Digital Commons Network^™

Wake-On-Anomaly Federated Architecture For Privacy-Preserving Poultry Health Early Warning, Mahmoud Aziz Louati

Masters Theses

Highly pathogenic avian influenza outbreaks, respiratory disease, heat stress, and silent equipment failures share one operational reality: they are detected too late because today’s poultry-health workflow is reactive, manual, and dependent on producers volunteering commercially sensitive data. This thesis presents a wake-on-anomaly federated architecture that addresses both the detection-latency problem and the privacy–adoption deadlock that has so far prevented cross-farm collaboration. The architecture is organized in two tiers. Tier 1 is a lightweight LSTM autoencoder that continuously screens four routine telemetry channels (water, feed, house temperature, activity proxy) and emits a per-window reconstruction-error score. A debounced k-of-m trigger with cooldown …

Seed Endophyte Bacillus Atrophaeus Colonizes Root And Shoot Tissues Providing Antifungal Activity During Wheat Seedling Establishment, Anagha Wankhade, Zhiting Xu, Ashlynn Clark, David Britt

Biological Engineering Student Research

Seed-associated endophytes become active during germination, playing important roles as early colonizers of plant tissues and contributing to plant health while residing in a protective niche. In this study, we characterized a wheat-derived bacterial isolate, JunSE1L, to determine its functional traits and ecological role in the plant microbiome. The isolate was identified as Bacillus atrophaeus based on 16S rRNA analysis. JunSE1L exhibited nutrient-dependent plasticity in colony architecture, forming robust hydrophobic biofilms and pellicles under rich nutrient availability while swarming and forming thin, often dendritic colonies under defined nutrition. JunSE1L produced highly surface-active compounds that lowered the surface tension of water …

Deforestation Dynamics In The Amazon: Impacts, Socio-Environmental Drivers And Restoration Pathways, Maria Natalia Rodriguez

Master's Projects and Capstones

The Amazon, which is the largest tropical rainforest in the world, experienced 542,581 km² of forest loss between the years 2000 and 2020. The process of deforestation endangers the ecological system results which maintain ecosystem connectivity and the Earth's climate system. The Amazon rainforest supplies essential ecological services which include maintaining soil fertility, storing carbon, purifying water and climate stability. The fundamental ecosystem of this area faces new threats because of increasing forest destruction. The research study adopts a combined methodology that uses Geographic Information Systems (GIS) with a comprehensive literature review to study Amazon deforestation patterns and its driving …

Examining The Ligands, Location, And Function Of Toll-Like Receptor 10, Kiefer Keanu Tam

Master's Theses

Toll-like receptors are a class of innate immune pattern recognition receptors that detect pathogen-associated molecular patterns and regulate downstream inflammatory responses. Toll-like receptor 10 remains the only human TLR whose ligand specificity, cellular localization, and immunological function are not fully defined. Emerging evidence suggests that TLR10 may play an anti-inflammatory role and can heterodimerize with TLR2 to modulate immune signaling. Previous studies from our laboratory demonstrated that stimulation with heat-killed Mycobacterium tuberculosis promotes TLR2-TLR10 heterodimerization and trafficking to the cell surface. In this study, we expanded our ligand panel to include additional gram-positive bacteria, particularly anti-inflammatory probiotic species, to further …

Watershed Amendments: Assembling New Pervious Ground From Landscape Waste, Sophie Kaplan-Bucciarelli

Masters Theses

In Providence, Rhode Island, much of the downtown area is built over a vast historic tidal estuary. Though we no longer see the salt marshes, wooded bluffs, or meadows that once characterized this landscape, we recognize their absence in contemporary crises of urban heat, flooding, polluted soils and stormwater runoff, and habitat loss. These conditions are particularly acute along the city’s industrialized river corridors, where vacant lots and parking areas sit idle, their history paved over and potential constrained by limited imagination and resources.

These lots - already experiments in fill and land building after centuries of disturbance - can …

Replication And Architectural Enhancement Of Omni Aggregation Networks, Matteo Calviello

Rose-Hulman Undergraduate Research Publications

Single Image Super-Resolution (SISR) reconstructs high-resolution images from low-resolution inputs, a capability valuable across many application domains. This thesis focuses on the replication and architectural enhancement of the Omni Aggregation Network (OAN), a lightweight super-resolution architecture designed to balance reconstruction quality with computational efficiency through a novel omni-axis self-attention mechanism.

Independent replication remains a persistent challenge in machine learning research, and this work addresses that issue directly. Initial replication attempts trailed the original reported results by approximately 6-10% in performance metrics before several undocumented implementation details were identified. After correcting these discrepancies, the replicated implementation achieved results within 4% of …

Somatic Prosthetics For Planetary Resonance, Disha Dharesh Kumar R

Masters Theses

This thesis investigates how industrial design can transcend extractive technological paradigms in favor of relational interfaces that foster planetary attunement. Framing the climate crisis as a 'crisis of imagination', the research challenges the Western bifurcation of nature and culture by drawing on Indic cosmologies- which recognize stones, plants, and ecosystems as conscious at different levels and participants in a shared cosmic field. By synthesizing research in Biosemiotics, Quantum Information Pansycishm, and Neuroscience, the project redefines intelligence as a distributed, more-than-human phenomenon.

The research materializes as a speculative design artifact: a device that functions as a somatic prosthetic for planetary resonance. …

In Silico Molecular Docking Study Of Antidiabetic Bioactive Compounds From Brotowali (Tinospora Cordifolia) Targeting Glut4 In Type Ii Diabetes Mellitus, Gita Euaggelion Tarigan, Surya Dwira

Indonesian Journal of Medical Chemistry and Bioinformatics

Type 2 diabetes mellitus (T2DM) is a global metabolic disorder characterized by insulin resistance and impaired glucose uptake. Despite the availability of pharmacological therapies, limitations such as adverse effects and high costs highlight the need for alternative therapeutic candidates. Tinospora cordifolia has been widely reported to contain bioactive compounds with antidiabetic potential; however, comparative evaluation of their interaction with glucose transporter type 4 (GLUT4) remains limited.

This study aimed to identify the most promising bioactive compounds from Tinospora cordifolia targeting GLUT4 using an in silico molecular docking approach, followed by pharmacokinetic and toxicity (ADMET) prediction. Molecular docking was performed using …

Heat Shock Factor 1 Signaling: A Novel Pathway Implicated In Rett Syndrome Pathophysiology, Sonia Gonzalez

Dissertations

Rett syndrome (RTT) is a severe neurodevelopmental disorder that is associated with loss-of-function mutations in the methyl-CPG binding protein 2 (MECP2) gene. There are limited therapeutic options to address the wide range of social, cognitive, motor, and respiratory symptoms that patients experience throughout their lifetime. To identify novel therapeutic targets, we leveraged a rare form of RTT known as MeCP2-mutation-negative or atypical RTT. Traditionally, RTT is first diagnosed clinically and then confirmed through the identification of mutations in the MECP2 gene. However, ~5% of RTT patients are found to be MeCP2-mutation-negative (atypical), despite sharing overlapping symptomology with typical RTT. We …

Capturing System Complexity In Maritime Decarbonization: A Multilayer Modeling Perspective, Maksym Chepeliev, Rene Banares-Alcantara, Lorenza Campagnolo, Ronald Apriliyanto Halim, Jim Hall, Gianandrea Mannarini, Hesam Naghash, Carlo Palazzi, Ramiro Parrado, Paola Rocchi, Alessandro Taberna, Soheil Shayegh

Department of Agricultural Economics Faculty Publications

No abstract provided.

Towards A Methodology For Form Creativity Of Building Envelope To Enhance Thermal Performance (Biomimicry As A Tool For Form Creativity), Amal Ebrahim Ahmed Hassanin, Marwa Atef Abd-Elhady

Mansoura Engineering Journal

It has become necessary to achieve thermal comfort for users in buildings, which enhances human ability to work, create, or rest and enjoy. Since the building envelope serves as the link between the inside and outside of the building, forming the building envelope creatively improves and enhances thermal performance of buildings, thus achieving thermal comfort for users. Nature is the primary teacher and source of creativity for humans. Therefore, Biomimicry was chosen as a tool for creative formation, and the descriptive analytical approach was used by analyzing an example where nature was simulated in the formation of the external envelope …

Patterns And Drivers Of Cladocera Community Structure In The Black Sea, Elena Bisinicu, Luminita Lazar

Turkish Journal of Zoology

Cladoceran community dynamics were examined in the Romanian sector of the Black Sea during the warm seasons of 2013– 2020, using Marine Reporting  Units (MRUs) to evaluate spatial heterogeneity across transitional, coastal, and  marine waters. Analyses of density, biomass, mean individual biomass (MIB), and  species composition revealed interannual fluctuations superimposed on strong  nearshore–offshore gradients, with higher values in transitional and coastal MRUs.  The assemblage was consistently dominated by Pleopis polyphemoides and Penilia  avirostris, which together accounted for most of the total abundance and biomass.  Multivariate analysis identified significant differences in taxonomic composition  across MRUs and years, while correlation analyses highlighted …

Endemism Patterns Of Leaf Beetles (Coleoptera: Chrysomelidae) In Türkiye, İsmai̇l Şen, Ali̇ Gök

Turkish Journal of Zoology

In this study, the distribution of endemic leaf beetles in Türkiye was analyzed  holistically at the provincial scale using species richness (ENR), corrected weighted  endemism (CWE), and range-restricted endemism (RRE) indices. A total of 95  endemic taxa were found in Türkiye and these taxa exhibited significant spatial  heterogeneity in terms of richness and extent of distribution. The Western and  Central Taurus Mountains and the Eastern Black Sea Region were found to be the  main centers of endemism, with high densities of narrowly distributed and  geographically restricted species. These patterns clearly demonstrate that key  biogeographic factors, such as steep elevation gradients, …

Dynamics Of Ant Activity Under Extreme Climatic Changes In 2024: Effects Of Temperature  And Humidity On Formica Rufa And Lasius Fuliginosus Behavior, Stanislav Stukalyuk, Mykola Kozyr, Vira Balabukh

Turkish Journal of Zoology

Global warming and extreme heatwaves, which can alter species distribution and ecosystem dynamics, have profound effects on forest ants. T‍his study investigated the impact of summer and autumn 2024 heatwaves on the activity, prey transport, and nest-building of Formica rufa Linnaeus, 1761 and Lasius fuliginosus (Latreille, 1798) in deciduous forests of Kyiv, Ukraine. Fieldwork was conducted from June to September 2024 in Holosiyivo Forest and the Feofaniya tract. Ant colonies were assigned to experimental plots, where logs were placed along foraging trails, or to control plots with unmanipulated ground-floor trails. The study included 10 F. rufa anthills for activity monitoring …

The Effect Of Spatial Scale Of Habitat On Abundance Of Roe Deer (Capreolus Pygargus) And Water Deer (Hydropotes Inermis Argyropus) During Summer In South Korea, Naeyoung Kim, Hyejin Kim, Hyoun-Gi Cha, Hyun-Su Hwang

Turkish Journal of Zoology

Understanding species-specific habitat preferences provides essential ecological  information about interactions among habitat components. In South Korea, roe deer  (Capreolus pygargus) and water deer (Hydropotes inermis argyropus) are the  dominant large herbivorous mammals of the family Cervidae. The increasing populations of these species have led to ecological and economic  challenges. Therefore, we investigated the effects of spatial scale characteristics on  the habitat preferences of roe deer and water deer. From June to August each year  between 2021 and 2023, we calculated the relative abundance index (RAI) using  camera-trap data and analyzed patch characteristics in the study area using remote  sensing techniques, …

The Impact Of Tgfβ Conditioning And Socs3 Expression On Cytokine Signal Transduction And Inflammatory Gene Expression In Fibroblasts, Morgan Anderson-Crannage

NYMC Student Theses and Dissertations

Inflammation is a major driver in many aspects of recessive dystrophic epidermolysis bullosa (RDEB) pathology, including impaired wound healing, fibrosis, and potentially cutaneous squamous cell carcinoma development. Fibroblasts, as key stromal cells in the dermis, are responsible for orchestrating inflammatory responses through the secretion of cytokines and chemokines upon stimulation with IL-1α or IL-6. Suppressor of Cytokine Signaling 3 (SOCS3) functions as a negative feedback regulator of cytokine signaling and has emerged as a key modulator of inflammatory responses in immune cells and fibroblasts. Transforming Growth Factor Beta (TGFβ), a known driver of fibrosis in RDEB, has been implicated in …

Assessment Of The Bioremediation Potentials Of Biosurfactant-Producing Bacterial Strains Recovered From Spent Engine Oil-Contaminated Environments In Southwest Nigeria, Nafisa Mohammed Babayola, Nasiru Bright Lecky, Chinweizu Obioma Onumaegbu, Olufunmiso Olusola Olajuyigbe, Martins Ajibade Adefisoye

Journal of Environmental Science and Sustainable Development

Environmental pollution from hydrocarbons and their derivatives is predominantly of anthropogenic origin, occurring mainly during mining, transportation, and storage. This often in an annual release of substantial amounts of pollutants into the environment. The effective restoration of petroleum-contaminated environments requires a series of interventions to remediate soil to its natural state. This study aimed to isolate and characterize biosurfactant-producing bacterial strains with potential bioremediation capabilities to assess the potential application for remediating soils polluted with spent engine oil in the Remo district, Ogun State. Bacterial isolates were recovered from soil samples collected from spent engine oil contaminated sites, using standard …

The Heterogeneous Response Of Astrocytes In Different Brain Regions Under Metabolic Stress, Pawan Kumar Thapaliya

USF Tampa Graduate Theses and Dissertations

Astrocytes play a central role in maintaining ionic homeostasis, neurotransmitter clearance, and brain en-ergy metabolism. Their excitability, reflected in activity-evoked intracellular sodium (Na+, [Na+]i) and calcium (Ca2+,[Ca+]i) dynamics, is increasingly recognized as a critical determinant of neuronal function and vulnerability, particularly under metabolic stress. Despite their importance, the mechanisms underlying astrocytic ionic signaling and its regional heterogeneity remain incompletely understood. In this thesis, I developed detailed computational and biophysical models to investigate astrocytic Na+ and Ca2+ dynamics, their bioenergetic consequences, and the roles of key ion transporters under physiological and metabolically stressed conditions, validating the models against experi- mental data. …

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …

Genomics And Bioinformatics Student Companion Workbook (First Edition), Na Xu, Tina Hu

Open Educational Resources

This Genomics and Bioinformatics Student Companion Workbook provides an integrated, hands-on introduction to the principles and applications of modern genomics and bioinformatics. Designed for undergraduate students, the workbook guides learners from foundational concepts of genome structure and sequencing technologies to advanced topics including variant analysis, comparative genomics, and multi-omics integration. Emphasizing the interplay between experimental biology and computational analysis, it introduces key analytical tools and biological databases that support genome interpretation and data-driven discovery.

Through a structured progression of chapters, students explore genome organization across diverse biological systems, from prokaryotes and viruses to complex eukaryotic genomes, and examine how genomic …

Scb252 Fundamentals Of Biotechniques Laboratory Manual, Na Xu, Hanqi Ye

Open Educational Resources

This laboratory manual for SCB252: Fundamentals of Biotechniques provides an integrated, hands-on introduction to core concepts and methods in modern biological research using Drosophila melanogaster as a model organism. The manual emphasizes laboratory safety, research integrity, and responsible conduct of research, alongside foundational experimental skills. Students are guided through key biological techniques including fly husbandry, genetic crosses, mutant analysis, microscopy, DNA extraction, polymerase chain reaction (PCR), gel electrophoresis, sequencing technologies, and bioinformatics tools such as BLAST and genome databases. Advanced modules introduce gene structure annotation, RNA-seq data analysis, and primer design, while fluorescence microscopy and protein analysis techniques further expand …

Virus-Like Particle Peptoid Conjugate As A Triple-Negative Breast Cancer Targeting Delivery System, Ricky Zhu

Chemistry Theses

Triple-negative breast cancer (TNBC), an aggressive form of breast cancer, characterized by its lack of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER2) poses a therapeutic challenge as common treatment options are rendered ineffective. Here is a strategy to develop a drug delivery system utilizing poly-glycinated LC129 8, a TNBC targeting peptoid, covalently attached to HK97 virus-like particles (VLP) containing a C-terminal LPETG sequence via a sortase mediated reaction. Using the properties of the cage-like structure of VLPs and the TNBC specificity of the LC129-8, high doses of chemotherapy can be efficiently loaded into the …

Determining Agricultural Literacy Proficiency Of Extension Professionals And Primary Volunteers In Mississippi, Molly Campbell

Theses and Dissertations

The development of agricultural literacy is a lifelong process, moving from gaining agricultural knowledge to communicating with others to applying to societal issues, and extends beyond the formal classroom. The Mississippi State University Extension Service has the ability to reach various audiences through educational programming, making them a potential catalyst for change in increasing agricultural literacy across the state. The study aims to determine the agricultural literacy levels of Extension professionals and primary volunteers in Mississippi and the factors potentially influencing these levels. Twenty-nine Extension professionals and eleven primary volunteers completed a survey of demographic questions and the Judd-Murray Agricultural …

The Development And Evaluation Of An Automated Tactical Tillage Tool To Identify And Control Weeds In Row-Crop Production Systems Using Vision-Based Machine Learning., Clara Anne Cobb

Theses and Dissertations

Controlling in-field weeds in row-crop production systems is vital to the success of the operation. To control weeds, most producers use combinations of weed control strategies, including tillage and herbicide applications. Cotton production operations across the country have been trending toward conservation tillage practices in an effort to minimize soil disruption and maintain crop residues on the soil surface. This practice, in addition to the adoption of herbicide-tolerant cotton varieties, has encouraged more use of chemical herbicides. The overuse of these herbicides has resulted in an increase in herbicide-resistant weeds, making weed control difficult for farmers. This research aimed to …

Patterns Of Molecular Evolution Driving Reproductive And Genomic Processes In Sauropsids, Taylor Green

Theses and Dissertations

Sexual reproduction is an important driver of genetic diversity and speciation through such forces as selection, mutation, and drift. Sauropsids are an appropriate clade to study shared molecular drivers of sexual and genomic evolution due to their genome architecture, sex determination mechanism (SDM) plasticity, and large syntenous genomic regions. Using comparative phylogenetic methods, I identify predictable patterns of selection in meiotic recombination genes and clade-specific drivers of recombination rate evolution. Then, leveraging whole genome sequencing, I demonstrate that American alligator genomes are characterized by an ancient loss of genetic diversity driven by drift and historic inbreeding. I also generate a …

Reproductive Genetics Of Caenorhabditis Nematodes, Dharani U. Matharage

Theses and Dissertations

Variation in reproductive traits and genome evolution reflects the interaction between selection, environment, and life-history. In the genus Caenorhabditis, recombination rate and sperm size exhibit a striking variation between strains and species. Here, Iintegrate three projects investigating recombination rate variation and recombination plasticity in C. elegans and sperm size divergence across Caenorhabditis species. First, I quantify recombination rates in two genetically distinct strains, N2 and CB4856, with different levels of laboratory adaptation using fluorescent markers spanning across gene-rich and gene-poor regions of the chromosome IV. I identify significant differences in recombination rate between the two strains within both gene-rich and …

Accuracy Of Parameter Estimation For A Simple Gene Regulatory Network Model Is Sensitive To Network Motif, Number Of Parameters Estimated, And Magnitude And Direction Of Regulatory Relationships, Nikki C. Chun, Kam Dahlquist

Honors Thesis

A gene regulatory network (GRN) is a set of transcription factors that regulate the expression of genes encoding other transcription factors. The dynamics of a GRN explain how gene expression changes over time. GRNmap is a MATLAB software package that uses ordinary differential equations to model dynamics of small-scale GRNs. We used the program to estimate production rates, expression thresholds, and regulatory weights for each transcription factor in three related literature-derived GRNs based on yeast cold shock microarray data previously collected in the Dahlquist Lab. We noticed large differences in estimated weight values when 1-2% of the expression values were …

Exploring Health Insurance’S Role In Chronic Disease Management Among Hispanics, Romelyn Dones

Seton Hall University Dissertations and Theses (ETDs)

This qualitative study examined how insured non-English- and English-speaking Hispanic adults perceive the role of health insurance in the management of chronic disease. Chronic conditions remain a leading cause of morbidity in the United States, and although prior research suggests that insurance coverage improves access to care, it does not always enhance how individuals understand or utilize support for chronic disease management. Limited research has explored how individuals with chronic conditions interpret the role of insurance in their daily self-management practices, particularly among Hispanic populations. Guided by Andersen’s Behavioral Model of Health Services Use, this study explored how contextual, enabling, …

Interpretable Deep Learning Models For Trustworthy Prediction Of Enzyme Functions, Louis Dumontet

UNLV Theses, Dissertations, Professional Papers, and Capstones

Trustworthy prediction of enzyme function from protein sequences remains a central challenge in computational biology, particularly when annotated data are limited, imbalanced, or incomplete. This dissertation develops interpretable deep learning methods for enzyme discovery and enzyme function prediction from amino acid sequences. First, it introduces PEPIC, an interpretable convolutional neural network for substrate-level prediction of hydrolytic plastic-degrading enzymes. Using curated and expanded sequence datasets, PEPIC improved predictive performance over benchmark methods, identified sequence regions aligned with catalytic and substrate-binding residues, and supported the discovery and experimental validation of a previously uncharacterized PET-degrading enzyme. Second, this dissertation investigates the integration of …

Community Development Professionals’ Perceptions Of Agritourism In Mississippi, Emma Jane Berry

Theses and Dissertations

Agritourism has emerged as a strategy for supporting rural economies, strengthening community identity, and increasing agricultural literacy. Although prior research has examined agritourism operators and visitors, limited attention has been given to the perceptions of community development professionals who influence local planning and program support. The purpose of this qualitative exploratory study was to examine community development professionals’ perceptions of agritourism’s role in community development, economic growth, and agricultural literacy in Mississippi. Guided by Social Exchange Theory, data were collected through two semi-structured virtual focus groups with 12 professionals representing Extension, tourism, economic development, and Main Street organizations. Data were …