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The Linc Complex Component Kms1 And Cenp-B Protein Cbp1 Cooperate To Enforce Faithful Homology-Directed Dna Repair At The Nuclear Periphery, Alyssa Laffitte

Yale Graduate School of Arts and Sciences Dissertations

DNA double-stranded breaks (DSBs) represent a danger to genome stability. Cells repair DSBs mainly through one of two pathways: canonical non-homologous end-joining (cNHEJ), which requires the direct ligation of the two DSB ends, or homologous recombination (HR), which involves the use of a homologous template to create a faithful repair product. While HR is often considered to be an error-free mechanism, the ultimate fidelity of this pathway depends on the ability of the cell to identify and engage with the correct homologous template. This is particularly challenging during repair of repetitive regions of the genome for which non-allelic sequences can …

Computational Study Of Redox-Active Protein Residues And Biological Proton-Coupled Electron Transfer, Qiwen Zhu

Yale Graduate School of Arts and Sciences Dissertations

Proton-coupled electron transfer (PCET) reactions are essential processes in biological systems, fundamental to various enzymatic functions and redox biology. Key to these reactions are redox-active residues, such as tyrosine and tryptophan, which enhance the efficiency and specificity of electron transfer events. This thesis investigates the thermodynamics, kinetics, and conformational influences of PCET in proteins involving these residues through three projects, each offering significant insights into the mechanisms and broader implications for biological function. The studies have focused on two protein systems: a simple de novo protein system, α3X, and ribonucleotide reductase, an enzyme critical to DNA synthesis. Combining a wide …

A Bioluminescent Approach To Coxiella Burnetii Pathogenesis: Development And Utilization Of An In Vivo Imaging Model, Jenna Myr Andrews

Yale Graduate School of Arts and Sciences Dissertations

Coxiella burnetii is a Gram-negative, obligate intracellular bacterium that infects livestock and causes Q fever in humans, which can range from acute flu-like symptoms to severe, persistent infections. C. burnetii relies on a Dot/Icm type IVB secretion system to translocate effector proteins, manipulating host cell processes to support intracellular replication. While axenic media have facilitated in vitro pathogenesis research, in vivo studies remain limited due to the classification of the virulent Nine Mile phase I strain as a category B select agent. Although the avirulent phase II strain RSA493 is exempt from this classification, it is rapidly cleared in immunocompetent …

Dysregulation Of Transcription And Mrna Processing In Splicing Factor Mutant States: Mechanistic Insights And Implications, Prajwal Chaitanya Boddu

Yale Graduate School of Arts and Sciences Dissertations

Recurrent mutations in RNA splicing factor (SF) genes, such as SF3B1, U2AF1, SRSF2, and ZRSR2, are key drivers of oncogenesis in various cancers, particularly clonal myeloid disorders like Myelodysplastic syndromes (MDS) and Acute Myeloid Leukemia (AML). Over the past decade, significant insights have been gained into their molecular mechanisms and effects on RNA splicing. These mutations are typically heterozygous and non-synonymous (except ZRSR2, which involves single-allele loss-of-function mutations) and are largely mutually exclusive, suggesting shared downstream mechanisms that prevent co-occurrence. Given their pre-eminent roles in splicing, most studies to date have primarily focused on the effects of SF mutations on …

Spatial Control Of Nonlinear Interactions In Multimode Fibers, Kabish Wisal

Yale Graduate School of Arts and Sciences Dissertations

In recent years, there has been significant advancement in controlling optical scattering by structuring the wavefront of the incident light, or `wavefront shaping'. Most applications of wavefront shaping have focused on linear scattering, but there is a growing interest in tailoring nonlinear scattering. In this thesis, we explore a new approach based on wavefront shaping for suppressing certain instabilities induced by nonlinear scattering in passive and active multimode fibers (MMFs). Specifically, we focus on suppressing stimulated Brillouin scattering (SBS) and transverse mode instability (TMI). A key motivation for our work is power scaling in high power fiber lasers and amplifiers, …

Elucidating Cell Intrinsic Regulators Of Cd8 T Cell Differentiation: Klf2 Maintains Effector Cd8 Lineage Fidelity, Eric Quinn Fagerberg

Yale Graduate School of Arts and Sciences Dissertations

CD8 T cells are an integral part of the immune system, principally responsible for the cytolytic clearance of virally infected and cancerous cells. They adapt to the nature of the immune response they are partaking in by adopting distinct cell fates through a process of highly coordinated differentiation. These fates are characterized by the activation and suppression of functional programs under the control of transcription factors and epigenetic machinery, which integrate cell extrinsic signals to drive differentiation. Here we elucidate the function of a group of transcription factors in dictating CD8 T cell differentiation in infection. We go on to …

Spink1-Col18a1 Crosstalk Shapes Epigenome And Drives Cancer Stemness In Pancreatic Ductal Adenocarcinoma, Haoyu Tang

Yale Graduate School of Arts and Sciences Dissertations

Pancreatic ductal adenocarcinoma (PDAC) is a devastating cancer with an increasing incidence and extremely dismal prognosis, due to early metastasis and the limited understanding of the mechanisms driving its progression. In this dissertation, by analyzing bulk transcriptomic profiles from PDAC patients with substantial differences in survival and deconvoluting the results using a single-cell transcriptome dataset of human PDAC, we identified serine protease inhibitor Kazal type 1 (SPINK1) as a crucial modulator of PDAC progression and patient survival. At the patient level, higher SPINK1 expression is correlated with shorter survival, and at the single cell level, SPINK1 expression showed dynamical changes …

Undergraduate Bulletin 2025-2026, Cuny John Jay College

College Bulletins

Covers academic year 2025-2026

Oltjona Muca Honors Portfolio, Oltjona Muca

Honors Capstone Portfolios

Oltjona Muca's honors portfolio captured in May 2025.

13. Mentorship Matters: Documenting The Unseen Impact Of Instructor-Student Relationships, Jeff Spears, Amanda Deliman, Hannah Mae Lewis, Jim Lamuth, Kim Hales

Documenting Teaching Excellence

This chapter explores the critical yet often unrecognized role of documenting instructor mentorship as a core component of teaching excellence in higher education. Mentorship encompasses a range of instructor-to-student interactions, including academic guidance, psychosocial support, research support (graduate and undergraduate), and career exploration for students (DeAngelo, Mason, & Winters, 2016; Thiry & Laursen, 2011). Despite its importance, mentorship is rarely documented comprehensively in teaching documentation portfolios (Ocobock et al., 2022). By systematically capturing the multifaceted impacts of mentorship, instructors enhance their teaching portfolio and contribute to the broader discourse on teaching excellence. This chapter aims to empower instructors to demonstrate …

Targeted Deletion Of Cxcl1 In Mscs Regulates Osteogenesis And Suppresses Bone-Metastatic Prostate Cancer, Catherine S. Johnson, Diane L. Costanzo-Garvey, Julio C. Valencia, Sanjana Rajgopal, Theodore Reed, Emma R. Brannon, Jeremy S. Frieling, Deanna Mosley, Todd A. Wyatt, Elijah F. Edmondson, Kabhilan Mohan, Grinu Mathew, Leah M. Cook

Journal Articles: Environmental, Agricultural & Occupational Health

Bone metastasis continues to be the greatest challenge in treating patients with prostate cancer despite ongoing research. In bone, prostate cancer tumors hijack normal bone remodeling processes to drive cancer progression. However, it is unclear how these interactions drive bone-metastatic prostate cancer growth in the bone environment. To understand the mechanisms associated with bone-metastatic prostate cancer regulation of mesenchymal stem cells (MSC), we previously identified that bone-metastatic prostate cancer induces MSC expression of the pro-inflammatory chemokine CXCL8 and its mouse functional homologue Cxcl1. To date, there has been little to no information about the role of CXCL1/8 in MSC biology …

Research News, Publications, 2025, Volume 2, Soumyajit Majumdar

Publications (2015-)

Publications that appeared during the period of April 1 - June 30, 2025.

Pediatric Acute Necrotizing Encephalopathy: A Case-Based Review Of Diagnosis And Outcomes, Chance Swanson Bs, Josh Jimenez Bs, Manav Patel Bs, Phillip Alexeev Bs, Kevin Hiatt Md

SPARK Symposium Presentations

Pediatric acute necrotizing encephalopathy (ANEC) is a rare condition characterized by precipitation of a viral illness, bilateral thalamic lesions on CT and MRI, and normal cell counts with increased protein in cerebrospinal fluid [1]. ANEC typically presents with a 6-18 month child that experiences fever, seizures, rapid alteration in level of consciousness, in addition to specific findings in brain imaging such as bilateral thalamic lesions with supra and infra-tentorial lesions of variable dimensions [2]. Although the pathogenesis is not fully understood, the absence of inflammatory cells on post-mortem analysis and the lack of consistent viral detection in CSF suggest that …

Abuse Of Power In The Workplace: The New Gender Discrimination Claims, June R. Carbone, Nancy Levit, Naomi Cahn

Articles

This article draws on our book, Fair Shake: Women and the Fight to Build a Just Economy, to show how the fight for gender equality has changed. Antidiscrimination laws took hold during an era of relative economic equality; the fight for gender equality was a fight to gain access to the rights of white men. Today’s economy creates much greater inequality and reserves the greatest rewards for a much smaller group, again predominately white and male, who can defy the rules and get away with it. In such contexts, anti-discrimination law premised on a fight for equality can provide only …

Shorebird Vigilance From Biological Influences, Ryan Abdilla

IdeaFest 2025

My research project involves researching two different species of wild shorebirds, Marbled Godwits and Eurasian Whimbrels, and studying which biological factors like predator abundance, tide height, foraging rates, and time of day play a role in vigilant behavior in these two shorebird species. We are looking to see how these rates and their factors differ between 5 different areas across the Arcata Marsh and if there are noteworthy changes in any of the listed factors between the two species and which ones play the biggest role in shorebird vigilance and which do not.

Revisiting The Fishes Of The Beartooth Butte Formation, Patience Brennan, Lucas Kebow, Allison Bronson

IdeaFest 2025

This research aims to address the species composition of Devonian fossil fish species from a formation in Wyoming called the Beartooth Butte. This location has not received much, if any, attention from paleoichthyologists since the fossils within the formation were originally described in 1932. These fishes were overlooked for botanical fossils, and historically yielded fragmentary material. However, specimens from a Cal Poly Humboldt excavation in 2017, not only include the second articulated fossil from the formation, but also the first 3D fossil recorded.

The Cycle Of Giving:, Sarai Brown

BYU Asian Studies Student Journal

On one hot summer day in the middle of a 3-month stint studying Mandarin Chinese at National Chung Hsing University (NCHU) in Taichung, Taiwan, my friends and I were desperate to sate our appetites after class, even in the atrociously hot and humid conditions. Most of our little group was drawn to a 牛肉麵 niúròu miàn (beef noodle) shop, but the thought of hot soup on a day like this drove me and a couple of others to continue our search. We stumbled upon another outdoor restaurant—though “restaurant” is perhaps a loose term for the holey-tent-covered food stand with mismatched …

2. Leveraging Open Pedagogy To Create An Authentic And Renewable Curriculum, Erin Mckenney, Sam Winemiller, Hillary Fox, David Tully, Will Cross

Open Educational Resources For and As Assessment

The high cost of course materials is a barrier for many students, and traditional assessments often fail to inspire engagement. To address these challenges, NC State University Libraries promotes open course materials and open-enabled practices. Since 2014, the Alt-Textbook Project has helped faculty incorporate Open Educational Resources (OER) into their syllabi, reducing textbook costs and supporting innovative educational approaches. This effort was enhanced with the Open Pedagogy Incubator, a multi- semester program bringing together librarians and interdisciplinary faculty to redesign courses around open- pedagogical practices. Dr. McKenney, an incubator participant, redesigned her advanced undergraduate course on Applied Ecology (AEC 400) …

Bibliography, Mary P. Bennett

Faculty/Staff Personal Papers

Bibliography of publications by Mary Bennett.

Harmonic Analysis Of Currents Within Humboldt Bay, Caitlin J. Williams, Ula Brucker, Jaden Mccarthy, Noe Noe Camarillo, Taylor Juchau, Steven Gracy, Max Serrano, Karina Bernbeck, Emma Modrick, Isabelle Marcus, Simon Kurciski, Isis Kees, Tamara Beitzel Barriquand

IdeaFest 2025

Multiyear time series of current data measured by 2 horizontal SonTek/YSI ADCPs placed mid-depth in the water column at 2 different locations in Humboldt Bay, CA, a shallow, tidally-driven estuary in northern California, were analyzed to determine the contributions of different harmonic frequencies within the bay. Spectral analysis of the time series revealed that the currents are dominated by several tidal harmonics. The 3 dominant frequencies include M2, K1, and O1, but their contribution varies spatially between the two station locations. Additional frequencies in the data indicate overtides, as well as potential interference with topography and the more variable wind-induced …

Agent-Based Modeling Of Microglia Metabolic Pathways: Implications In Alzheimer’S Disease, Abigail Penland, Cheyenne Ty, John Gerving, Martín Mendoza-Ceja, Megan Pratt

IdeaFest 2025

Alzheimer’s Disease (AD) is a neurological disorder that destroys memory and other cognitive functions. Several scientific findings have connected dysfunctional microglia, a type of immune cell, to AD progression. We created an agent-based model to simulate the interactions between microglia and their environment, addressing dysfunctional microglia's effect on AD. Our model represents a two-dimensional slice of the hippocampus, depicting microglia's ability to move, metabolize glucose, and interact with the blood brain barrier and amyloid beta plaques. We applied treatments of metabolic boosting and exercise to our model to study how varying treatment intensities can impede AD progression.

Change In Snowmelt Timing And Its Effects On The Green-Up Timing Of Mixed Conifer Forests, Tully Leonard, Rachel Torres

IdeaFest 2025

Shifts in the timing of snow-pack melt influences the phenological cycles of evergreen forest in the Sierra Nevada mountain range; this can lead to potential alterations in the timing and duration of green-up in these forests. This can affect the forest’s resilience to ecological disturbances, like wildfires or insect outbreaks. In order to investigate these patterns this study uses data from the National Ecological Observatory Network (NEON), which monitors the green-up of the forest and the snow depth. In addition, the snow water equivalent (SWE) data from the National Water and Climate Center (NWCC) was used to approximate the amount …

Edge Effects On Salamander Morphology In The Arcata Community Forest., Blake Knapp

IdeaFest 2025

This project examines how edge effects influence the weight and snout-to-vent length (SVL) salamanders (Order Caudata) in the Arcata Community Forest. Effects, caused by habitat fragmentation, can alter environmental conditions such as temperature, humidity, and soil composition, potentially affecting salamander physiology and well-being. The study aims to investigate whether salamanders living near forest edges exhibit different morphological characteristics compared to those in interior habitats. If salamanders in the Arcata Community Forest are impacted by edge effects, then there will be a significant correlation between snout to vent lengths (SVL) and weight and distance from the edge.

Remote Sensing For Forest Health And Wildfire Mitigation, Jonathan David Juarez, Rachel Torres

IdeaFest 2025

Forest ecosystems are vital for maintaining biodiversity, stabilizing soil, and regulating water cycles. However, frequent wildfires, extended droughts, and declining vegetation health are placing these ecosystems at risk. This research will explore how remote sensing tools and available data such as soil moisture, vegetation indices, and phenology can be used to assess forest health and mitigate wildfire risks.

Assembly And Testing Of A Closed Cycle Cryostat, Chris Maguire

Science University Research Symposium (SURS)

Closed cycle cryocoolers are commonly used in laboratories as they provide long-term, low-cost, low-maintenance operation. This project covers the assembly and testing of an Advanced Research Systems DE-202 closed cycle cryostat to provide a low temperature apparatus for undergraduate research and advanced laboratory projects. This system is useful for many applications including optics, condensed matter physics, spectroscopy, electrical characterization, microscopy, superconductivity, crystallography, and biological studies.

Cryostat assembly involved research and planning to build a custom frame for the cryocooler, assemble vacuum, water, gas and electrical systems, leak test, and fit components to laboratory utilities. Once setup is complete, the actual …

Utilizing Β-Gal To Visualize Selective Transport Of The Ssa4 Gene In S.Cerevisiae, Ian M. Staertow, Rebecca L. Adams Phd

Science University Research Symposium (SURS)

In eukaryotic cells such as Saccharomyces cerevisiae, protein synthesis begins with the transport of mRNA from the nucleus to the cytoplasm. In order for mRNA to leave the nucleus, it must first bind to specific transport proteins which can then facilitate transport via the nuclear pore complex (NPC), a selectively permeable membrane within the cell's nuclear envelope. Under environmental stress, such as heat shock, S. cerevisiae cells modulate transport rates. In this case, in heat stress or “heat shock” most mRNA transcripts will remain in the nucleus. The SSA4 transcript encodes for a chaperone protein which facilitates the subsequent export …

Harvesting Humans, Joanmarie Ilaria Davoli

Belmont Law Review

This Article examines allegations of systematic forced organ harvesting by the People’s Republic of China and argues that existing U.S. federal criminal law provides an underutilized mechanism to deter American participation in that industry. Tracing the historical development of China’s transplant system—from the use of executed prisoners to the alleged targeting of prisoners of conscience, including Falun Gong practitioners and Uyghurs—the Article situates organ procurement practices within broader human rights and genocide concerns. It contends that despite congressional hearings, resolutions, and proposed sanctions, meaningful deterrence has been limited. The Article advances a novel enforcement theory: prosecution of U.S. persons under …

Exploring Belmont’S Herbarium, Corinne Parker, Darlene Panvini

SPARK Symposium Presentations

The Belmont University Herbarium is a collection of plant samples used to document species. These specimens have been collected by Belmont students since 1973, helping to document the flora of Middle Tennessee. This semester, the specimens were organized and their identifications were confirmed. Updating the herbarium’s organizational system allowed for some specimens that were not fully prepared to be identified and processed, increasing the number of specimens that the university can use for teaching and research purposes. The number of specimens, families, and commonly collected families will be reported. Recommendations will be provided for further collecting to expand the herbarium …

Teaming With Technology: Adaptive Automation In Joint Cognitive Systems For Industry 5.0, Jessica Johnson

Virginia Digital Maritime Center (VDMC) Faculty Publications

Adaptive automation enables dynamic reallocation of functions between people and autonomous agents to improve performance in complex work. This paper presents a meta-analysis of experimental and quasi-experimental studies (2000-2025) on joint cognitive systems in industrially relevant contexts, quantifying effects on task performance, safety/failure management, workload, trust, and learning. Across studies, adaptive automation reliably reduces operator workload and shows moderate gains in task performance and safety, with healthier trust dynamics when adaptations are triggered by human-state or event cues, made transparent to the user, and remain rapidly overridable. Risks emerge when performance-triggered switching is opaque or poorly timed, which can erode …

Efficacy Of Deferoxamine Mesylate In Serum And Serum-Free Media: Adult Ventral Root Schwann Cell Survival Following Hydrogen Peroxide-Induced Cell Death, Yee Hang Ethan Ma, Abhinay R. Putta, Cyrus H. H. Chan, Stephen R. Vidman, Paula V. Monje, Giles W. Plant

Neurosurgery Faculty Publications

Schwann cell (SC) transplantation shows promise in treating spinal cord injury as a pro-regenerative agent to allow host endogenous neurons to bridge over the lesion. However, SC transplants face significant oxidative stress facilitated by ROS in the lesion, leading to poor survival. deferoxamine mesylate (DFO) is a neuroprotective agent shown to reduce H₂O₂-induced cell death in serum-containing conditions. Here we show that DFO is not necessary to induce neuroprotection under serum-free conditions by cell survival quantification and phenotypic analysis via immunohistochemistry, Hif1α and collagen IV quantification via whole cell corrected total cell fluorescence, and cell death …