Digital Commons Network^™

Pathways, Outputs And Impact Of Nih-Supported Bioinformatics And Genomics Graduate Trainees In Africa, Daudi Jjingo, Andrew Walakira, Suhaila Hashim, Cisse Cheickna, Ronald Galiwango, Caleb Kibet, Florence N. Kivunike, Gerald Mboowa, Fredrick Elishama Kakembo, Babajide Ayodele, Jean Baka Domelevo Entfellner, Santie De Villiers, Karen Wambui, Segun Fatumo, Tinashe Chikowore, John Mukisa, Alfred Ssekagiri, Nicholas Bbosa, Julius Mulindwa, Samuel Kyobe, Mike Nsubuga, Grace Kebirungi, Eric Katagirya, Savannah Mwesigwa, Ibra Lujumba, Rogers Kamulegeya, Samuel Kirimunda, Stephen Kanyerezi, Shahiid Kiyaga, Ivan Sserwadda, Davis Kiberu, Daniel Masiga

All Peer-Reviewed Publications

Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes of nucleic acid sequencing. Concurrently, epidemiological studies and clinical records are generating enormous amounts of data amenable to disease modeling, machine learning, and artificial intelligence techniques. Bioinformatics and data science expertise is therefore essential for improved population health. Accordingly, in 2012, the US National Institutes of Health (NIH) in partnership with the Wellcome Trust, and with support from the African Society for Human Genetics, initiated the H3Africa (Human Heredity and Health in Africa) consortium. One of its key goals was to …

Ecological Intensification Of Maize-Kale Systems In Kenya By Biofertilization And Push-Pull Management Shifts Nematode Communities, Agnes Kiriga, Johnnie Van Den Berg, Frank Chidawanyika, Solveig Haukeland, Bianca Greyvenstein, Dennis Beesigamukama, Chrysantus M. Tanga, Sevgan Subramanian, Daniel M. Mutyambai

All Peer-Reviewed Publications

Plant-parasitic nematodes (PPNs) pose a persistent threat to vegetable production in Kenya, contributing to reduced yields and soil degradation. The management of PPNs in vegetables in Kenya has largely remained unaddressed. The integration of ecological intensification strategies such as the vegetable integrated push-pull (VIPP) system and the use of black soldier fly frass fertilizer (BSFF) is gaining traction in sustainable agriculture. The aim of this study was to determine the effects of integrating VIPP and BSFF on nematode abundance and diversity in maize-kale cropping systems. Field trials were conducted in two different agroecological zones in Kenya. Field treatments involved plots …

The Association Between Social Vulnerability And Racial Disparities In Preterm Birth, Anita Pershad, Gabby Adams, Lindsay Robbins, George Saade, Tetsuya Kawakita

Department of Obstetrics & Gynecology Faculty Publications

Objective

To evaluate the association between county-level social vulnerability and preterm birth and assess whether racial disparities vary across levels of vulnerability.

Methods

This cross-sectional study utilized restricted Centers for Disease Control and Prevention natality data from 2023. We included Black or White births with singleton pregnancies across 3123 US counties from 50 US states and the District of Columbia. Participants were grouped into quartiles based on the county-level Social Vulnerability Index (SVI), with quartile 4 representing the most socially vulnerable populations. The primary outcome was preterm birth, defined as delivery before 37 weeks. Secondary outcomes included small for gestational …

Mapping Robusta Coffee (Coffea Canephora) Cropping Systems In Uganda: A Two-Step Pixel And Sub-Pixel Based Approach With Sentinel-2 Data, Getachew Kebede, Bester Tawona Mudereri, Onisimo Mutanga, Tobias Landmann, John Odindi, Natacha Motisi, Fabrice Pinard, Henri E.Z. Tonnang, Elfatih M. Abdel-Rahman

All Peer-Reviewed Publications

Coffee is a highly valued commodity and a widely consumed beverage, playing an important role in global trade. However, coffee farming landscapes are increasing transitioning into smaller-scale agricultural setups. This transformation highlights the critical need for accurate classification and mapping of coffee cropping systems (CS), especially in countries like Uganda, where dense vegetation and complex terrain present substantial challenges to traditional land survey methods. Moreover, understanding the spatial distribution of Robusta coffee (Coffea canephora) CS is essential for developing site-specific management strategies, guiding extension services, and informing evidence-based policy decisions. To address this gap, the present study aimed to enhance …

Navigating Language, Faith, And Identity: A Case Study Of Language Policies In Indian Transnational Families In Saudi Arabia, Muhammad Alasmari, Rashad Ahmed, Amna Shamim, Nief Aied Al-Gamdi

Research, Publications & Creative Work

This study investigates the family language policies (FLPs) of two North Indian Muslim families residing in Saudi Arabia, focusing on how they navigate multilingualism to balance cultural heritage, religious practices, and sociolinguistic adaptation. Using Spolsky’s FLP framework and a qualitative case study approach, the research examines the dynamic roles of Urdu, Arabic, and English in these households. Semi-structured interviews were conducted with mothers and children to explore language ideologies, practices, and management strategies. The findings reveal that Urdu serves as a cornerstone of cultural identity, while Arabic is pivotal for religious education and social integration. English plays a supplementary role …

Mathematicly Rigorous Quantum General Relativity, I: Pure, James Glimm

Department of Applied Mathematics & Statistics Faculty Publications

A pure general relativity (quantum or classical) is one lacking in matter. Such a field has a Lorentzian space time geometry. A renormalization perturbative expansion, truncated to all finite orders, establishes both the quantum and the general relativity theory with full mathematical rigor.

The Boson Yang-Mills Field: The Loop Expansion, James Glimm

Department of Applied Mathematics & Statistics Faculty Publications

This paper demonstrates convergence of the loop expansion for Yang-Mills fields.

The loop construction of perturbation theory is based on the axial gauge, ghost states, the BRST framework and the Gribov extension of the Hamiltonian, with a loop expansion cutoff to all finite orders for the dynamics.

The construction is established by renormalized perturbation theory convergent to all finite orders.

Two distinct Yang-Mills theories are constructed, one based on short distance asymptotics and the other based on long distance asymptotics.

The construction depends on an assumed principle of a maximum rate of entropy production.

The paper has sufficient generality to …

The Pure Yang-Mills Field, Repeated Blowups, James Glimm

Department of Applied Mathematics & Statistics Faculty Publications

The temporal scaling of the quantum Yang-Mills solution is characterized by analytic solutions for a limited time interval, ended by a discontinuity (blowup).

For general initial conditions, there will be a finite series of these discontinuities.

The time asymptotic limit of this series of discontinuities is given as the mean of these solutions, starting with the mean of the initial data. The time asymptote is the solution in $\mathcal{S}'$ of the heat equation as a stochastic process.

The time asymptote satisfies the cluster axiom, to complete the requirements for a solution of the Millennium Yang-Mills problem.

The principle of a …

The Red Hands Of Ulster, Philip Metres

2026 Faculty Bibliography

No abstract provided.

Autonomy Without Alignment: Professional Development And The Fragmented Ai Landscape In Higher Education, Kelly D. Muller

Essays in Education

Higher education’s strong commitment to autonomy and academic freedom has produced a fragmented and ethically inconsistent approach to artificial intelligence (AI) professional development. As AI reshapes teaching, assessment, authorship, and academic integrity, faculty responses range from prohibition to enthusiastic adoption, often without shared institutional guidance. Current professional development efforts are largely optional, tool-focused, and reactive, leaving instructors to construct individual ethical frameworks while students encounter inconsistent expectations across courses. This variability raises concerns about equity, accountability, and institutional risk. Drawing on scholarship related to academic freedom, AI governance, and diffusion of innovation, the article proposes a three-layer model that reframes …

Regional Oceanographic Controls On Water Column Nitrogen Fixation In Northern Australian Waters, Douglas G. Capone, Ajit Subramaniam, Yubin Raut, Joseph P. Montoya, Margaret R. Mulholland, Rachel Ann Foster, Miles Furnas, Edward J. Carpenter

OES Faculty Publications

Large blooms of the diazotrophic cyanobacteria, Trichodesmium, have been re-ported along the north coast of Australia and are readily evident in remote sensing images. During a research cruise in November 1999, we sampled from Townsville to Broome, examined Trichodesmium population densities and their rates of carbon and N₂ fixation alongside microscopy-based cell counts of them and other cyanobacte-rial diazotrophs. Additionally, we also enumerated the picophytoplankton community using flow-cytometry, measured bulk chlorophyll concentrations, carbon and N₂ fixation rates, and water column hydrography, enabling comparison of diazotrophic and picophytoplankton functional groups across the system. Agglomerative hierarchical clustering analysis of physicochemical oceanographic …

Unintended Consequences Of Estuarine Management Within The Trajectory Of Recovery: Examples From The Chesapeake Bay, Jessica S. Turner, Fei Da, Molly M. Mitchell

OES Faculty Publications

Estuaries are vital ecosystems that support biodiversity, human populations, and economic activities such as fisheries, aquaculture, and tourism. Managing estuarine systems often involves interventions to regulate sediment and nutrient inputs with the goal of improving water quality, and subsequently the economic values of the estuary. However, these management strategies can produce unintended consequences. The Chesapeake Bay is an estuary recovering from eutrophication which provides clear case studies for these patterns. In the Chesapeake Bay, decreased sediment inputs, resulting from shoreline stabilization and watershed modifications, can impair marsh resilience to sea level rise and disrupt sediment-light-algal interactions affecting water clarity. Likewise, …

Revisiting The Life Cycle Of Margalefidinium Polykrikoides Group Iii, Eduardo Pérez-Vega, Kenneth N. Mertens, Pjotr Meyvisch, Margaret R. Mulholland

OES Faculty Publications

Dinoflagellates produce cysts as a strategy to withstand environmental stressors, with nutrient depletion generally considered a key trigger for cyst production. Resting cysts are thick-walled, typically composed of one to several layers, and characterized by a prolonged dormancy period. In contrast, pellicle cysts possess a thin, single wall and exhibit no dormancy or a markedly shorter dormancy than resting cysts of the same species. Margalefidinium polykrikoides produces pellicle and resting cysts, whereas its congener, M. fulvescens, has been shown to produce pumpkin-like structures. Using phase-contrast microscopy, time-lapse microscopy, FlowCam, and attenuated total reflection Fourier transform infrared microspectroscopy (ATR μ-FTIR), …

Ai-Powered Immune Cell Knowledge Graph (Ickg) With Granular Immune Contexts Enables Immune Program Interpretation, Shan He, Yukun Tan, Qing Ye, Matthew M Gubin, Merve Dede, Hind Rafei, Weiyi Peng, Katayoun Rezvani, Vakul Mohanty, Ken Chen

Faculty, Staff and Student Publications

The widespread application of single-cell and spatial omics to models and patient samples has transformed immune cell profiling across physiological conditions. However, knowledge of immune cell states, functions, and gene regulation remains fragmented across publications, limiting our ability to synthesize insights and derive mechanistic understanding from the literature. To address this gap and facilitate literature integration, we constructed Immune Cell Knowledge Graphs (ICKGs)-four cell type-specific graphs derived from over 24,000 cancer immunotherapy-focused PubMed abstracts using large language models (LLMs) with "human verifiable" validation. Unlike conventional databases, which provide context-agnostic pathways, ICKGs capture directed, literature-supported relationships among genes, pathways and immune …

Outcomes Of Patients With Melanoma Brain Metastases Treated With Ipilimumab And Nivolumab With Or Without Upfront Comprehensive Stereotactic Radiosurgery, Troy J Kleber, Denái R Milton, Subhiksha Srinivasan, Bikash Panthi, Warren Floyd, Eric A Goethe, Michael A Davies, Hussein A Tawbi, Isabella C Glitza Oliva, Diana Kaya, Jing Li, Todd A Swanson, Subha Perni, Martin C Tom, Chenyang Wang, Sujit Prabhu, Jeffrey S Weinberg, Ian E Mccutcheon, Caroline Chung, Sherise D Ferguson, Thomas H Beckham

Faculty, Staff and Student Publications

Background: The efficacy of ipilimumab and nivolumab (ipi/nivo) for melanoma brain metastases (MBMs) has been previously reported, leading to uncertainty regarding the optimal role of comprehensive stereotactic radiosurgery (cSRS). We therefore conducted a single-institution retrospective study to compare outcomes of upfront versus deferred cSRS for MBM treated with ipi/nivo.

Methods: We identified patients who started ipi/nivo for newly diagnosed MBMs between 2018 and 2023, with or without upfront cSRS. Patients with >15 MBMs, leptomeningeal disease, or whole-brain radiotherapy at baseline were excluded. Outcomes were compared using multivariable regression and reported as adjusted hazard ratios (aHRs) with 95% CIs.

Results: Of …

Reply To: Late Nonrelapse Mortality: A Hidden Risk In Triplet Therapy For Idh-Mutated Aml?, Jennifer Marvin-Peek, Courtney D Dinardo

Faculty, Staff and Student Publications

No abstract provided.

Test-Retest Apparent Diffusion Coefficient Reproducibility In Head And Neck Cancer Using A 15-T Mr-Linac, Brigid A Mcdonald, Dina El-Habashy, Renjie He, Sam Mulder, Sarah Mirbahaeddin, Abdallah S R Mohamed, Sara Ahmed, Yao Ding, Jihong Wang, Stephen Y Lai, Alex Dresner, John Christodouleas, Clifton D Fuller

Faculty, Staff and Student Publications

Purpose

To evaluate the reproducibility of apparent diffusion coefficient (ADC) measurements in head and neck squamous cell carcinoma (HNSCC) using a 1.5-T MR-linac (MRI-guided linear accelerator) system.

Materials and Methods

In this retrospective study, conducted between February 2021 and January 2024, patients with HNSCC lesions underwent echo-planar imaging diffusion-weighted MRI on a 1.5-T MR-linac system at two time points before the start of radiation therapy. Mean and median ADC values and volumes were measured for each lesion. Absolute and percent reproducibility coefficients (RCs) were calculated. Linear regression analyses and F tests were performed to determine whether the lesion volume or …

Perspective: Radiotherapy And Body Composition: Unmet Needs In Low- And Middle-Income Countries, Alexia J Murphy-Alford, Aaron J Grossberg, Vickie E Baracos, Maha Barbar, Judy Bauer, Jonathan P Bennett, Elena Fidarova, Clifton D Fuller, Anastassia Löser, Amy C Moreno, Anurima Patra, Deepa Puttaswamy, David I Rosenthal, Judy Schoeman, Yavuz Anacak

Faculty, Staff and Student Publications

Radiotherapy plays a vital role in cancer treatment, yet its effects on patients' nutritional status can precipitate muscle loss, with significant implications for treatment tolerance and outcomes. Evidence from high-income countries increasingly links radiation-induced muscle loss to adverse clinical outcomes. In contrast, low- and middle-income countries face a stark evidence gap, despite the heightened vulnerability of cancer patients in these settings due to delayed diagnosis, limited access to care, and high rates of co-morbidities. This paper highlights the critical gaps in nutritional care for radiotherapy patients in low- and middle-income countries.

Genomic Determinants Of Response And Resistance To Pirtobrutinib In Relapsed/Refractory Chronic Lymphocytic Leukemia, Jennifer R Brown, Bastien Nguyen, Sai Prasad Desikan, Helen Won, Shady I Tantawy, Samuel C Mcneely, Narasimha Marella, Hetal S Randeria, Lauren M Hanson, Andrew Parker, Salomé Calado Botelho, Jennifer A Woyach, Krish Patel, Constantine S Tam, Toby A Eyre, Chan Y Cheah, Nirav N Shah, Paolo Ghia, Wojciech Jurczak, Minna Balbas, Binoj Nair, Paolo Abada, Chunxiao Wang, Denise Wang, Lindsey E Roeker, Varsha Gandhi, William G Wierda

Faculty, Staff and Student Publications

Pirtobrutinib, a noncovalent, reversible Bruton tyrosine kinase inhibitor (BTKi), demonstrated efficacy in patients with chronic lymphocytic leukemia (CLL), resistant to covalent BTKi (cBTKi). We analyzed genomic correlations with response and resistance to pirtobrutinib in relapsed/refractory (R/R) patients with CLL pretreated with cBTKi enrolled in the phase 1/2 BRUIN trial. DNA sequencing was performed on peripheral blood mononuclear cells at baseline, on treatment, and at progressive disease (PD). Common alterations at baseline included mutations in BTK (43%), TP53 (38%), SF3B1 (25%), NOTCH1 (23%), ATM (19%), XPO1 (11%), PLCG2 (9%), BCL2 (8%), and 17p deletion (28%). Common baseline BTK mutations included C481S …

Integrating Telehealth Into Advanced Health Assessment: A Bimodal Approach, Heather M. Jones, Tracy Alam, Beth A. Ammerman, John Jardine, Carolyn Rutledge

Ellmer School of Nursing Faculty Publications

The expansion of telehealth emphasizes the need for advanced practice registered nurses (APRNs) to develop competencies in telehealth technology and techniques. Limitations in physical assessments and the lack of comprehensive telehealth curricula in APRN programs have been identified as barriers to students' preparedness and confidence in performing telehealth assessments in clinical practice. This project evaluated integrating telehealth content into an advanced health assessment course with both in-person and online laboratories. Presurveys and postsurveys showed increased student confidence and competency in telehealth skills across both modalities. These findings support incorporating standardized telehealth education into APRN curricula to enhance telehealth clinical readiness.

Critical And Exegetical Notes And Discourses On The Gospels. Volume 2, Luke And John, Andrew Carroll

Heritage Material

No abstract provided.

What Church Planters Need : How Community, Training, & Intentional Relationships Fuel Church Growth, Carolina G. Miller

Heritage Material

No abstract provided.

Successful Evangelism, Or, Life And Labors Of Rev. E. A. Fergerson, W.B. Yates

Heritage Material

No abstract provided.

Helen Ruth Chambers Papers - Accession 1748, Helen Ruth Chambers Wren

Manuscript Collection

The Helen Ruth Chambers Papers document the undergraduate experience of Helen Ruth Chambers Wren (1909–1985) during her years as a student at Winthrop College, from the late 1920s through her graduation in 1931 with a Bachelor of Arts and Sciences. Helen was one of three sisters that graduated from Winthrop including Ella Margaret Chambers (Class of 1929) and Dorothy Chambers (Class of 1935). The collection consists primarily of student publications, academic work, and ephemera reflecting campus life, student organizations, and intellectual culture during this period.

Materials include a Winthrop College commencement announcement and program from 1929; student handbooks published by …

An Exploration Of Knowledge-Sharing Behaviour Within A Community-Based Service Provider: A Reflexive Thematic Analysis, Paul Mcmanus

Doctoral

This qualitative research examines the knowledge-sharing (KS) behaviour of employees within a non-profit organisation (NPO) based in Dublin, Ireland. This NPO is a community-based service provider that supports people with disabilities and their families. It operates under the aegis of the Health Service Executive (HSE). The ability of employees to share knowledge is fundamental to the sustained care of society’s most vulnerable. Research on employees’ KS behaviour remains underrepresented within the non-profit sector. This gap in knowledge aligns with the NPO’s view that its KS environment requires improvement. In response to the literature review, a developed taxonomy conceptualises the organisation …

Brief Therapy Dog Interactions May Increase Self-Efficacy And Lower Perceived Stress And Cortisol In High School Students: A Preliminary Study, Dawn Melzer, Deirdre Yeater, Madison Derubis, Christiana Rose Kohlroser, Barbara J. Pierce

Psychology Faculty Publications

The present study examined changes in high schoolers’ perceived stress, general self-efficacy and cortisol levels after a brief interaction with a certified therapy dog. High school students completed self-report measures of perceived stress and general self-efficacy and provided salivary cortisol samples both before and after a 10-min interaction with a certified therapy dog. Following the interaction, students reported reductions in perceived stress scores, exhibited lower salivary cortisol concentrations and demonstrated increases in self-efficacy scores compared to before the interaction. Although higher self-efficacy scores were observed, general self-efficacy is generally regarded as a stable construct; therefore, these findings may reflect a …

Llamoco: Instruction Tuning Of Large Language Models For Optimization Code Generation, Zeyuan Ma, Yue-Jiao Gong, Hongshu Guo, Jiacheng Chen, Yining Ma, Zhiguang Cao

Research Collection School Of Computing and Information Systems

Recently, combining the strength of large language models (LLMs) and Evolutionary Computation (EC) has shown promising results for addressing optimization problems. It typically involves either iterative next-step solution seeking or directly prompting LLMs to generate critical optimization codes. However, these methods often suffer from low computational efficiency, high sensitivity to prompt design, and a lack of domain-specific knowledge. We introduce LLaMoCo, the first instruction-tuning framework designed to adapt LLMs for solving optimization problems in a code-to-code manner. LLaMoCo features a comprehensive instruction set that includes code-style problem descriptions as input prompts and robust optimization codes from expert EC optimizers as …

Generalized Visual Relation Detection With Diffusion Models, Kaifeng Gao, Siqi Chen, Hanwang Zhang, Jun Xiao, Yueting Zhuang, Qianru Sun

Research Collection School Of Computing and Information Systems

Visual relation detection (VRD) aims to identify relationships (or interactions) between object pairs in an image. Although recent VRD models have achieved impressive performance, they are all restricted to pre-defined relation categories, while failing to consider the semantic ambiguity characteristic of visual relations. Unlike objects, the appearance of visual relations is always subtle and can be described by multiple predicate words from different perspectives, e.g., “ride” can be depicted as “race” and “sit on”, from the sports and spatial position views, respectively. To this end, we propose to model visual relations as continuous embeddings, and design diffusion models to achieve …

Graduate Student Retention: Examining Why Master’S Students Leave And What Motivates Their Return In A Large Public University System, Sonja Prophete

Theses and Dissertations

Graduate student persistence is a relatively unexplored area in the literature of higher education studies; specifically, at a multi-institutional scale at the master's level. This research study examines the factors which cause students to discontinue their master's degrees, and what conditions could possibly support them returning to their program at a large urban public university system. The current study was guided by Hoyt and Winn's (2004) distinction between non-returning students, and Bean & Metzner's (1985) theoretical model of student attrition. A sequential mixed-methods study was conducted to examine the institutional and environmental influences on students' decision-making processes.

The quantitative data …

The Gendered Path Of Least Resistance: First Entry And Exit Behaviors Of Public And Nonprofit Employees, Tiana Marrese, Ying Liu, Femida Handy

Political Science Faculty Publications

Public and nonprofit organizations exhibit high rates of female employment often attributed to sector structures and social roles. To better understand how individual behaviors dynamically contribute to these distinctive ratios, we deconstruct public and nonprofit employment into gendered patterns of attraction and attachment. Using duration analysis and following a cohort from the National Longitudinal Survey of Youth 1997, this research finds that women demonstrate a higher attraction to their first public and nonprofit job compared to men, evidenced through a faster rate of entry into this employment. There are no significant gender differences when considering the duration of an individual's …