Digital Commons Network^™

From Sequence To Allostery: How Amino Acid Differences Rewire Coupled Conformational Heterogeneity In The Ptp Enzyme Family, Shivani Sharma

Dissertations, Theses, and Capstone Projects

Protein Tyrosine Phosphatases (PTPs) are critical regulators of cellular signaling, and their activity is often modulated through allosteric mechanisms. Allostery is defined as a chemical or conformational change in one site of the protein due to a binding event at another site. Although several studies have investigated aspects of allostery in PTPs, the mechanistic foundations underlying allosteric regulation remain poorly understood. Despite a highly conserved catalytic domain across PTPs, regions with low or no conservation suggest potential "rewiring" of allosteric networks. This raises key questions about the universality versus individuality of allosteric mechanisms across the PTP family.

In this work, …

Understanding Why Individuals Maltreated As Children Do Not Retrospectively Self-Report, Kristin S. Lynch

Dissertations, Theses, and Capstone Projects

Individuals with documented histories of childhood maltreatment who do not retrospectively self-report these childhood experiences demonstrate better emotional and psychological outcomes in adulthood. Understanding why these individuals do not retrospectively self-report is important for the development of effective interventions focused on mitigating the long-term consequences of maltreatment. The current study compared maltreated individuals who did not retrospectively self-report (O-R group) to those who did retrospectively self-report (O+R group) to examine theoretical explanations related to intentional nondisclosure (i.e., social desirability and discomfort during the interview) and memory processes (i.e. infantile amnesia, use of mental health services, avoidant coping …

Potential Role Of A Ruthenium-Based Compound Ru-Im In The Treatment Of Triple Negative Breast Cancer, Rachele Rameau

Dissertations, Theses, and Capstone Projects

Triple negative breast cancer (TNBC) is an aggressive and heterogeneous molecular subtype of breast cancer that has limited available treatments. The organometallic cationic ruthenium derivative Ru-IM was found to be highly water soluble, was differentially toxic for breast cancer cells and tumors, and was involved in the pI3K/AKT/mTOR pathway. However, a full understanding of genetic and epigenetic factors that can be part of regulatory mechanisms of Ru-IM is yet to be determined. Epigenetic assays including DNA methylation, histone acetylation and histone deacetylation were performed with the half inhibitory concentration (IC50) values of Ru-IM. Bisulfite sequencing of untreated and treated MDA-MB-231 …

Dónde Están: Searching For Desaparecidos Of The Argentine Dirty War, Paula Fleischer

Dissertations, Theses, and Capstone Projects

This project is a data physicalization textile representing the 30,000 'desaparecidos' from the Argentine Dirty War of late 1970s. The large quilt visualizes the official count of 9,000 missing persons in the shape of a headscarf worn by their mothers and grandmothers, while the overall dimensions of the quilt acknowledges 30,000 missing persons. The quilt and accompanying missing persons posters encourage the viewer to interact with the data, however the observed reluctance to engage influenced the direction of this discussion about the hegemonic disinclination to get involved when authority figures 'disappear' fellow residents of our communities.

Low-Resource Ecoacoustic Audio Classification, Enis Berk Coban

Dissertations, Theses, and Capstone Projects

Ecoacoustic monitoring via machine learning enables scalable analysis but is often constrained by labeled data scarcity, particularly in remote regions like the Arctic. This thesis confronts low-resource ecoacoustic audio classification by developing and evaluating complementary machine learning methodologies. We introduce EDANSA, the first publicly available, expert- labeled Arctic dataset of its kind, curated via novel active learning, alongside a baseline CNN. We systematically evaluate transfer learning, showing general audio embeddings effectively bootstrap classifiers for challenging Arctic sounds, significantly outperforming direct label mapping. Optimizing label utility, we investigate standard data augmentation and introduce novel audio data valuation via Shapley values, revealing …

Giving Voice To The Frames Of War: A Digital Humanities Framework For Evaluating War Crimes Databases, Leila Markosian

Dissertations, Theses, and Capstone Projects

Developments in digital technologies have complicated existing debates around the ethics of cataloging war crimes and human rights violations. Digital humanities methods of evaluating digital scholarship can help to construct a framework for evaluating war crimes databases, a process which requires a fine-tuned critical analysis aimed towards understanding the purpose of compiling the database, the platform or media template through which the database is presented, and the communicative potentials of the database. The following paper presents a survey of the existing literature on war crime databases and the politics of memory; a model of how war crimes database analyses may …

Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu

Dissertations, Theses, and Capstone Projects

This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

“Justice, Justice Pursue”: Coworker Reactions To Religious Workplace Accommodations, Joshua A. Nagel

Dissertations, Theses, and Capstone Projects

This study examines coworker reactions to religious accommodations in the workplace, a growing necessity as religious diversity increases, and recent legislation strengthens protections for religious observances. Religious accommodations can provoke perceptions of differential treatment, impacting coworker morale, cooperation, and organizational cohesion. While extensive research exists on disability accommodations, religious accommodations differ fundamentally as they often relate to moral beliefs and are viewed variably in terms of necessity and controllability. Drawing on organizational justice theories, this dissertation applies and modifies Colella’s (2001) and Colella et al.’s (2004) models for coworker perceptions of distributive and procedural fairness of disability accommodations to the …

Retinal Precursor Cell Enriched Multiomic And Pseudo-Time Analysis Of Developing And Reprogrammed Photoreceptors, Brendon M. Patierno

Dissertations, Theses, and Capstone Projects

The vertebrate retina is a complex tissue made up of seven major cell subtypes which during development must differentiate and localize into a highly organized structure. These neuronal cells do not regenerate if damaged or diseased, and the progressive deterioration of cone photoreceptor cells is the leading cause of age related blindness. Currently there are no cures for this disease, but one promising therapeutic avenue is cell transplantation research. If we can further elucidate the gene regulatory networks that define cone cell development, this knowledge could be applied to the generation of healthy cone cells in clinically relevant models.

The …

Nonlinear Diffusion, Hydrodynamic Cascades And Jamming In Kinetically Constrained Systems: Insights From Lattice Gas Models, Abhishek Raj

Dissertations, Theses, and Capstone Projects

This dissertation investigates non-linear diffusion processes and emergent dynamical phenomena in kinetically constrained lattice gases. Two central models are considered: a one-dimensional lattice gas exhibiting a diffusion cascade triggered by hydrodynamic nonlinearities and a triangular ladder exclusion model that undergoes a jamming transition. The former demonstrates stretched exponential decay consistent with non-perturbative long-time tails, while the latter illustrates how classical-quantum mappings yield insight into glassy dynamics and mobility constraints. Through a combination of numerical simulations, analytical perturbation theory, and mean-field approximations, the work uncovers mechanisms underlying anomalous transport, jamming transitions, and the breakdown of perturbative hydrodynamics.

The Sonic Hedgehog Effector Smoothened Modulates Cholinergic Interneuron Activity, Physiology, And Striatum-Dependent Behaviors, Santiago Uribe-Cano

Dissertations, Theses, and Capstone Projects

The striatum is a central node in action selection and associative learning, integrating cortical, thalamic, and neuromodulatory input. Among its principal modulators, dopamine (DA) and acetylcholine (ACh) are known for their temporally coordinated yet mechanistically distinct influences on striatal output. However, the upstream signals that regulate their dynamic interplay, particularly within cholinergic interneurons (CINs)—the primary source of striatal ACh—remain incompletely characterized. This dissertation investigates the role of Smoothened (Smo), a G protein-coupled receptor (GPCR) effector of Sonic Hedgehog (Shh) signaling, in modulating ACh signaling dynamics in the striatum.

Building on evidence that midbrain DA neurons co-release Shh and that CINs …

Teaching And Technology: "You Can't Just Do The Same Thing Online", Sakina Laksimi

Dissertations, Theses, and Capstone Projects

This dissertation examines how faculty at the City University of New York navigated the abrupt transition to online teaching during the COVID-19 pandemic, revealing how pedagogy is shaped by technological, institutional, and social conditions. Drawing on twenty-two interviews with twelve faculty across eight disciplines, I use a grounded theory approach to analyze how instructors adapted courses, reimagined assessment, and sustained connection with students amid crisis. Three overlapping pedagogical orientations emerged: improvisational, relational, and design-based teaching. These approaches highlight how faculty balanced responsiveness, care, and intentional course design in environments mediated by digital platforms and marked by inequity. The study situates …

Non-Linear Heart Rate Variability: Investigating Cardiac Complexity Of Psychopathic Traits, Khaya A. Roach

Dissertations, Theses, and Capstone Projects

Psychopathy is a complex personality disorder characterized by distinct emotional and interpersonal deficits, and affects approximately 25% of the prison population and 4.5% of nonincarcerated populations. The manifestation of psychopathy can be understood through two distinct variants, each demonstrating unique etiological pathways and clinical presentations. Primary psychopathy is characterized by core interpersonal and affective deficits, including shallow emotions and manipulativeness, while demonstrating reduced autonomic responsivity and lower anxiety levels. Secondary psychopathy presents with higher levels of impulsivity, anxiety, and emotional dysregulation, showing stronger associations with various psychopathologies. Treatment outcomes also vary between the variants, with primary psychopaths typically showing poor …

Mechanistic Insights Into The Neuroprotective Effects Of The Antidepressant Agomelatine In Alzheimer's Disease, Grace Terry

Dissertations, Theses, and Capstone Projects

Alzheimer’s Disease (AD) is a complex neurodegenerative disease that has limited treatment options and no cure. AD is characterized by robust pathology including extracellular amyloid beta plaques, intracellular neurofibrillary tangles, neuronal and synaptic loss, neuroinflammation, and brain atrophy. AD presents with cognitive decline and memory loss but only years after neuropathology has started to accumulate. This robust pathology has made AD difficult to treat and highlights the need for therapeutics that modulate multiple pathways. Agomelatine (AGO) was selected by a high-throughput machine learning drug repurposing algorithm by our collaborator Dr. Lie Xie (Hunter College Dept. of Comp. Sci.) as having …

Repurposing Atractylenolide Iii, A Natural Anti-Inflammatory Compound, For Alzheimer’S Disease, Angela M. Steele

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a debilitating neurological condition ranked as the fifth leading cause of death in adults over the age of 65. Despite the severity, 98% of drugs have failed as treatments for AD. Current novel drug development approaches have been unable to produce a disease-modifying treatment as they often have a one-target approach, not accounting for the complex nature of the disease. One of the hallmarks of the disease, inflammation, may provide a better target for treatment because it interacts with multiple facets of the disease. Drug repurposing to identify compounds that mitigate inflammation in AD could provide …

The Architecture Of Exclusion: Disability, Race, And The History Of New York City’S 600 Schools, Francine Almash

Dissertations, Theses, and Capstone Projects

This dissertation investigates the largely erased history of New York City’s 600 schools—segregated public schools created to house students labeled as emotionally disturbed or socially maladjusted. These institutions, operating throughout the mid-20th century, disproportionately served Black and Puerto Rican youth, many of whom were placed in these schools under vague behavioral criteria and with little to no pathway for return to general education settings.

Combining archival research, longitudinal policy analysis, historical media review, and critical race and disability studies frameworks—including DisCrit (Disability Critical Race Theory)—this project situates the 600 schools at the intersection of institutional racism and ableism. It argues …

Bmp Signaling Co-Regulation Of Immune Response And Lipid Metabolism, Katerina K. Yamamoto

Dissertations, Theses, and Capstone Projects

The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that …

Investigating The Role Of Early Growth Response 1 (Egr1) Gene In Riluzole-Induced Apoptosis In Osteosarcoma, Syeda Maryam Azeem

Dissertations, Theses, and Capstone Projects

Osteosarcoma is a rare but aggressive bone malignancy most commonly affecting adolescents and young adults (AYA). With 5-year survival rate stagnating over the last four decades despite the advancements in multi-modal therapy, drug repurposing offers a rapid path to new osteosarcoma treatments. Recent studies suggest that Riluzole, a drug approved for amyotrophic lateral sclerosis (ALS), may be repurposed for osteosarcoma treatment due to its ability to slow tumor progression and induce apoptosis. Previously, we have shown that Riluzole increases reactive oxygen species (ROS), activating c-Abl, which phosphorylates YAP in the nucleus. YAP then forms a complex with p73 to enhance …

Behavioral Biomarkers Of Vulnerability In The Aba Model, Nora Ozer

Dissertations, Theses, and Capstone Projects

Anorexia nervosa (AN) is a severe psychiatric disorder with the highest mortality rate among mental health conditions, yet effective biological treatments remain limited. The activity-based anorexia (ABA) paradigm, which combines food restriction with wheel access to model the hyperactivity and self-starvation cycle characteristic of AN, shows considerable individual variability in vulnerability. Understanding what predisposes certain individuals to develop the full ABA phenotype while others remain resilient could inform early intervention strategies for human AN. This study employed continuous behavioral monitoring technology to identify early predictors of vulnerability to activity-based anorexia in mice, with the goal of discovering behavioral biomarkers that …

The Role Of Parent Psychiatric Symptoms In The Intergenerational Continuity Of Child Neglect: A Prospective Examination, Cody D. Stitzel

Dissertations, Theses, and Capstone Projects

Parental history of childhood neglect is a risk factor for offspring neglect. When a parent and their offspring both experience neglect in childhood, the phenomenon is referred to as the intergenerational continuity of child neglect. Understanding how child neglect is continued from one generation to the next is essential for creating effective interventions and prevention strategies that may help break the cycle. Since links between childhood neglect and heightened risk for various psychiatric symptoms have consistently been identified in research, as well as links between various psychiatric symptoms and heightened risk for child neglect, it may be that parents’ psychiatric …

Wavelength And Luminance Interaction On Spatio-Temporal Contrast Sensitivity Function, Taylan S. Ergun

Dissertations, Theses, and Capstone Projects

Contrast sensitivity (CS) measures the ability to discriminate objects from their backgrounds under varying conditions(Campbell & Robson, 1968). Contrast sensitivity is important for navigating the real world and operating under different light conditions. The contrast sensitivity function (CSF) reflects how the visual system performs under different conditions. This measure is crucial in assessing the health of the visual system (Chen & Gardner, 2021). CSF contributes to a deeper understanding of how the visual system processes and integrates properties of light to create visual sensation and perception. Human contrast sensitivity depends on the viewing conditions such as field size, luminance, color, …

Liberated Learning Spaces: A Visual Playlist, Tarilyn R. Little

Dissertations, Theses, and Capstone Projects

Liberation can be defined as “the act of setting free” or “being free from limits on thoughts and behavior.” Both an action and a state of being, liberation has long been centered as a key function of education, particularly for those who live in historically and systemically marginalized identities. Despite the long-standing existence of liberation-focused pedagogies and activism aimed at transforming schools and students’ lived experiences, educational institutions in the United States have struggled to live out these ideals, often sustaining and replicating systems and practices of oppression. Drawing on historical and contemporary conversations in education and psychology, Liberated Learning …

The Role Of Water In Peptide Behavior And Peptide-Based Water-Responsive Crystals, Janel Jannette Rivera Cancel

Dissertations, Theses, and Capstone Projects

Water plays a crucial role in shaping the behavior and function of biomolecules across the liquid, supercooled, and glassy states. This thesis presents a dual approach combining computational simulations and experimental investigations to explore the influence of water on biomolecular systems, particularly peptide-based materials. We employ molecular dynamics simulations to study the hydration-dependent structural dynamics of homopolymer peptides. Simulations were carried out across a range of temperatures and pressures to analyze changes in hydration and structural stability, shedding light on the behavior of peptides under supercooled and glassy conditions. These studies are especially relevant for understanding biomolecular stability in cryopreservation. …

Improving The Assessment Of Functional Ability In Older Adults, Aneela Rahman

Dissertations, Theses, and Capstone Projects

Deficits in instrumental activities of daily living (IADL) are a hallmark of dementia, and the unprecedented aging of the population strongly motivates early identification of older adults at-risk for functional decline. In 2015, the White House Conference on Aging emphasized the need to improve detection of diminished capacity across important areas of functioning. To date, there is very limited research on early IADL changes in cognitively unimpaired (CU) individuals and those with subjective cognitive decline (SCD) and mild cognitive impairment (MCI), who may be in early preclinical dementia stages. Additionally, little is known about how changes in functional brain networks …

Nurses’ Knowledge About Assisted Reproductive Methods And Their Awareness About It In Potential Immune-Related Outcomes Of Conceived Children, Salma Abd-Elatty Moawed, Abdallah Ahmed Said

Nursing

Abstract A rising worldwide health concern, infertility is impacted by a number of environmental and lifestyle factors. With cutting-edge methods like intrauterine insemination, intracytoplasmic sperm injection, and in vitro fertilization, assisted reproductive technology gives infertile couples hope. Because they provide clinical care, education, and emotional support before, during, and after assisted reproductive technology procedures, nurses are essential to its success. The purpose of this study is to assess nurses’ knowledge and awareness about assisted reproductive methods and the immune outcomes among the resulting children. A structured interview questionnaire will be used to gather data from 130 nurses as part of …

Single Nuclei Transcriptomics Reveals Cellular Diversity In Tsc Subependymal Giant Cell Astrocytomas, Jennie C. Holmberg, Vijay Shankar, Rachel A. Lyman, Trudy F.C. Mackay, David M. Feliciano

Publications

Tuberous sclerosis complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that are a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing. SEGAs contain several cell types. In contrast to unaffected samples, SEGAs have pronounced vasculature, more endothelial cells, increased perivascular macrophages, less myelination, and altered …

Integrated Systems Biology Identifies Disruptions In Mitochondrial Function And Metabolism As Key Contributors To Hfpef, Andrew A. Gibb, Kyle Lapenna, Ryan B. Gaspar, Nadina R. Latchman, Yinfei Tan, Carmen Choya-Foces, Jake E. Doiron, Zhen Li, Huijing Xia, Michael P. Lazaropoulos, Mariell Conwell, Thomas E. Sharp, Traci T. Goodchild, David J. Lefer, John W. Elrod

School of Graduate Studies Faculty Publications

Heart failure with preserved ejection fraction (HFpEF) accounts for ∼50% of HF cases. The ZSF1-obese rat model recapitulates clinical features of HFpEF including hypertension, obesity, metabolic syndrome, exercise intolerance, and diastolic dysfunction. We utilized a systems-biology approach to define the metabolic and transcriptional signatures to gain mechanistic insight into pathways contributing to HFpEF development. Male ZSF1-obese, ZSF1-lean hypertensive controls, and WKY (wild-type) controls were compared at 14 weeks of age for extensive physiological phenotyping and left ventricle (LV) tissue harvesting for unbiased-metabolomics, RNA-sequencing, and mitochondrial morphology and function. Utilizing ZSF1-lean and WKY controls enabled a distinction between hypertension-driven molecular changes …

Trends In Genitourinary Tumors: Academic Center Experience Over 16 Years, Samah N. Saharti, Fawaz M. Almutairi

Saudi Medical Journal

ABSTRACT Objectives: To analyze the trends, histopathological characteristics, and demographic distribution of genitourinary (GU) tumors at a major academic center in Jeddah, Saudi Arabia, over a 16-year period (2007–2023). Methods: A retrospective review of electronic medical records was conducted, including all histologically confirmed cases of GU tumors. Data on patient demographics, tumor type, and histopathological findings were extracted and analyzed using descriptive and inferential statistical methods. Results: A total of 1,791 GU tumor cases were identified. Bladder cancer was the most prevalent (42%), followed by prostate cancer (21%) and renal cell carcinoma (21%). Testicular and ureteral tumors were less common, …

Unmasking Iron Deficiency And Iron Deficiency Anemia In Saudi Arabia: Data From A Large Private Sector Lab, Osman O. Radhwi, Omar M. Raslan, Eman M. Mansory

Saudi Medical Journal

ABSTRACT Objectives: This study investigates the prevalence of iron deficiency anemia (IDA) in Saudi Arabia, analyzing variations by gender, age, and geographical region. Methods: An observational, cross-sectional analysis was conducted from January 2014 to February 2024 using data from Al Borg laboratories, including ferritin levels, demographics, and routine hematological results. Results: The study included 420,956 individuals, with 73% being female and 94% over 15 years old. The IDA was found in 19.8% of patients, Non-Anemic Iron Deficiency (NAID) in 23.7%, and other anemias in 9.6%. Females represented 93% of those with IDA and NAID. All patients under 12 were anemic, …