Digital Commons Network^™

The Antifungal Mechanism Of Entv-Derived Peptides Is Associated With A Reduction In Extracellular Vesicle Release, Giuseppe Buda De Cesare, Melissa R Cruz, Shane A Cristy, Luis A Vega, Robert Zarnowski, Shantanu Guha, Danielle A Garsin, Michael C Lorenz

Faculty, Staff and Student Publications

Candida albicans, an opportunistic fungal pathogen, causes systemic and superficial infections, especially in immunocompromised patients. Treatment of fungal infections is complicated by limited antifungal options and the development of drug resistance. Previous work from our group demonstrated the efficacy of the anti-virulence peptide EntV and shorter variants against C. albicans infection in various animal models, including mouse models of oropharyngeal candidiasis and disseminated infection and a rat venous catheter model. However, the mechanism of action, which abrogates fungal virulence without fungicidal or fungistatic activity, has remained unknown. We used a combination of cell biological, biochemical, genomic, and genetic approaches to …

Mechanisms Underlying Treatment-Resistant Depression: Exploring Sex-Based Biological Differences, Francisco E R Da Silva, Atakan Yucel, Antonio P M Menezes, Ana C Ruiz, Marcela C Carbajal Tamez, Giselli Scaini

Faculty, Staff and Student Publications

Treatment-resistant depression (TRD) represents a severe and complex subtype of major depressive disorder (MDD), affecting approximately 30% of patients who fail to respond adequately to multiple standard antidepressant therapies. While the pathophysiology of TRD remains incompletely understood, emerging evidence suggests that sex-based biological differences might influence its onset, progression, and treatment response. Women are disproportionately affected by depression and are more likely to experience residual symptoms and treatment resistance, potentially due to hormonal fluctuations, immune system differences, and variations in brain circuitry and neuroplasticity. This narrative explores the current literature on the mechanisms underlying TRD, with a particular emphasis on …

Rna-Binding Proteins Mediate The Maturation Of Chromatin Topology During Differentiation, Bondita Dehingia, Małgorzata Milewska-Puchała, Marcin Janowski, Mahmoud-Reza Rafiee, Misbah Abbas, Jan Senge, Dietrich Walsh, Jacqueline Severino, Debadeep Chaudhury, Sajjad Iqbal, Rogelio Montiel-Manriquez, Sylwia Jankowska, Peyman Zare, Wolfgang Huber, Jianliang Xu, Rafael Casellas, Timo Zimmermann, Paweł Dłotko, Jeroen Krijgsveld, Aleksandra Pękowska

Faculty, Staff and Student Publications

Topologically associating domains (TADs) and chromatin architectural loops impact promoter-enhancer interactions, with CCCTC-binding factor (CTCF) defining TAD borders and loop anchors. TAD boundaries and loops progressively strengthen upon embryonic stem (ES) cell differentiation, underscoring the importance of chromatin topology in ontogeny. However, the mechanisms driving this process remain unclear. Here we show a widespread increase in CTCF-RNA-binding protein (RBP) interactions upon ES to neural stem (NS) cell differentiation. While dispensable in ES cells, RBPs reinforce CTCF-anchored chromatin topology in NS cells. We identify Pantr1, a non-coding RNA, as a key facilitator of CTCF-RBP interactions, promoting chromatin maturation. Using acute CTCF …

Wuse-Oil Compound 03 Mitigates Radiation-Induced Oral Mucositis By Modulating Oral Microbiota To Mediate Tlr4/Nf-Κb Pathway And Inhibit M1 Macrophage Polarization, Liqun Jia, Rong Huang, Chen Chen, Feng Teng, Tian Gu, Li Ma, Jingyi Long, Zihan Jin, Dong Li, Dongmei Chen, Yanni Lou

Faculty, Staff and Student Publications

Background: Radiation-induced oral mucositis (RIOM) is a prevalent condition among patients with head and neck cancer undergoing radiotherapy. It is characterized by a high incidence and severe symptoms that significantly compromise patients' quality of life. Currently, there exists no consensus regarding an effective treatment modality. Wuse-oil Compound 03 (WC03), a Traditional Chinese Herbal Medicine, demonstrates potential in managing RIOM.

Purpose: This study aims to investigate the efficacy of WC03 in treating RIOM through the modulation of oral microbiota and associated biological pathways.

Study design: Mechanism study experimental design.

Methods: A rat model of RIOM was established via radiation exposure. WC03 …

Comparative Pathology Boards Facilitate The Translation Of Knowledge Between Canine And Human Cancer Patients, Jessica A Beck, Christina Mazcko, Sara Belluco, Mireille Bitar, Daniel Brat, Rati Chkheidze, Chad Frank, Caterina Giannini, Craig Horbinski, Jason T Huse, Jennifer W Koehler, Andrew D Miller, C Ryan Miller, M Gerard O'Sullivan, Joanna J Phillips, Daniel R Rissi, Courtney R Schott, Anat Stemmer-Rachamimov, Stephen Yip, Amy K Leblanc

Faculty, Staff and Student Publications

Comparative pathology boards bring together anatomic pathologists with expertise in canine and human histology to identify shared features, including immune or TME components, tumor subtypes, or prognostic tissue biomarkers. This article summarizes feedback to improve future initiatives and enhance the translational relevance of comparative oncology for human patients.

Launching! To Adulthood, A Culturally Adapted Treatment Program For Military-Dependent Autistic Young Adults And Their Military Parents: A Pilot Study, Antonio F Pagán, Jordan Kenemore, Maj Mark Ahlenius, Linda Hernandez, Stephen Armstrong, Katherine A Loveland, Ron Acierno

Faculty, Staff and Student Publications

Introduction: Military-dependent young adults (17-25 years old) with autism spectrum disorder (ASD) face significant barriers to accessing services during their transition to adulthood. Frequent relocations, disrupted care, and limited ASD-tailored interventions exacerbate the challenges for these families, with many young adults experiencing a "service cliff" as they age out of pediatric care and school-based services. Addressing these gaps is critical, particularly given the rising mental health challenges and executive dysfunction in this population. This study evaluates the preliminary efficacy of an adapted telehealth intervention, the Military-Launching! program, designed to support young adults with ASD and their military families.

Materials and …

The Crisis Of Safety, Well-Being, And Belonging Facing Lgbtq Children: Mad/Crip Of Color Critique Towards A Curriculum Of Radical Care, Jameson Goetz

Dissertations, Theses, and Capstone Projects

In this thesis, I turn toward the study of educational experience, defined broadly to include lived experiences both within and outside of formal schooling institutions. I approach curriculum as an ongoing project of self-understanding in which one becomes mobilized for engaged pedagogical action alongside others in the pursuit social justice. I am guided by the following question, foundational to the field of curriculum studies: for those of us who work alongside LGBTQ children, what knowledge is of most worth? Critically reflecting on ways of working alongside LGBTQ children in the pursuit of social justice, I formulate a mad/crip of color …

The Georgian Of Heritage Speaker Children, Cass Lowry

Dissertations, Theses, and Capstone Projects

This dissertation presents three research articles united in the goal of describing the Georgian language as it is spoken by heritage speakers in the Brooklyn diaspora. The Georgian heritage speaker subjects recruited for these studies were children due to immigration patterns at the time when experimental data was collected. Their production of morphosyntactic inflection and pronouns is compared to adult and child homeland speakers.

Heritage speakers of Georgian demonstrate the following divergences from homeland and standard language comparisons. Nominal case inflection is most affected in heritage production, as heritage speakers use a default case or collapse Georgian's split-ergative and inverse …

Investigation Of Motor Neuronal And Circuit Level Mechanistic Determinants Of Spinal Excitability Following Cst Injury, Thelma Bethea

Dissertations, Theses, and Capstone Projects

The corticospinal tract (CST) is the primary descending motor pathway in mammals, essential for precise, dexterous movements, especially in humans and nonhuman primates. Damage to the CST, such as from spinal cord injury (SCI), impairs skilled motor function and triggers maladaptive changes including aberrant proprioceptive afferent sprouting and increased spinal excitability. These changes are closely linked to both muscle weakness and the development of hyperreflexia, compounding the functional deficits. Animal models of SCI are valuable for investigating mechanisms of injury and recovery, though traditional models often limit the ability to isolate circuit-specific contributions. To address this, I employed selective unilateral …

The Evolution And Reproduction Of Andean Miconia (Melastomataceae), Juan Angulo

Dissertations, Theses, and Capstone Projects

Understanding the factors that shape diversification and distribution in tropical plant lineages is central to explaining the origins of Neotropical biodiversity. Assessing evolutionary history with trait evolution and climatic niche dynamics provides key insights into the drivers of diversification and biogeography, while natural history data remains critical for these evolutionary studies. The Tropical Andes, with its exceptional biodiversity and environmental heterogeneity, offers an ideal setting to explore these processes. In this dissertation, I investigate how reproductive systems, climatic niche dynamics, and pollination strategies influence the evolution and biogeography of Miconia III, a large and ecologically diverse clade in the …

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 …

Love Amid The Rage: Feminist Affect In Women's Life-Writing, Genesis Siverio

Dissertations, Theses, and Capstone Projects

The aim of this thesis is to show the ways women’s emotions or affect, particularly rage and love, are described by women writers in their most intimate stories. I discuss the way emotion has been demeaned, and how feminist scholars have instead viewed the body as a place of insight, reclaiming a knowledge from the senses. In the midst of white supremacy and heteropatriarchy, women give voice to their affectual experiences and cultivate the feelings they have so often been denied. Focusing on the particular ways women’s anger manifests in their lives and in their bodies, I zoom in on …

Imagined Empires: Roman And Chinese Constructions Of One Another In Antiquity, Elizabeth S. Tsang

Dissertations, Theses, and Capstone Projects

This thesis examines how the Roman and Han Chinese empires conceptualized one another during the first centuries CE, despite never establishing sustained direct contact. It argues that mutual perceptions were shaped less by firsthand experience than by mediated reports, commodities, and the political interests of intermediaries. The study proceeds in four parts. The first explores how Roman authors employed the ethnonym Seres to frame China as a land of wonder, wealth, and alterity. The second analyzes the Chinese designation Da Qin, showing how it projected Han imperial ideals outward by casting Rome as a mirror-image polity. The third turns to …

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 …

Scripted For Surveillance: Parole Revocation Hearings And The Performance Of Procedure In New York, Kelsey G. Greeff

Dissertations, Theses, and Capstone Projects

This thesis examines parole revocation hearings in New York as complex performances that extend carceral control beyond prison walls. Drawing on a composite vignette from the Bronx parole court, it analyzes the interplay between procedural reform, constitutional due process, and neoliberal governance. Using a dramaturgical framework informed by Michel Foucault’s discourse analysis and Judith Butler’s theory of performativity, the study identifies four interrelated processes: the judge as director, who orchestrates hearings according to institutional priorities; normalization, where repetition embeds structural inequality as routine; type-marking, the classification of parolees into predefined roles through accumulated records and cues; and the extension of …

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 …

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 …

Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio

Dissertations, Theses, and Capstone Projects

The origin and maintenance of the tropical montane diversity have been evaluated over multiple decades using various techniques and perspectives. Despite major progress in understanding phylogenetic relationships, diversification patterns, distributional data, and general ecology in the Andean biota, large gaps in our understanding remain, particularly in the synthesis across scales. To fill these gaps, I aimed to explore patterns and processes that underlie species diversification in birds of the tropical Andes of South America by combining different approaches using phenotypic, phylogenetic, and genomic data in multiple temporal and spatial scales.

In the first chapter, I examined the macroevolutionary patterns of …

Alerted And Anxious? The Effects Of Mobile Crime Alerts On Perceptions Of Personal And Public Safety, Amanda C. Benjamin

Dissertations, Theses, and Capstone Projects

Mobile crime alert platforms promise to enhance personal and public safety by delivering frequent notifications about nearby dangers—claims that, until now, have not been experimentally tested. For-profit applications like Citizen deliver real-time, geo-targeted push notifications about nearby crime incidents to over 9 million users, often operating outside the bounds of institutional oversight. Although marketed as tools to enhance awareness and protection, these platforms may simultaneously empower users through information while also potentially amplifying anxiety, heightening threat perceptions, and eroding trust in community. Despite their increasing prominence and integration into public safety communications, the psychological and behavioral impacts of mobile crime …

The Question Of Money: State, Protest, And Informal Currencies In The Wake Of Greece’S Economic Crisis, Helen Panagiotopoulos

Dissertations, Theses, and Capstone Projects

Monetary unions are designed to foster political, social, and economic integration among member states by enabling the free movement of people, goods, services, and capital. Yet when a member nation faces economic crisis, citizens may respond by creating monetary systems of their own. This research asks whether such practices are simply demonstrations of human resiliency and adaptability, or whether they also challenge the very idea of a shared market and currency that do not align with national identity. Greece offers a crucial case for this inquiry. Following the 2008 debt crisis, austerity measures led to economic depression, mass unemployment, and …

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 …

Choreographies Of Care: Disability And Relationality In Performance, Kiera Bono

Dissertations, Theses, and Capstone Projects

My dissertation explores enactments of what I am calling “choreographies of care” in interdisciplinary performance practices in the 21^st century. Working across disability studies, race and ethnicity studies, queer theory, and performance studies, I investigate the ways in which chronically ill and disabled artists have generated multisensorial movement, sound, and performance works that resist normative understandings of time, space, bodies, and interactions between bodies. Focusing mostly on performances and events that I have attended in New York City or virtually over the past decade, my project engages directly with disability arts communities in which I have been deeply embedded …

Leveraging Stellar Chemistry For A Global View Into The Atmospheres Of Brown Dwarfs And Giant Exoplanets, Emily Calamari

Dissertations, Theses, and Capstone Projects

In the era of the James Webb Space Telescope (JWST), it is now possible to examine substellar mass atmospheres in unparalleled detail and precision. However, unraveling the complicated thermodynamics and chemistry in these atmospheres remains a challenge. Atmospheric retrievals are a leading data-driven technique capable of recovering an object’s fundamental parameters such as mass, radius, effective temperature, gravity, cloud structure and composition and chemical abundances. However, in directly imaged or isolated worlds, constraining and/or interpreting these fundamental parameters can be difficult, particularly as retrieval models try to parameterize the overall impact of clouds.

For my dissertation, I turned to main …

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 …