Digital Commons Network^™

Two Decapod Crustaceans, Panopeus Herbstii And Petrolisthes Armatus, Stabilize Their Gaze Using Achromatic Visual Cues, But Not The Angle Of Linearly Polarized Light, M. Janakis, S. Guirges, A. C. Grant, I. Paris, E. F. Lopresti, Daniel Isaac Speiser

Faculty Publications

No abstract provided.

Comprehensive Study Of Imidazole-Based Hydrazones: From Design, Synthesis, And Characterization To In Vitro And In Silico Antiproliferative Activity Analysis, Ömer Di̇lek

Turkish Journal of Chemistry

The aim of this study was to synthesize novel imidazole-cored hydrazones and investigate their cytotoxic activities against human breast and lung cancer cell lines using in vitro and in silico techniques. For this purpose, 5 novel compounds (6 and 7a–7d) were synthesized. The structures of the synthesized compounds were confirmed using spectroscopic methods. The cytotoxic effects were evaluated against human lung (A549) and breast (MCF-7) cancer cell lines using the MTT assay. All synthesized compounds had higher cytotoxic activity against MCF-7 cells (IC50 < 9.262 μM) than the control drug cisplatin. However, their cytotoxic activity against A549 cells (IC50 > 2.605 μM) was lower than that of cisplatin. Except for compound 7d in the A549 cell line, …

A Disposable Biosensing System For Analysis Of Ca125 In Real Human Serum Samples, Meltem Afşar, Berfi̇n Vural, Meli̇ke Bi̇lgi̇ Kamaç, Mustafa Kemal Sezgi̇ntürk

Turkish Journal of Chemistry

Several biomarkers have been developed to track the development of ovarian cancer and identify the illness at an early stage. A promising development for ovarian cancer is using cancer antigen 125 (CA125). The objective of this work is to identify the CA125 marker by utilizing an indium tin oxide polyethylene electrode. The advantage of the designed biosensor is that it is very cheap, disposable, practical, and easy to use. The necessary parameters for the developed biosensor have been optimized in detail. Repeatability, reproducibility, regeneration, storage, and selectivity studies have been completed to characterize the proposed biosensor. Electrochemical impedance spectroscopy and …

Mechanisms Of Ssdna Gap Resection In Brca1-Proficient And -Deficient Cells, Isabelle Seppa

Arts & Sciences Graduate Student Theses and Dissertations

Single-stranded (ss) DNA gaps are potentially genome-destabilizing structures that require prompt repair (or filling) to prevent DNA breakage and genome instability. We previously showed that gap repair is defective in cancer cells with deficiencies in the breast cancer susceptibility gene BRCA1. These findings explain why ssDNA gaps accumulate in BRCA1-deficient cells in response to therapies that target DNA, such as platinum-based compounds, or therapies that inhibit specific repair pathways, such as PARP inhibitors (PARPi). We also discovered that gap repair can be restored in BRCA1-deficient cells by inhibiting MRE11 nuclease activity, indicating that nuclease processing plays a central role in …

Anti-Inflammatory Diet And Probiotic Supplementation As Strategies To Modulate Immune Dysregulation In Autism Spectrum Disorder, Carlos Andrés Naranjo-Galvis, Diana María Trejos-Gallego, Cristina Correa-Salazar, Jessica Triviño-Valencia, Marysol Valencia-Buitrago, Andrés Felipe Ruiz-Pulecio, Luisa Fernanda Méndez-Ramírez, Jovanny Zabaleta, Miguel Andres Meñaca-Puentes, Carlos Alberto Ruiz-Villa, Marcela Orjuela-Rodriguez, Juan Carlos Carmona-Hernández, Luisa Matilde Salamanca-Duque

School of Medicine Faculty Publications

Background/Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental condition associated with behavioral and cognitive impairments. Increasing evidence also links ASD with systemic immune dysregulation, including abnormal cytokine profiles and chronic low-grade inflammation. Emerging evidence suggests that targeted dietary strategies and probiotic supplementation may modulate immune responses and gut–brain interactions in patients with ASD. This study aimed to evaluate the immunomodulatory effects of a structured anti-inflammatory diet (NeuroGutPlus) compared to multi-strain probiotics in children with ASD. NeuroGutPlus is a nutritionally complete anti-inflammatory dietary protocol that targets gut integrity, inflammation, and mitochondrial function. It includes a diet low in gluten, FODMAPs, casein, …

Dominant Tree Species As A Driver Of Forest Herb Community Assembly: The Peculiar Case Of Pawpaw (Asimina Triloba), Anna Wassel

Arts & Sciences Graduate Student Theses and Dissertations

Understanding the drivers of community assembly is a key goal in ecology and conservation. One way to better understand community assembly is to understand how the presence or absence of dominant species– highly abundant species with a proportionally large effect on the ecosystem–affects assembly. This approach allows for a more generalized understanding of community assembly based on the presence or abundance of one species rather than pairwise interactions among all species in a community. In forests, studies on dominant tree species have focused on how they affect patterns of species diversity. In contrast, surprisingly little is known about how dominant …

Ghosts Of Predators Past: Um Student Studies Raccoon Scent Memory, Clara Turnage

University of Mississippi News

OXFORD, Miss. – They are known for their clever paws and masked faces, but raccoons might also have an unexpected survival skill: remembering scents of predators they have never met.

The Impact Of Interactive Read-Alouds On Students’ Literacy Development, Kaitlyn Hill

Theses and Dissertations

This thesis examined how multicultural interactive read-alouds support first-graders’ literacy skills and cultural awareness. Multicultural literature was used to conduct interactive read-alouds to first-grade students. A look across all data sources suggested three main themes that occur throughout the research study. These themes included student engagement and questioning, making connections by experiencing culture through an authentic lens, and developing cultural awareness and empathy for those who are different. It was evident that incorporating multicultural literature into classroom instruction had a positive impact on students’ literacy development and cultural awareness. The data suggested that these multicultural texts supported the students’ development …

Difference In High School Geometry End-Of-Year State Exam Scores Between Three Different Retake Time Frames, Christina Noel Walton

Walden Dissertations and Doctoral Studies

A grading policy was implemented in a Northeastern suburban public school district that left it to curriculum teams to define the amount of time between the original test and its retake resulting in a slight decrease in high school students’ geometry end-of-year state exam scores. Guided by Bloom’s theory of mastery learning, the purpose of this quantitative causal-comparative study was to investigate if there were statistically significant differences between high school students’ geometry end-of-year state exam scores or between high school students’ geometry math growth scores when controlling for the preassessment score differentiated by three schemes of retake timing: short-term, …

Anti-Tumor Activity Of Camptothecin Analog Conjugate Of An Rspo4-Based Peptibody Targeting Lgr4/5/6 In Preclinical Models Of Colorectal Cancer, Yukimatsu Toh, Ling Wu, Jianghua Tu, Zhengdong Liang, Adela M Aldana, Jake J Wen, Li Li, Sheng Pan, Julie H Rowe, Martha E Hensel, Carolyn L Hodo, Rick A Finch, Kendra S Carmon, Qingyun J Liu

The Brown Foundation: Institute of Molecular Medicine

Background: Antibody-drug conjugates (ADCs) are a significant advancement in targeted cancer therapy, but none are approved for colorectal cancer (CRC). LGR4/5/6, highly expressed in most CRCs, are promising targets. While LGR5-targeting ADCs show strong anti-tumor effects, their efficacy is limited by LGR5 loss in some CRC cells. RSPO4, a natural ligand for LGR4/5/6, binds all three receptors with high affinity. This research develops RSPO4-based peptibody drug-conjugates (PDCs) to simultaneously target LGR4/5/6, offering a novel therapeutic approach for CRC.

Methods: LGR4/5/6 expression in CRCs was analysed using RNA-seq datasets and Western blot. Peptibody binding affinities were measured, conjugated to camptothecin analog, …

Reconciling Harm Reduction Philosophy And Approaches Among Abstinence-Only Substance Abuse Treatment Professionals, Amy Rose Ashton-Williams

Walden Dissertations and Doctoral Studies

Historically, substance use disorder (SUD) treatment in the United States has been firmly grounded in abstinence-only treatment approaches. Harm reduction as a treatment model has gained additional traction. With increased rates of opioid use, overdoses, and advancements in medications for SUDs, harm reduction treatment approaches are becoming more important to improve lives of people who use drugs. Little is known about how counselors who have been educated, trained, and deliver abstinence-based SUD treatment reconcile use of harm reduction into their practice. To address this gap in literature, a generic qualitative study was conducted using the social constructivism theory. A purposive …

Applying Machine Learning To Developmental Psychopathology, Robert Jesus Jirsaraie

McKelvey School of Engineering Graduate Student Theses & Dissertations

Psychopathology arises from a combination of many contributing factors, which can include genetic predispositions, family history, environmental stressors, developmental processes, and psychosocial dynamics. Each of these contributing factors has been researched for decades, and their influences on mental health have been well documented. In recent years, there has been a growing enthusiasm for integrating these risk factors using machine learning. However, there are a wide array of data-driven frameworks that have been implemented, and the relative strengthens of each approach is not clear. Through of series of four research studies, we examined each data-driven approach in terms of its potential …

Intravital Optical Imaging Of Peripheral Nerve Injury Response, Igor Luzhansky

McKelvey School of Engineering Graduate Student Theses & Dissertations

Peripheral nerve injuries in animal models require imaging approaches that can reveal the dynamic, multiscale process of regeneration over time without disrupting repair mechanisms. Traditional methods lack the ability to visualize cellular behavior and matrix remodeling continuously. We present an imaging technique based on an implantable nerve window and fluorescent labeling, enabling high-resolution, longitudinal cellular-scale observation of peripheral nerve regeneration in living mice. We first evaluated near-infrared fluorophore-conjugated fibrin as a transient marker for early regenerative tissue within nerve guidance conduits. Imaging performed upon surgical re-exposure of the nerve revealed the incorporation of fibrin into early-stage regenerative cables, with gradual …

Large-Scale Modeling And Inference Of Non-Stationary Brain Dynamics, Addison Schwamb

McKelvey School of Engineering Graduate Student Theses & Dissertations

Neural modeling has long been a tool for understanding the brain's function, in both healthy subjects and those experiencing neural pathologies. These models have captured structures in the brain ranging in spatial scale from the subcellular level to the whole-brain level, and processes ranging in temporal scale from milliseconds to multiple hours. Currently, however, there are very few dynamical systems models of whole-brain activity, and the modeling methodologies that do exist rely on neural data modalities which are impractical for use in clinical settings. At the same time, a wealth of data is being generated by patients undergoing clinical monitoring. …

Spatial Patterns In Electronic Health Record Data-Based Predictive Modeling: A Case Study Of Prenatal Care And Preeclampsia, Abigail Lewis

McKelvey School of Engineering Graduate Student Theses & Dissertations

The electronic health record (EHR) documents interactions between patients and healthcare systems and is widely used for secondary research on health outcomes due to broad adoption. While EHR data support efficient clinical informatics research, they are subject to biases stemming from healthcare seeking behavior, health system attributes, and individual or environmental characteristics. Place-based characteristics, in particular, strongly influence when and how patients access care and shape health outcomes. These biases in EHR data can affect predictive modeling pipelines which leverage them, contributing to variation in model performance across groups. In healthcare, where predictive models are increasingly used to guide care, …

Harnessing Metabolic Modeling And Artificial Intelligence For Next-Generation Bioproduction, Zhengyang Xiao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Bioproduction in microbial hosts faces two main challenges: (1) unique metabolism of each species is difficult to generalize, and it requires precise quantification before metabolic engineering. (2) Past experiment data are fragmented in different studies, making it difficult to combine these non-standardized data for future experiment design. These challenges lead to high costs and risks in scaling up biomanufacturing processes, where R&D requires substantial budgets and iterative experiments are expensive. This thesis addresses both challenges through two research pillars. Part I uses 13C metabolic flux analysis (MFA) and genome-scale model (GSM) to investigate metabolic limitations in bioproduction hosts. In Escherichia …

Moment Ensemble Approaches For Estimation And Robust Quantum Control, Andre Luiz Paes De Lima

McKelvey School of Engineering Graduate Student Theses & Dissertations

Large-scale population dynamics governed by ensemble systems present significant challenges due to their inherently high dimensionality. Recent advances have demonstrated the effectiveness of moment-based methods (particularly those employing polynomial bases such as Legendre and Chebyshev polynomials) when integrated with optimization techniques for control design in ensemble systems. However, these methods have not been extensively explored for enhancing robustness against systematic noise, nor have they been widely applied to complex quantum systems involving multi-parameter configurations and entanglement phenomena. In this work, we extend the application of moment methods in ensemble systems through two projects. Initially by developing a Kalman filter analogue, …

Towards Graph Foundation Models: Few-Shot And Zero-Shot Learning On Graphs, Hao Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Graphs naturally model complex relationships and interactions across various domains, including social networks, biological systems, and recommender platforms. Graph Neural Networks (GNNs) have emerged as powerful tools for learning effective graph representations through iterative message passing, significantly improving performance in tasks such as node classification, link prediction, and graph classification. However, the success of GNNs largely depends on abundant labeled data, posing challenges in practical scenarios where labeled data is scarce or unavailable. This dissertation addresses these challenges by exploring few-shot and zero-shot learning within the graph domain. We first propose COLA, a self-supervised few-shot node classification method that exploits …

Computational Imaging Under Incomplete Information, Weijie Gan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Computational imaging is a pivotal field that synergizes physical measurement principles with advanced algorithms to generate visual information. An important task in this field is solving imaging inverse problems that aim to reconstruct high-quality images from observed measurements. Model-based deep learning (MBDL) has emerged as a particularly powerful tool for tackling these inverse problems by integrating machine learning (ML)-driven priors with knowledge of the imaging physics. This dissertation focuses on the pervasive challenge of informational incompleteness in computational imaging, arising from various practical and physical limitations, that hinder the widespread adoption of ML-driven computational imaging algorithms in practice. This includes: …

Faster, Higher, Stronger: Modern Methodologies For The Calibration, Exploration, And Utilization Of Agent-Based Models, David O'Gara

McKelvey School of Engineering Graduate Student Theses & Dissertations

Increases in computing power and availability have led to the widespread use and adoption of agent-based models (ABMs) in the physical, biological, and social sciences. At their core, ABMs represent a novel paradigm for scientific inquiry: their micro-level specification allows for the simulation of the individual components of a system which yields a deeper understanding of dynamic processes such as contagion and adaptive decision-making when used appropriately. However, several hurdles exist when attempting to use ABMs to their full potential. In this thesis, we will explore and address several challenges in designing and utilizing ABMs, with a focus on applying …

Smartphone Attachment In Emerging Adults : Impacts On Mental Health Through Basic Psychological Needs, Jialin Xiao

Lingnan Theses (MPhil & PhD)

In the digital era, smartphones have become integral to daily life, fulfilling various emotional needs. Mirroring human attachment, past studies have found people can develop three types of attachment to smartphone: secure (comfortable, dependable connection), anxious (intense emotional reliance with separation anxiety) and avoidant (preference for independence from one’ s phone) attachment. However, little is known about how these types of smartphone attachment relate to mental health over time. Moreover, the mechanism underlying the relationship between smartphone attachment and mental health is unknown. To fill these gaps, based on the attachment theory, this study examined the longitudinal associations between smartphone …

Transmission Patterns That Reduce Population Size Without Increasing Disease Prevalence: Masting And Chronic Wasting Disease In White-Tailed Deer, Virginia Kanzinger, Karen C. Abbott

Faculty Scholarship

How individuals use space and, thus, the rate and the nature of their interactions with others are shaped by their environment. Exogenous changes that alter aggregation patterns, such as resource pulses, can therefore have a significant impact on seemingly unrelated processes like disease spread. White-tailed deer (Odocoileus virginianus) aggregate in oak forests during mast events, and chronic wasting disease (CWD) transmission patterns vary with deer density, so we hypothesize a link between the masting cycle and CWD dynamics. We investigate various possible effects of masting on deer, including shifts to more frequency-dependent CWD transmission due to aggregation, as well as …

Theoretical Study On Electronic And Optoelectronic Properties Of Some C^N^N- And C^C^C-Chelated Iridium(Iii) Complexes For Oleds, Ayhan Üngördü

Turkish Journal of Chemistry

The electronic and optoelectronic properties of 8 C∧N∧N- and C∧C∧C-chelated Ir(III) complexes were investigated using density functional theory at the Becke-style 3-parameter Lee-Yang-Par and triple zeta plus polarization level. Based on reorganization energy calculations, complex 7 was identified as a promising ambipolar material, while complexes 1 and 2 had efficient hole transport properties. Complex 8 had low ionization potential and is therefore a strong candidate for hole transport applications. Complex 4 had high electron affinity and therefore has potential as an effective electron acceptor material. Photophysical analysis showed that all complexes had phosphorescent properties, with complexes 5 and 6 showing …

A Decision Model For Enhancing Reaction Yield: Pd(Ii) And Pt(Ii) Metal Insertion To Free Porphyrin, Özay Özaydin, Emel Önal

Turkish Journal of Chemistry

Chemical synthesis experiments are crucial for developing new materials, yet their inherent complexity and variability often lead to suboptimal results, causing significant resource and time wastage. This study proposes a novel decision support model to enhance the success rate of macromolecule synthesis experiments for sensor applications. The model leverages principles of experimental design and decision-making. We identified synthesis alternatives through a literature review and expert consultations, narrowing it down to 6 alternatives for metal salts, 3 for reactant mole ratios, 5 for organic solvents, 3 for reaction temperatures, and 4 for reaction times. Considering the time and cost constraints, this …

Synthesis, Characterization, And Drug Release Properties Of Enzyme-Responsive Oxamide-Bridged Mesoporous Organosilica Nanoparticles, Yaşar Gök, Hali̇l Zeki̇ Gök, Osman Tayyar Arli, Tuğçe Türkaslan

Turkish Journal of Chemistry

In this study, we report a novel enzyme-responsive mesoporous organosilica nanocarrier (MON) and its drug delivery properties in the presence of the trypsin enzyme. The mesoporous organosilica nanocarrier was synthesized by using the oxamide bridged bissilyl compound (2) and 1,4-bis(triethoxysilyl)benzene (BTSB). To compare the enzyme responsiveness of MON, the reference periodic mesoporous organosilica (PMO) nanocarrier was also synthesized using BTSB only. The structural determinations of the synthesized organic compounds were carried out by 1H, 13C-NMR, FT-IR, and MS, while FT-IR, XRD, SEM, EDS, transmission electron microscopy (TEM), TGA, and N2 sorption analyses were used for the characterization of MON and …

Relationships Between Household Economic Distress And Child Mental Health: Determinants, Mechanisms, And Interventions, Yuanyuan Yang

Brown School Graduate Student Theses and Dissertations

Economic inequality has grown dramatically worldwide, creating serious problems for children and families. At the same time, child and adolescent mental health problems have reached crisis levels, yet many of them cannot access treatment. Researchers have studied how economic inequality affects mental and behavioral health, but most of this work focuses on adults rather than children. This dissertation used recent data from the Panel Study of Income Dynamics (2019 and 2021 waves) to unpack the complex relationships between household economic distress and child mental health across multiple levels, including individual, family, school, and community factors in the United States. This …

Asymmetric Fgf Receptor Dimerization: Implications For Fgf23 Biology And Drug Discovery, Mohammed S. Razzaque, Moosa Mohammadi

School of Medicine Publications

Fibroblast growth factor 23 (FGF23) requires both αKlotho and heparan sulfate proteoglycans (HSPGs) as obligatory coreceptors to bind, dimerize, and activate its FGF receptors (FGFRs) in the kidney, thereby regulating mineral ion and vitamin D homeostasis. Cryogenic electron microscopy studies reveal that FGF23 signaling proceeds through an asymmetric 1:2:1:1 FGF23–FGFR–αKlotho–HS assembly. According to this structural model, αKlotho simultaneously anchors FGF23 and one FGFR chain, referred to as the primary receptor (FGFRP), to form a 1:1:1 FGF23-FGFRP-αKlotho triplex, which boosts FGF23-FGFRP interaction. Subsequently, the HS coreceptor aids the triplex in recruiting a second FGFR chain, or secondary receptor (FGFRS), leading to …

Extended Survival With Pancreatic Carcinosarcoma: A Case Report And Literature Review, Tian Xiao, Claire Browne, Morgan Black, Celia Marginean, Elena Tsvetkova

Faculty, Staff and Students Publications

Pancreatic carcinosarcoma is a rare and aggressive malignancy that can mimic pancreatic adenocarcinomas in presentation but often has different disease biology and different responses to conventional treatment for pancreatic adenocarcinoma. Case reports have documented a 5-year overall survival of approximately 13% only if the disease is caught at an earlier stage and is amenable to multi-modality treatment, including surgery, chemotherapy, and radiation. In the advanced stage, treatments do not often provide benefit, and patients may decline rapidly. There are currently no studies demonstrating survival benefits with chemotherapy in patients with metastatic carcinosarcoma, owing to both the rarity and the often …

Improving Automated Deep Phenotyping Through Large Language Models Using Retrieval-Augmented Generation, Brandon T Garcia, Lauren Westerfield, Priya Yelemali, Nikhita Gogate, E Andres Rivera-Munoz, Haowei Du, Moez Dawood, Angad Jolly, James R Lupski, Jennifer E Posey

Faculty, Staff and Students Publications

Background: Diagnosing rare genetic disorders relies on precise phenotypic and genotypic analysis, with the Human Phenotype Ontology (HPO) providing a standardized language for capturing clinical phenotypes. Rule-based HPO extraction tools use concept recognition to automatically identify phenotypes, but they often struggle with incomplete phenotype assignment, requiring significant manual review. While large language models (LLMs) hold promise for more context-driven phenotype extraction, they are prone to errors and "hallucinations," making them less reliable without further refinement. We present RAG-HPO, a Python-based tool that leverages retrieval-augmented generation (RAG) to elevate accuracy of HPO term assignment by LLM. This approach bypasses the limitations …

Cationic Liposome Nanoparticles For Drug Delivery To The Inner Ear, Firas Al-Ashker

Master's Theses (2009 -)

Cisplatin is a widely used chemotherapy drug associated with a high incidence of hearing loss, particularly in younger patients. This ototoxicity is linked to the drug’s long-term accumulation in the cochlea, where it can persist for years following treatment. Current clinical interventions, such as sodium thiosulfate (STS), offer partial protection against hearing loss but are limited by poor drug penetration into the inner ear. The objective of this study was to develop and evaluate a targeted drug delivery platform capable of overcoming anatomical and physiological barriers to reach the cochlea more effectively. Specifically, we aimed to design cationic liposome nanoparticles …