Digital Commons Network^™

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

Lethal Autonomous Weapons Systems And The Principles Of Distinction And Proportionality, Nicholas Cromie

Dissertations, Theses, and Capstone Projects

Lethal Autonomous Weapons Systems (LAWS) challenge the core principles of International Humanitarian Law (IHL), distinction and proportionality, by delegating life-and-death decisions to algorithms rather than human judgment.  This dissertation examines whether LAWS can conform to these principles and, if so, under what conditions.  Through process tracing, the study traces the historical integration of disruptive weapons technologies, including chemical, biological, nuclear, and armed drones, into IHL-compliant frameworks or their exclusion via prohibition.  Each case reveals distinct pathways: outright bans for indiscriminate or inherently inhumane systems (chemical and biological weapons), normative restraint and limited acceptance despite destructive power (nuclear weapons) and phased …

Deficient Executive Control In Transformer Attention, Suketu Chandrakant Patel, Hongbin Wang, Jin Fan

Publications and Research

Although transformers in large language models (LLMs) effectively implement a self-attention mechanism that has revolutionized natural language processing, they lack an explicit architecture for the executive control of attention found in humans, which is essential for resolving conflicts and selecting relevant information in the presence of competing computations and is critical for adaptive behavior. To investigate the impact of this limitation in LLMs, we employed the classic color Stroop task, widely regarded as the gold standard, to test the executive control of attention in these models. Our results revealed a typical conflict effect of underperformance in terms of accuracy in …

The Effect Of The Chemical And Microbiological Structure Of Biofilms On The Growth Of Oyster Spats In The Hudson River, June L. Rahman

Student Theses and Dissertations

Eastern oysters (Crassostrea virginica) are sessile suspension feeding bivalves that improve water quality through filtration and reef formation, making them crucial to the health oftheir native ecosystems. Establishing oyster habitats is a priority in Hudson River restoration efforts following significant population declines due to over harvesting, habitat loss, and pollution. Oyster spat production and attachment are influenced by biofilms; however, it is not well known how biofilm properties, such as bacterial taxonomic composition and EPS content, affect oyster larval attachment in the Hudson River. We hypothesized that intertidal surfaces,which are more exposed sunlight, would develop photosynthetic biofilms that enhance oyster …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Examining Whether The Relationships Between Specific Psychiatric Diagnoses And Both Adolescent Suicide And Reoffending Are Moderated By Sex, Michael T. Baglivio, Katherine Jackowski, Brooke Neupaver, Grayson Black, Bailee Perry, Kevin T. Wolff

Publications and Research

The current study examines the relationships between specific psychiatric diagnoses and both adolescent suicide and reoffending, the implications of adverse childhood experiences on these outcomes, and assesses whether these relationships are moderated by sex. Using a multilayer multiyear statewide sample of 6,515 adolescents who completed juvenile justice residential placements, logistic regression and moderation models were used to examine these relationships. Findings demonstrate that the rate of suicidal ideation was 2.5 times higher for female youth, while the recidivism rate was 1.7 times higher for males. Psychiatric diagnoses prevalence ranged from 65.9% for conduct disorder to less than 1% for personality …

Beyond "Bad Apples": Political Identity, Moral Interpretation, And Institutional Response To Abuse, Laura Werner

Student Theses

This thesis examines how psychological explanatory frameworks and structural institutional response interact to shape how domestic violence and sexual abuse are understood and addressed. Drawing on behavioral design theory and John Dewey's transactional approach to experience, I argue that harm is interpreted through mental models that simultaneously shape both individual perception and institutional action. Using survey data from 736 participants, I demonstrate that endorsement of the "bad apples" explanatory framework, attributing abuse primarily to a small group of deviant individuals, is predicted by psychological essentialism, belief in a just world, social dominance orientation, and political conservatism. These findings suggest that …

Exploring Biogeographical Ancestry Inference Of New York Residents Using A 45 Indel Panel, Amanda Martinez

Student Theses

Biogeographical ancestry (BGA) inference is an important tool in forensic science, providing supplemental information when comparison/reference DNA is not available for traditional DNA analyses. Insertion/deletion polymorphisms (INDELs) have been used in the last decade as ancestry-informative markers (AIMs) for BGA inference because they can be easily adapted to forensic-type samples and are determined using low cost and easy processing methods. Limited research has attempted to estimate ancestry and admixture in United States (U.S.) populations. This study evaluated the effectiveness of a 45- and 21- INDEL panel to measure population admixture proportions of four different origins (African, European, East Asian and …

Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos

Student Theses and Dissertations

Microtubules, composed of a/b-tubulin heterodimers, play a central role in breast cancer tumor growth by polymerizing, leading to metastasis and depolymerizing, contributing to proliferation. Human enzymes protein kinase Ca (PKC-a) and cyclin-dependent kinase 1 (Cdk-1) mediate phosphorylation at sites a:Ser165 and b:Ser172, respectively, influencing the growth of microtubules. It is possible that alternating phosphorylation at these sites contribute to an a/b-tubulin “toggle switch” that mediates microtubule instability and tumor growth.

The project investigates the influence of the toggle switch model on microtubule stability by determining the impact of mutants (a:S165D, a:S165N, a:S165S_P, b:S172S_P and a:S165S_P/b:S172S …

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 …

Proximal Stress And Gender Identity: The Role Of Internalized Transphobia In Future Expectations, Maribelle Almonacy

Student Theses and Dissertations

Transgender and non-conforming (TGNC) youth and young adults are more likely to experience symptoms of posttraumatic stress due to identity-specific abuse. Studies on the impact of trauma on negative expectations in high-risk youth show a high association between pessimism, nihilism, and instability. Internalized transphobia, similarly, is correlated with negative mental health outcomes, such as depression and anxiety, and the internalization of social messages and discrimination. These studies are not specific to the experiences of gender minorities and do not explore the intersections of internalized stressors or trauma in young adults. To address this gap in literature, this study sought to …

Hidden In The Mist: Three New Species Of Salamanders Of The Genus Pseudoeurycea (Amphibia: Plethodontidae) From Oaxaca, Mexico, Eduardo A. Aguilar-Herrera, Salomón Sanabria-Urbán, Dulce L. Flores-Martínez, José David Gómez-Tapia, Misael Seba-Chacha, Leopoldo D. Vázquez-Reyes, Francisco A. Rivera-Ortíz, Patricia Ramírez-Bastida, Bruno Cortés-Ortiz, R. Alejandro Calzada-Arciniega, Etienne U. Avila-Ortega Avila-Ortega, Dónovan I. Víquez-Vega, Omar Hernández-Ordoñez, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another …

Psy 1100 Writing Intensive Syllabus, Jos Khan

Open Educational Resources

This is an ZTC/OER syllabus for a PSY 1100 writing intensive course at Kingsborough Community College.

The Effects Of Cinnamaldehyde On Tetrahymena Thermophila, Sydney Kurland

Publications and Research

In addition to their common use as spices in cooking and baking, cinnamon plants, Cinnamomum zeylanicum and Cinnamomum cassia for example, have long been used in herbal remedies worldwide. Cinnamon contains many vital oils and active compounds including cinnamaldehyde (CMD). Numerous studies looking at potential therapeutic effects of cinnamon have demonstrated its antioxidant, anti-inflammatory, and antimicrobial properties (1, 2, 3).   Therefore, it is important to continue studying the efficacy, benefits, and mechanisms of action of cinnamon and CMD to have a complete understanding of its full potential. Tetrahymena thermophila is a ciliated protozoan commonly used as a model organism to …

Trauma, Memory, And Decision-Making: How Covid-19 Shaped Autobiographical Memories And Risky Decision-Making In Young Adults, Rachel Seo

Student Theses

Autobiographical memory is a critical component of the memory process that guides future behaviors by relying on past personal experiences connected to major public events. This decision-making process is heavily influenced by trauma exposure and post-traumatic stress disorder (PTSD) symptoms, as they may guide individuals to riskier behaviors. The COVID-19 pandemic represents a global traumatic stressor that contributed to shifts in behavioral outcomes post-pandemic. Despite research showing associations between memory accessibility, traumatic symptoms, and decision-making, there is limited research on health-related behaviors and post-pandemic behavioral outcomes in individuals with high trauma exposure specifically from the pandemic. The present study investigates …

Hannah, Nora Brigid Monahan

Theses and Dissertations

Hannah is a contemporary adaptation of Henrik Ibsen's Hedda Gabler, which reimagines Ibsen's heroine as a "stealth" (or undetected) transsexual woman living among the American conservative elite in Washington D.C. Newly married to George Taylor, a charismatic but financially strained far-right media personality, Hannah struggles to maintain the façade she has constructed when Eliot Loving, a volatile political streamer and figure from past, reappears in her life. Their collision, orchestrated by the manipulative power-broker Judge Brock, upends Hannah's sense of self and forces her into a desperate struggle for her own autonomy and security. In a deliberate subversion of …

Ephemeral System, Shibo Chan

Theses and Dissertations

Ephemeral System examines systems, feedback, repetition, and material fragility through a kinetic wax sculpture repeatedly dragged across a wooden ramp. Drawing from cybernetics, absurdist waiting, and personal mourning, the work explores how bodies and systems wear themselves down through continuous operation.

Monitoring Biodiversity Growth In An Oyster Reef Restoration: Understanding How Oyster Reef Life Cycle May Impact Biodiversity., Gabriel A. Roses

Theses and Dissertations

Oyster reefs are vital to marine ecosystem health, improving water quality and providing food and habitat for diverse species. We assessed biodiversity changes for a proposed oyster reef restoration site to help guide management, future assessment, and deepen understanding of how oyster reefs function and their ecosystems dynamics.

A Meta-Analysis Of The Impact Of Narrative Perspective On Trauma Recall Outcomes, Samantha R. Lefton

Theses and Dissertations

This study is a meta-analysis of trauma, linguistics, and emotional reactivity, examining how narrative perspective relates to emotional experiences of trauma recall. Synthesizing narrative, affective forecasting, and memory research, it finds narrative distancing to be associated with a decrease in emotional reactivity, bridging clinical psychology and applied linguistics.

Bugs, Birds, Blue: Queer Ecologies Of Embodiment, Kinship, And Survival, Celeste B. Newcomb

Theses and Dissertations

bugs, birds, blue is a multi-channel audiovisual installation that examines queer ecology as a framework for understanding transgender embodiment, kinship, and survival amid environmental crisis and ongoing political attacks on trans life (Mortimer-Sandilands and Erickson). Through sculpture, projection, sound, reflective surfaces, and biological imagery, the installation places human bodily matter alongside microbial and aquatic life forms to challenge narratives that frame trans existence as unnatural, recent, or isolated. Instead, the work proposes transness as relational, adaptive, and deeply entangled with broader ecological systems. The installation is composed of two interconnected environments. On one side of the space, three aquariums rest …

Synthetic Explorations Towards Phenyl Benzazepine-Inspired Scaffolds And Synthesis Of Minor Cannabinoid Derivatives, Vishwashiv Kumar Emogaje

Theses and Dissertations

D1R is a compelling therapeutic target for correcting dopaminergic imbalances. However, existing ligands exhibit suboptimal pharmacokinetic properties. As such, we synthetically explored untouched structural modifications to the phenyl benzazepine scaffold. Cannabinoid-based molecules also display potential to treat neurological maladies and cancer. We synthesized Cannabichromene derivatives and uncovered enhanced anticancer activities.

They Returned Fighting: World War I, Disillusionment, And The Remaking Of African-American Political Life In New York City, Michael Frank

Theses and Dissertations

They Returned Fighting examines how Black New Yorkers used World War I service, wartime activism, and postwar protest to press claims to citizenship and democracy, even as racial violence, discrimination, and contested public memory exposed the limits of that belonging in New York City and the United States.

Surface Gestures: Contemporary Sculpture, Material, And The Possibilities Of Finish, June Kitahara

Theses and Dissertations

Through the work of Tiona Nekkia McClodden, Patty Chang, and Jes Fan, alongside performance, cinema, cultural figures, and twentieth-century sculpture, the thesis argues that the surface of contemporary works reveals the inextricability of aesthetics from technologies of gendered racialization, sexuality, and sensation.

The I Need More Time Machine, Suzanne L. Schulz

Theses and Dissertations

The I Need More Time Machine imagines alternatives to gendered overwork and exhaustion. Incorporating animation and the interviews of twelve NYC-based female and nonbinary artists who are caretakers and full-time workers, the film dwells in spaces of fatigue and repetition — from the vantage point of commuting — then draws on forgotten feminist and utopian housing blueprints to create science fiction-inspired, fantasy-imbued sites for gendered flourishing. The animated fantasy segments imagine elastic time, deep rest, experiments in collaboration, and liberating feminist spatial possibilities

Do Clothes Make The Man? Ftm Crossdressing In The 18th-19th C. Anglo-American World, Aidrian Graber

Theses and Dissertations

This paper seeks to analyze the legacy of "Female Husbands" and other female-to-male crossdressers in the 18/19th c. Anglo-American world and how such people can illuminate the field of transgender history.

One Long Yawn, Dylan Musler

Theses and Dissertations

Dylan Musler contextualizes her painting and ceramic work. She explores themes around time, the grotesque, transference, holes, and dirty snow piles.

Genetic Screen For Regulators Of Pol4, A Dna Repair Polymerase In Saccharomyces Cerevisiae, Pasang Dolma Sherpa

Theses and Dissertations

In Saccharomyces cerevisiae, DNA polymerase 4 (POL4) is the beta repair polymerase, the product of the POL4 gene, and is involved in base excision repair (BER) and microhomology-mediated end joining (MMEJ). Despite its involvement in these repair pathways and its conservation across eukaryotes, deletion of POL4 shows no detectable phenotype under standard laboratory conditions. I hypothesized that unknown genes act as backup systems, providing redundant activities that allow pol4Δ cells to survive. To test this, a genetic screen for mutants showing synthetic lethality with pol4Δ was implemented. I constructed a strain lacking the POL4 gene and carrying …

Lemonade Everything Was So Infinite, Lauren Cline

Theses and Dissertations

In “Lemonade Everything Was So Infinite,” artist Lauren Cline uses her process-based approach to painting as a metaphor for the relationship between mundanity and eternity. Utilizing various frameworks, including the autobiographical writings of Hélène Cixous and the theology of Simone Weil, as well as examples from her own artworks,  the artist suggests that there is a universal human need for the dissipation of the singular, isolated self, and explores various ways that this can be achieved.

Voyager, Ben K. Voss

Theses and Dissertations

This thesis explores painting as a site of meditation, time and (un)knowability.