Digital Commons Network^™

Cross-Modality Learning For Predicting Ihc Biomarkers From H&E-Stained Whole-Slide Images, Amit Das

Computer Science Senior Theses

Hematoxylin and Eosin (H&E) staining is a cornerstone of pathological analysis, offering reliable visualization of cellular morphology and tissue architecture for cancer diagnosis, subtyping, and grading. Immunohistochemistry (IHC) staining, an important ancillary study, provides molecular insights by detecting specific proteins within tissues, enhancing diagnostic accuracy, and improving treatment planning. However, IHC staining is costly, time-consuming, and resource-intensive, requiring specialized expertise. To address these limitations, this study proposes HistoStainAlign, a novel deep learning framework that predicts IHC staining patterns directly from H&E whole-slide images (WSIs) by learning joint representations of morphological and molecular features. The framework integrates paired H&E and IHC …

Don’T Take St. Anselm For A Marriage Therapist: The Utility Of Substitutionary Atonement Theology In Light Of Feminist Critiques, Abigail Elizabeth Livengood

Honors Projects

In light of feminist critiques from the twentieth and twenty-first century, this paper returns to Anselm’s Cur Deus Homo to examine the earliest expression of the Substitutionary Atonement Model. While acknowledging the harmful rhetoric attached to the model which has been brought to light by feminist theologians, this work examines Anselm's characterization of God, Jesus, and suffering from within his medieval worldview. In addition, this paper utilizes understandings of Christ held by historical women and survivors themselves to provide further context for Anselm’s understanding. Ultimately, this paper asserts that while feminist theologians raise important concerns about the dangers of Substitutionary …

Functional Resilience Of Healthcare In The Critical Juncture Of The Covid-19 Pandemic, Avner Kronisch, Christian Bongiorno, Kerane Smith, John Baker

Working Papers Series

This paper offers a comparative analysis of eight national healthcare systems—spanning democracies, autocracies, and various institutional models—to evaluate resilience during the COVID-19 pandemic. Drawing on Shvetsova et al.’s framework of informational and authority redundancies, and Parker & Klein’s “choke point” theory of healthcare rationing, we examine how institutional structure shaped pandemic response, system adaptability, and continuity of non-COVID services. Using indicators like life expectancy, under-five mortality, hospital capacity, cancer survival, and excess mortality, we explore how systems absorbed shock and maintained essential care. We find that decentralized and polycentric governance structures, when paired with coordination and resource adequacy, enhanced resilience—exemplified …

Usa V. Barron Thomas

2025 Decisions

USDC for the Middle District of Pennsylvania

S. M. V. Freehold Regional High Sch Dist Board Of Education

2025 Decisions

USDC for the District of New Jersey

The (Dis)Continuity Of Meaning In John Dewey’S Experience And Nature, Harrison S. Jackson

Center for Dewey Studies Essay Award

Experience and Nature proposes a naturalistic empiricism emphasizing continuity. This paper will argue that this continuity is threatened by Dewey’s anthropocentric in its account of meaning, which is only found in humans but is necessary for the perception of objects, communication, and social existence. Given contemporary research in ethology, Dewey’s denotative method requires a modification of this account. I will propose Merleau-Ponty’s notion of sense or the neuroscientific theory of enactivism as supplements preserving embodiment and social communication while being more continuous. Finally, I examine some recent applications of Dewey’s naturalism and show how they modify this account of meaning.

Systems, Methods, And Media For Monitoring The Production Process Of A Product, Chris Peter Tsokos, Lohuwa Mamudu

USF Patents

In accordance with some embodiments, systems, methods, and media for monitoring a production process of a product are provided. In some embodiments, a system comprises a remote server, a communications connection between the remote server and a facility database, at least one processor coupled to the communication system, and a memory device having stored thereon a set of computer readable instructions. The set of computer readable instructions cause the at least one processor to: receive a first set of data related to the production process, calculate a first monitoring index indicator for the production process based on the first set …

Shedding Light On Inequities Of Power Outages Through Data Transparency, Kelly A. Stevens, Sanam K. Aksha, Mohammad Siddiqur Rahman, Elizabeth Trader, Herbert Longenecker, Rebecca Entress, Thomas Wahl, Christopher Emrich, Kristopher O. Davis

Faculty Publications

In a changing climate, the electricity grid is increasingly exposed to more extreme weather that results in significant power outages. Further, lower income and racial-ethnic minority households are more likely to experience a higher frequency and duration of power outages compared to less socially vulnerable groups. The literature on the unequal impacts of power outages is a new, growing area of research that has been stymied in part due to the difficulty acquiring high spatial resolution, historical power outage data from utilities. In this Perspectives article, we review the availability of power outage data, and what can be learned from …

Shedding Light On Inequities Of Power Outages Through Data Transparency, Kelly A. Stevens, Sanam K. Aksha, Mohammed Siddiqur Rahman, Elizabeth Trader, Herbert Longenecker, Rebecca Entress

Faculty Publications

In a changing climate, the electricity grid is increasingly exposed to more extreme weather that results in significant power outages. Further, lower income and racial-ethnic minority households are more likely to experience a higher frequency and duration of power outages compared to less socially vulnerable groups. The literature on the unequal impacts of power outages is a new, growing area of research that has been stymied in part due to the difficulty acquiring high spatial resolution, historical power outage data from utilities. In this Perspectives article, we review the availability of power outage data, and what can be learned from …

Machine Verification Of Correctness For A Concurrent Union-Find Object, Karun Ram

Computer Science Senior Theses

We consider a family of near-optimal randomized multiprocessor implementations for the union-find problem due to Jayanti and Tarjan–known as the Jayanti-Tarjan Randomized-Linking (JT-RL) union-find objects–and provide the first formal and fully machine-verified proof of their strong linearizability (i.e., correctness). Their algorithms are efficient both in theory and in practice: numerous benchmarking works demonstrate that they perform faster, or as fast, as all other known implementations for the union-find object on both CPUs and GPUs.

The correctness of the JT-RL algorithms is subtle, which motivates the need for formal verification. To this end, we first specify the JT-RL objects in TLA+, …

The Case For Visual Art In Overcoming The Double Empathy Problem, Katelyn Milea Rose Nilson

Theses and Dissertations

A person's cognitive environment--made up of their thoughts, experiences, and tendencies--can affect how they empathize with others. Those with significantly different cognitive environments, such as autistic and neurotypical individuals, may have a difficult time empathizing with one another. This study aimed to facilitate empathy between the two groups by aligning their cognitive environments through discussion about visual art. Five autistic neurotypical dyads completed three discussion sessions where they observed and journaled about a piece of art, discussed their thoughts with each other, and filled out a questionnaire about their experience. All participants also completed a post-study interview. Data from questionnaires, …

Houthi Maritime Terrorism: Severing The Iranian Lifeline, Raul (Pete) Pedrozo

International Law Studies

The Houthis have carried out an unprecedented assault on commercial shipping and foreign warships operating in international waters off the Arabian Peninsula that has changed the face of maritime terrorism. These waters are a strategic corridor that facilitates international trade and the movement of naval forces from Europe and the Americas to the Middle East and Asia via the Suez Canal. As a result of the Houthi attacks, most shipping companies rerouted their vessels around Africa via the Cape of Good Hope, which adds significant costs and adversely affects the global supply chain, increasing inflation, and exacerbating food insecurity in …

Current Issues In Oral Health: Introduction To The Special Issue, Nejat Düzgüneş

Pacific Faculty Work

No abstract provided.

New Definitions Of Library Use: Experimentation, Discovery, And Creation (Edc) Within A Library, Holt Zaugg

Faculty Publications

Why did you do this activity, project, or research?

Over the last decade, libraries have shifted from being primarily repositories for information and resources to active learning centers. Physical resources (e.g., books, journals, manuscripts) have moved to online access. Librarian roles have adjusted how they help patrons find and access resources in their local library and beyond, resulting in impactful input on research, learning, and scholarly endeavors. Additionally, due to a reduced need for storing materials, libraries have developed collaborative and innovative spaces to meet patrons’ needs. These spaces include group study rooms, experiential studios, makerspaces, green rooms, and podcast …

Public Health Simulation Infused Program (Pship) Toolkit, Desiree A. Díaz, Mindi Anderson, Francisco Guido-Sanz, Peggy Hill, Samantha Stephenson, Heather Peralta, Syretta Spears, Geraldine Luzincourt

Faculty Scholarship and Creative Works

Project Narrative

PURPOSE AND NEED

Purpose: Priorities set forth by the Health Resources & Services Administration (HRSA) are addressed in the proposed simulation program in an effort to meet curricular needs and foster care to the medically underserved in Florida, further exposing students to public healthcare needs. Interprofessional (nursing and social work) and intraprofessional (undergraduate nurse and Nurse Practitioner [NP]) instruction is essential in the simulation-based education (SBE) program, promoting important content on identifying risk factors and health assessment of the medically underserved community (MUC) (Education Priority 2, §831). Coordination of medical care is a vicarious learning opportunity for all …

Nazor V. Sydney Sol Group, Ltd.

All Decisions

In this loft tenant action, the court modified the lower court's order, reinstating claims for rent overcharge, unjust enrichment, and breach of warranty of habitability. The court held that court-ordered use and occupancy payments are not "voluntarily paid" rent under MDL § 302(b), allowing these claims to proceed in a related action. The court also reinstated a claim for accounting of the security deposit and attorneys' fees, finding the landlord failed to prove non-commingling. However, claims for harassment, retaliatory eviction, and constructive eviction were dismissed.

Artificial Intelligence And Astronomy: Lab Manual For Generative Ai-Based Learning Activities, Vasiliy Znamenskiy

Open Educational Resources

This lab manual introduces community college students to the intersection of artificial intelligence (AI) and astronomy through hands-on, inquiry-based activities. It explores how generative AI platforms—ranging from text-based chat systems to image and video generators—can enhance scientific understanding, creativity, and critical thinking in space science education. Students engage with tools such as ChatGPT, Gemini, DALL·E, and Synthesia to formulate and evaluate astronomy-related questions, generate scientifically inspired visualizations, and produce dynamic representations of cosmic phenomena. Through structured exercises, the manual promotes digital literacy, fosters analytical skills, and illustrates how AI assists in astronomical research, including data analysis, image enhancement, spacecraft autonomy, …

Visualizing Sustainability Data With Ai, Matthew Van Dyke, Emily Chen, Hayden Le, Dorothy Xu

Computer Science and Engineering Senior Theses

EcoVisor is a prototype system for extracting, structuring, and visualizing sustainability related metrics from natural language articles. The project integrates a FastAPI backend with a Next.js frontend to transform raw text or article URLs into structured sustainability data, detect trends over time, and generate visual outputs for users. Key capabilities include automated scraping of web articles for sustainability semantics, sustainability related metric data extraction, post-processing of extracted values into cleaned segments and sentences using HTML parsing, grouping of metrics by category and year, generation of Chart.js visualizations, and production of concise “comic brief” summaries for accessible storytelling. EcoVisor aims to …

Stroke Survivors: Predicting Cognitive Outcomes By Stroke Severity, Caregiver Factors, & Social Determinants Of Health, Jason Alexander Blake

All ETDs from UAB

Physical and cognitive disabilities are common following a stroke, often leading to significant changes in survivors' daily lives and increasing dependency on caregivers. These changes can include involuntary retirement, loss of independence, and decreased social engagement, which may necessitate adjustments in living arrangements and long-term care. This dissertation investigates the predictors of cognitive outcomes in stroke survivors, with a particular focus on the roles of stroke severity and caregiver factors. Utilizing data from the REasons for Geographic and Racial Differences in Stroke (REGARDS) project, this research captures the different predictors of post-stroke cognition through biennial assessments. Through longitudinal studies, this …

Experiences Of Discrimination And Neighborhood Cohesion In Risk Of Poor Mental Health Outcomes Among Older, Community-Dwelling Participants In The Regards Study, Marquita S. Brooks

All ETDs from UAB

Mental health disorders impact approximately 14% of persons aged 65 and older and often are undertreated or underrecognized. Assessment of factors that link environmental, sociocultural, behavioral, and biological factors to overall health and disease is integral to guiding research on health disparities in older populations. Although research suggests associations between environmental factors (i.e., discrimination and neighborhood cohesion) and mental health outcomes, there is limited research on these factors within the U.S. Therefore, our study assessed the relationship between discrimination, neighborhood cohesion, and mental health outcomes in the REasons for Geographic and Racial Differences in Stroke (REGARDS) study, a national, prospective …

Examining Risk And Protective Factors Of African Americans Who Use Substances, Dominique Ashonta Black

All ETDs from UAB

African Americans (AAs) are less likely to report internalized symptoms and substance use compared to other racial groups but tend to report more severe symptoms related to either condition. Research suggests internalized symptoms and substance use share a causal relationship or an underlying factor that contributes to both conditions. Risk factors such as stress, discrimination, and trauma strengthen the relationship between anxiety and substance use in AAs. A higher prevalence of stress, discrimination, and trauma exposure was found in AAs when compared to other racial groups, increasing AAs risk for internalized symptoms and substance use. While it is important to …

Interrogating The Dispersal Process And Relevant Genes In Vibrio Fischeri, Jeremy Esin

Dissertations

Biofilms are aggregates of bacteria encased in a matrix that shields bacteria from environmental hazards. These structures are formed in response to cues from the environment and drive colonization of new niches. Biofilms can be both beneficial and detrimental. Largely, research focuses on biofilms that have negative outcomes in clinical, environmental, and economical settings. However, the value of beneficial biofilms is recognized and studied. The marine bacterium Vibrio fischeri is part of a model system for studying symbiotic biofilms in a eukaryotic host. V. fischeri produces a transient biofilm at the surface of a specialized light organ and then disperses …

Restoration Of The Tumor Suppressor Function Of Y220c-Mutant P53 By Rezatapopt, A Small-Molecule Reactivator, Anna M Puzio-Kuter, Lizhong Xu, Mary Kate Mcbrayer, Romyr Dominique, Hongju H Li, Bruce J Fahr, Alyssa M Brown, Amy E Wiebesiek, Brandon M Russo, Chris L Mulligan, Hong Yang, Josh Battaglia, Kimberly A Robell, Dafydd H Thomas, Kuo-Sen Huang, Alexander Solovyov, Benjamin D Greenbaum, Jonathan D Oliner, Thomas W Davis, Melissa L Dumble, Melissa L Johnson, Shunbin Xiong, Peirong Yang, Guillermina Lozano, Marc M Fellous, Binh T Vu, Alison M Schram, Arnold J Levine, Masha V Poyurovsky

Faculty, Staff and Student Publications

Restoration of the tumor suppressor function of tumor-associated p53 mutants, including the Y220C substitution, has posed a significant challenge for therapeutic discovery. In this study, we describe rezatapopt (PC14586), part of a series of compounds designed to reactivate the p53 Y220C mutant. These compounds restore p53 tumor suppressor function by correcting its conformation and enabling it to bind DNA and activate downstream target genes, thus inducing antiproliferative changes in tumor cells. Our findings are supported by biochemical and structural analysis, in vitro and in vivo transcriptomics, and functional data, revealing the recovery of multiple aspects of the wild-type p53 program. …

Comparing Emotional Facial Expressions Produced During Personal Narrative Discourse By People With And Without Aphasia, Chloe K. Houghton

Theses and Dissertations

This study investigated the differences in emotional facial expressivity between people with aphasia (PWA) and control participants during emotional discourse tasks. Participants consisted of 26 PWA and 26 control participants from Aphasia Talk Bank who retold a stroke or illness story and an important life event story, totaling 104 video files. Undergraduate research assistants were trained to code emotional facial expressions according to valence, intensity, and duration utilizing a modified Facial Expression Coding System (FACES; Kring & Sloan, 1991). Dependent variables included positive frequency, negative frequency, positive intensity, and negative intensity. Results from this study demonstrate that female participants used …

Posterior Predictive Design For Phase I Clinical Trials, Chenqi Fu, Shouhao Zhou, J Jack Lee

Faculty, Staff and Student Publications

Interval-based designs represent cutting-edge adaptive methodologies for phase I clinical trials to identify the maximum tolerated dose (MTD). These designs exhibit robust performance comparable to more intricate, model-based designs, and their pretabulated decision rule enables them to be implemented as simply as the conventional algorithm-based designs. In this paper, we introduce the posterior predictive (PoP) design, a novel interval-based design that leverages advanced Bayesian predictive hypothesis testing techniques for dose escalation and de-escalation. Our work moves beyond the existing model-assisted interval-based designs by achieving global optimality in dose transition. Theoretically, the global optimality ensures that the proposed design can consistently …

A Novel Cardiomyopathy Phenotype Linked To A Chd7 Missense Variant, In Young Park, Chih-Wei Hsu, Karim Bouazoune, Christina E Espindola, Madeline Hannah Mclaughlin Armond, Cristian Coarfa, Sandra L Grimm, James F Martin, Donna M Martin, Cheryl Lyn Walker

Center for Medical Ethics and Health Policy Staff Publications

Loss of function in the chromatin remodeler CHD7 causes CHARGE syndrome, characterized by variable penetrance and diverse abnormalities. However, establishing genotype-phenotype correlations has been challenging, as most CHD7 inactivating mutations are null alleles. Through CHD7 missense variant analysis at potential phosphorylation sites, we identified T730 (T720 in mice) as a critical residue associated with pathogenesis. Using a CHD7 T730 missense variant (Chd7T720A) and a frameshift null allele (Chd7fs) in a mouse model, we found that Chd7fs/fs mice were non-viable, while Chd7fs/+ mice exhibited haploinsufficiency-related circling behavior. Notably, Chd7fs/T720A mice died before postnatal …

In Situ Structure And Assembly Of The Abc-Type Tripartite Pump Macab-Tolc, Tong Huo, Wenfang Zhang, Zhili Yu, Wei Zheng, Yaoming Wu, Qiuyu Ren, Zekai Wan, Junli Cao, Zhao Wang, Xiaodong Shi

Faculty, Staff and Students Publications

The MacAB-TolC tripartite efflux pump is widely distributed in Gram-negative bacteria, extruding antibiotics and virulence factors that lead to multidrug resistance and pathogenicity. However, the in situ structure and assembly mechanism of MacAB-TolC remain unclear. Here, we resolve the in situ structures of the MacAB-TolC efflux pump in Escherichia coli by electron cryo-tomography and subtomogram averaging. In the cells without antibiotic treatment, we observe a fully assembled MacAB-TolC pump. When Escherichia coli cells are treated with erythromycin, in addition to the tripartite pumps, we also discover the emergence of MacA-TolC subcomplexes without MacB, indicating flexible binding of MacB in the …

Phage-Induced Protection Against Lethal Bacterial Reinfection, Yikun Xing, Haroldo J Hernandez Santos, Ling Qiu, Samantha R Ritter, Jacob J Zulk, Rachel Lahowetz, Kathryn A Patras, Austen L Terwilliger, Anthony W Maresso

Faculty, Staff and Students Publications

Bacteriophages, or phages, are viruses that target and infect bacteria. Due to a worldwide rise in antimicrobial resistance (AMR), phages have been proposed as a promising alternative to antibiotics for the treatment of resistant bacterial infections. Up to this point in history, phage use in preclinical animal studies, clinical trials, and emergency-use compassionate care cases has centered around the original observation from 1915 showing phage as lytic agent, and thus a treatment that kills bacteria. Here, we describe an activity associated with phage therapy that extends beyond lytic activity that results in long-term protection against reinfection. This activity is potent, …

Correlations Within And Between Highly Multiplexed Proteomic Assays Of Human Plasma, Mary R Rooney, Jingsha Chen, Christie M Ballantyne, Ron C Hoogeveen, Eric Boerwinkle, Bing Yu, Keenan A Walker, Pascal Schlosser, Elizabeth Selvin, Nilanjan Chatterjee, David Couper, Morgan E Grams, Josef Coresh

Faculty, Staff and Students Publications

Introduction: The number of assays on proteomic platforms has grown rapidly. The leading platforms, SomaScan and Olink, have strengths and limitations. Comparisons of precision on the latest platforms-SomaScan 11k and Olink Explore HT-have not yet been established.

Methods: Among 102 participants in the Atherosclerosis Risk in Communities Study (mean age 74 years, 53% women, 47% Black), we used split plasma samples to measure platform precision. CV and Spearman correlations were calculated for each assay. Cross-platform agreement was assessed for overlapping proteins.

Results: SomaScan 11k demonstrated a median correlation of 0.85 for the 10 778 assays and a median CV of …

Beyond The Surface: Mapping Dde's Metabolic Footprint On Adolescent Obesity, Zhenjiang Li, Shudi Pan, Brittney O Baumert, Jiawen Carmen Chen, Jesse A Goodrich, Hongxu Wang, Sarah Rock, Justin Ryder, Damaskini Valvi, Todd Jenkins, Stephanie Sisley, Xiangping Lin, Scott M Bartell, Thomas H Inge, Stavra Xanthakos, Brooklynn Mcneil, Anna R Robuck, Catherine E Mullins, Sandrah P Eckel, Rob S Mcconnell, Michele A La Merrill, Douglas I Walker, David V Conti, Lida Chatzi

Faculty, Staff and Students Publications

Background: Bariatric surgery is an intervention for severe obesity, leading to significant weight loss and metabolic improvements. However, the release of lipophilic chemicals accumulated in adipose tissue during weight loss presents a unique clinical challenge and research opportunity. Dichlorodiphenyldichloroethylene (DDE) is a persistent organic pollutant increasingly recognized as obesogen, while the biological mechanisms through which DDE influences body mass index (BMI) and waist circumference remain underexplored.

Objectives: We aimed to identify metabolic signatures mediating the association between DDE exposure and weight loss by plasma and adipose tissue metabolomics.

Methods: We conducted a longitudinal study involving 60 adolescents with severe obesity …