meaningful and contextual learning experiences. This study aimed to develop and evaluate an interactive biotechnology e-module based on in silico vaccine design to improve students’ biological literacy. The study employed Educational Design Research (EDR) using the Hannafin and Peck model, which consists of three phases: needs assessment, development, and implementation. The participants included 73 tenth-grade science students and one biology teacher from SMAN 68 Jakarta, Indonesia. The e-module was developed using Canva and Heyzine to create an interactive flipbook integrating …

Principal Leadership As A Predictor Of Teacher Performance: Evidence From An Indonesian Elementary School, Irminapinem Pinem, Antonius Remigius Abi, Hamela Sari Sitompul

Jurnal Pendidikan Sains

Teacher performance is a critical determinant of educational quality and student achievement, making the identification of factors that influence teacher effectiveness an important area of educational research. Among these factors, principal leadership has been recognized as a key organizational variable that shapes teachers’ professional practices and instructional performance. This study aimed to examine the relationship between principal leadership and teacher performance at State Elementary School Raya Kahean, Simalungun Regency, Indonesia. The study employed a quantitative correlational research design involving 52 teachers selected through total sampling. Data were collected using two structured questionnaires measuring principal leadership and teacher performance. The principal …

Association Of Household Economic Status And Birth Order With Stunting Among Children Aged 24-35 Months: Malawi Mics 2019–20, Sibongire B. Ngoma, Asri C. Adisasmita, Renti Mahkota, Septyana Choirunisa, Melisa Nyamukondiwa

Jurnal Epidemiologi Kesehatan Indonesia

Stunting remains a major public health concern in Malawi, with a national prevalence of 35.5% among children under five. However, evidence on the independent and combined effects of household economic status and birth order on stunting among Malawian children aged 24-35 months remains limited. This study aimed to examine the independent and combined association of household economic status and birth order with stunting among children aged 24-35 months in Malawi. A secondary data analysis of a cross-sectional 2019-20 Malawi Multiple Indicator Cluster Survey (MICS) was conducted, and the final sample comprised 2,764 children aged 24-35 months with complete data. Stunting …

A Review On Nanoparticles: Classification And Roles In Plant Systems, Muhammad Junaid Zafar, Muhammad Shafiq, Muhammad Azeem Rana

Journal of Bioresource Management

Nanotechnology has been a new paradigm of the twenty-first century with several good breakthroughs. These tiny particles, known for their outstanding qualities, are enjoying an increasing influence in many research fields concerning foodstuff, cosmetics, electronics, and pharmacology. Synthesis of nanoparticles includes utilizing chemical processes with reducing agents, alongside employing physical techniques such as top-down and bottom-up approaches for NP formation. The biological approach, known as green synthesis, utilizes plant extracts to ensure increased safety. Biological methods also involve bacteria and fungi, known as the major sources of nanoparticles. It is acknowledged as the most effective and environmentally conscious approach, attributed …

Economic Performance And Technical Efficiency Of “Small-Scale” Vegetable Production In Ido Local Government Area Of Oyo State, Nigeria, Taiye Oluwasola Babatunde, Oluyemisi Omowunmi Babatunde

Journal of Bioresource Management

A study was carried out to examine the economic performance of small-scale vegetable farmers and how effectively they are using their resources in Ido Local Government Area of Oyo State. The study involved eighty vegetable farmers who were chosen randomly, and information was gathered from them using structured questionnaires. Different tools such as budget analysis, linear regression, frequency distribution, percentages, and the stochastic frontier production function were used to examine the data that was collected. The results indicated that about 41.3 % of the farmers were between the ages of 41 and 50. Most of the people who answered were …

Crispr/Cas9-Based Genome Editing: Understanding Differences In Dna Repair Pathways, Profiles, And Outcomes, Samuel Effah, Shirley Barrera, Nahia Urturi Ortiz, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the …

Antimicrobial Resistance Profiles And Clinical Dynamics Of Listeriosis In Small Ruminants: A One Health Review, Muhammad Aqeel, Pervez Ahmed Khoso, Amjad Hussain Mirani, Dildar Hussain Kalhoro, Abdul Ahad Soomro

Journal of Bioresource Management

Although the incidence of listeriosis is much lower in small ruminants, it has implications for food safety, herd health and appropriate antibiotic usage as well as zoonotic potential. Both have been reported to be robust pathogens and Listeria monocytogenes is generally recognized as the most common etiologic agent, but in ovine or caprine abortion it should be included as a significant differential diagnosis. This is a narrative one health review that summarizes status of the information published to date on the epidemiology and clinical signs of infection, resistance patterns found and diagnosis and prevention methods employed in small ruminant populations. …

Essential And Non-Essential Amino Acid Composition Of Hilsa (Tenualosa Ilisha) Fish In Different Fishing Regions Of Bangladesh, Mohajira Begum, Md. Moshfekus Saleh-E-In, Md. Zia Uddin Al Mamun, Umma Fatema Shahjadee, Farha Matin Juliana, Md. Sabir Hossain

Journal of King Abdulaziz University: Marine Science

Hilsa, Tenualosa ilisha (Hamilton, 1822), is one of the favourite and popular tropical fish in the people of South-East Asia due to its delicious taste and flavour. This study investigates the comprehensive amino acid profiles of various fishing locations of Bangladesh to assess the protein quality and nutritional values. Fourteen free amino acids were identified from the six riverine locations of Bangladesh. The total free amino acid (TAA) contents were ranged from 11.60 g/100 g in Cox's Bazar to 13,40 g/100 g in Kirtonkhola for raw fish. In the case of smoked treated, the TAA ranged from 14.01 g/100 g …

Operational Risk Assessment Of Ship To Shore Petroleum Transfer Using Fuzzy Rule-Based Bayesian Networks, Ayman F. Alghanmi

Journal of King Abdulaziz University: Marine Science

Petroleum ports represent critical infrastructure in global energy supply chains, where operational risks during ship-to-shore transfer operations can lead to catastrophic consequences including environmental damage and human casualties. Despite rigorous safety protocols, these facilities remain vulnerable to operational hazards in dynamic maritime environments. This research aimed to develop and apply a hybrid Fuzzy Rule-Based Bayesian Reasoning (FRBBR) model to identify, evaluate, and prioritize operational hazards during crude oil transfer operations at petroleum port berths, with a case study conducted in Saudi Arabia, addressing the challenge of risk assessment where historical data is limited.
The research employed a mixed-methods approach combining …

Revolutionizing Coral Research: The Power Of Holo-Omics, Mohammad M. Binsarhan

Journal of King Abdulaziz University: Marine Science

This mini-review highlights the emerging field of holo-omics and its application in unraveling the complex dynamics of the coral holobiont. Corals exist as meta-organisms, closely interacting with a diverse microbiota including bacteria, archaea, microeukaryotes, viruses, and algal symbionts. Understanding these intricate relationships is critical for assessing coral health, stress responses, and resilience to environmental change. We explore the application of meta-omics approaches such as metabarcoding, metagenomics, meta-transcriptomics, metabolomics, and proteomics in profiling coral-associated microbial communities and their functions. The review sheds light on the methodological advantages and limitations of each approach, as well as some of the technical challenges involved …

Microalgae As Sustainable Biofactories For Bioplastic Production: Challenges And Future Perspectives: A Review, Zahraa Hussein Obaid, Noor S. Naji, Jasim M. Salman, Layla Mustafa A.A. Alkatrani

Journal of King Abdulaziz University: Marine Science

The widespread use of traditional plastics, combined with their slow breakdown, has exacerbated environmental and health problems. Therefore, it has become imperative to find alternatives. Due to their simplicity of cultivation, quick growth, tolerance to challenging growing conditions, and low cost, microalgae are being used more frequently as a bio-source for bioplastics lately. Additionally, a variety of biopolymers, including polyhydroxybutyrate, polylactic acid (PLA), starch, polyhydroxyalkanoates (PHA), protein, and cellulose, could be produced by microalgae. These polymers show promising qualities including biodegradability, biocompatibility, and non-toxicity under various cultivation conditions. The purpose of this study is to demonstrate the potential of microalgae …