Digital Commons Network^™

Rethinking Large-Scale Phylogenomics With Eukphylo V.1.0, A Flexible Toolkit To Enable Phylogeny-Informed Data Curation And Analyses Of Diverse Eukaryotic Lineages, Laura A. Katz, Marie Leleu, Godwin Ani, Rebecca Gawron, Auden Cote-L'Heureux

Biological Sciences: Faculty Publications

Eukaryotic diversity is largely microbial, with macroscopic lineages (plants, animals, and fungi) nesting among a plethora of diverse protists. Our understanding of the evolutionary relationships among eukaryotes is rapidly advancing through ’omics analyses, but phylogenomic analyses are challenging for microeukaryotes, particularly uncultivable lineages, as single-cell sequencing approaches generate a mixture of sequences from hosts, associated microbiomes, and contaminants. Moreover, many analyses of eukaryotic gene families and phylogenies rely on boutique data sets and methods that are challenging for other research groups to replicate. To address these challenges, we present EukPhylo v.1.0, a modular, user-friendly pipeline that enables effective data curation …

Climate Change And Digital Nations: Harnessing The Metaverse To Perpetuate Small Island Statehood, Nicole Bessette

Villanova Environmental Law Journal (1991 - )

No abstract provided.

Office Of Research, Economic Engagement And Outreach Update, June 11, 2025, Office Of Research, Economic Engagement And Outreach

Office of Research, Economic Engagement and Outreach

No abstract provided.

Green Technologies For Isolating Bioactives From Plant-Based Food And Their Applications In Human Health And Longevity, Vibha Gajbe, Azza S. Naik, Roji Waghmare, Shuchi Midha

Research Outputs: 2025-Present

No abstract provided.

Modernism’S Mythic Mothers: Queering Motherhood Through Classical Matrilineage, Samantha Marie Lepak

Dissertations

I position this dissertation at the intersection of modern/contemporary literature, queer/feminist theory, and ancient Greek classics in the hopes of better understanding the spaces in which they meet, engaging with writers from the late modernist era to the present in order to highlight the connections between theories, themes, and practices of queerness from the modernists forward. Using the work of H.D. and writers following in her footsteps, I argue that exploring adaptations of Greek classics written primarily by female and gender-variant authors from the modernist era forward illuminates the extent to which the classics enables writers to “think queerly,” considering …

Anthropogenic Litter In Freshwater Ecosystems: Effect On Ecosystem Processes And Spatial Distribution, Emily Johnson

Master's Theses

The rapid increase of plastic production and disposal into the environment has resulted in anthropogenic litter (i.e., trash; AL) becoming a global problem. In aquatic ecosystems, macro- and microplastics are long-lived, mobile, and interact with the physical and chemical components of aquatic ecosystems. Our objectives were to: (1) assess the impact of microplastic pollution on the ecosystem processes of ecosystem metabolism and N2 flux in an oligotrophic lake and (2) to assess the abundance and assemblage of anthropogenic litter in a large urban river. For objective (1), we added microplastics at a range of concentrations to littoral mesocosms. Ecosystem metabolism …

Citrullinated Eno1 Vaccine Enhances Pd-1 Blockade In Mice Implanted With Murine Triple-Negative Breast Cancer Cells, Ricardo A León-Letelier, Alejandro M Sevillano-Mantas, Yihui Chen, Soyoung Park, Jody Vykoukal, Johannes F Fahrmann, Edwin J Ostrin, Candace Garrett, Rongzhang Dou, Yining Cai, Fu-Chung Hsiao, Jennifer B Dennison, Eduardo Vilar, Banu K Arun, Samir Hanash, Hiroyuki Katayama

Faculty, Staff and Student Publications

Background/Objectives:Cancer vaccine targets mostly include mutations and overexpressed proteins. However, cancer-associated post-translational modifications (PTMs) may also induce immune responses. Previously, our group established the enzyme protein arginine deiminase type-2 (PADI2), which catalyzes citrullination modification, is highly expressed in triple-negative breast cancer (TNBC), promoting antigenicity.

Methods: Here, we show the workflow of designing citrullinated enolase 1 (citENO1) vaccine peptides identified from breast cancer cells by mass spectrometry and demonstrate TNBC vaccine efficacy in the mouse model. Immunized mice with citENO1 peptides or the corresponding unmodified peptides, plus Poly I:C as an adjuvant, were orthotopically implanted with a TNBC murine …

Inactivation Of The Fusobacterium Nucleatum Rnf Complex Reduces Fada-Mediated Amyloid Formation And Tumor Development, Timmie A Britton, Ju Huck Lee, Chungyu Chang, Aadil H Bhat, Yi-Wei Chen, Rusul Mohammed Ali, Chenggang Wu, Asis Das, Hung Ton-That

Faculty, Staff and Student Publications

The Gram-negative anaerobe Fusobacterium nucleatum is an oral oncobacterium that promotes colorectal cancer (CRC) development with the amyloid-forming cell surface adhesin FadA integral to CRC tumorigenesis. We describe here molecular genetic studies uncovering a novel mode of metabolic regulation of FadA-mediated tumor formation by a highly conserved respiratory enzyme known as the Rnf complex. First, we show that genetic disruption of Rnf, via rnfC deletion, significantly reduces the level of fadA transcript, accompanied by a near-complete abolishment of the precursor form of FadA (pFadA), reduced assembly of FadA at the mature cell pole, and severe defects in the osmotic stress-induced …

Role Of Glucuronoxylomannan And Steryl Glucosides In Protecting Against Cryptococcosis, Gabriel Soares Matos, Tamara L Doering, Et Al.

2020-Current year OA Pubs

The development of vaccines for fungal diseases, including cryptococcosis, is an emergent line of research and development. In previous studies, we showed that a

Mapping Vascular Network Architecture In Primate Brain Using Ferumoxytol-Weighted Laminar Mri, Joonas A Autio, Ikko Kimura, Takayuki Ose, Yuki Matsumoto, Masahiro Ohno, Yuta Urushibata, Takuro Ikeda, Matthew F Glasser, David C Van Essen, Takuya Hayashi

2020-Current year OA Pubs

Mapping the vascular organization of the brain is of great importance across various domains of basic neuroimaging research, diagnostic radiology, and neurology. However, the intricate task of precisely mapping vasculature across brain regions and cortical layers presents formidable challenges, resulting in a limited understanding of neurometabolic factors influencing the brain's microvasculature. Addressing this gap, our study investigates whole-brain vascular volume using ferumoxytol-weighted laminar-resolution multi-echo gradient-echo imaging in macaque monkeys. We validate the results with published data for vascular densities and compare them with cytoarchitecture, neuron and synaptic densities. The ferumoxytol-induced change in transverse relaxation rate (ΔR

Plug And Coil Procedure For Management Of Large Postinfarct Ventricular Septal Defect, Hussam Al Hennawi, Sergio Flores, Michael Little, Lacy Harville, Ahmad Almomani, Muhammad Hammadah

Abington Jefferson Health Papers

Acute surgical mortality for postinfarction ventricular septal rupture remains alarmingly high at approximately 50%. In comparison, medical mortality is nearly 100% and likely exceeds historical levels because of the declining frequency of these acute surgeries, with many surgeons now performing fewer than 1 or 2 annually. Percutaneous device closure has become a feasible option for managing postinfarction ventricular septal defects in carefully selected patients. However, this technique may be associated with challenges such as significant residual shunting, delayed endothelialization, hemolysis, and extended hospital stays. Here, we present a novel approach using coil packing to enhance closure and reduce shunting.

Animal Well-Being, Sentience And The Rights Of Nature, Andrew N. Rowan

WellBeing News

The article highlights how acknowledging animal sentience supports the growing movement to grant legal rights to nature. This shift encourages a more compassionate and sustainable relationship between humans, animals, and the environment.

U.S. Animal Shelter Demographics: Trends & Issues, Andrew N. Rowan

WellBeing News

This article reviews key trends in U.S. animal sheltering, including major declines in euthanasia and intake. It also highlights ongoing issues like regional disparities and resource gaps that impact shelter operations.

Effect Of Post-Operative Clothing, Bandage, And Collar Application On Stress After Ovariohysterectomy In Cats, Çağatay Esin, Seba Raouf, Gülşah Saral, Büşra Uzun

The Thai Journal of Veterinary Medicine

Ovariohysterectomy is a common surgical procedure in veterinary medicine, not only for reproductive control but also for conditions like pyometra, metritis, mammary tumors, and other reproductive disorders. Pain in cats occurs as a response of the body and is accompanied by various physiological and behavioral changes. Pain in cats, though prevalent, is often under-recognized and inadequately treated. The Glasgow pain scale is a psychometrically designed tool for assessing acute pain in veterinary patients. Serotonin (5-HT), a biogenic monoamine derived from tryptophan, functions as a mood-regulating neurotransmitter and may decrease following surgical interventions. This study aimed to evaluate post-operative pain and …

On The Concepts Of Culture, Education, And Language, Augusto Boal

Spect-actor: A Journal of Pedagogy & Theatre of the Oppressed

No abstract provided.

On The Concepts Of Modern And Archaic, Augusto Boal

Spect-actor: A Journal of Pedagogy & Theatre of the Oppressed

No abstract provided.

What's So Funny About Theatre Of The Oppressed?, Jennifer Schaupp

Spect-actor: A Journal of Pedagogy & Theatre of the Oppressed

This article examines my 2023 Pedagogy and Theatre of the Oppressed Conference virtual workshop within the framework of comedy and embodiment. It considers the activities I facilitated and their origins along with my perception of participant reaction for other educators and facilitators to adapt for their own educational experiences.

Roles Of Nigerian Ulama In Politics And Nation-Building: The Controversy, Achievements And Recommendations, Abdulkadir Salaudeen, Saidu Ahmad Dukawa

Future Journal of Social Science

Religion and politics in Islam are not watertight compartments. In Islam, it is impossible to separate the state from religion because Islam is a state in the political sense and a religion in the spiritual sense. It is true that state-religion-separation is the norm in the secularist West. It is not true in Islam where state and Islam are indivisibly connected. Despite the interconnectedness between Islam and politics, a lot of people see participation of ulama in politics as an abomination due to the current of apolitical Islam that is sweeping across the circle of ulama. Focusing on Nigeria, this …

The Paper King, Eric A. Keldani

Night Flight: Online Literary Journal

No abstract provided.

Collection Of Poetry By Me, Joseph K. Pearson

Night Flight: Online Literary Journal

No abstract provided.

Incidence Of Scabies Among Patients Attending Al-Faihaa Educational Hospital In Basra Province / Iraq., Sarah Kamal Naser

Maaen Journal for Medical Sciences

Background: In 2017, scabies was officially classified as a neglected tropical illness by the World Health Organization (WHO), in an attempt to raise awareness and support initiatives to eradicate it. Additionally, the WHO's strategy for neglected tropical diseases 2021-2030 has recently included scabie, intended to prevent the Sustainable Development Goals from being neglected, in recent years, scabies appears to have grown widespread in Iraq most likely as a result of the country's densely populated areas and high levels of interpersonal interaction, this study fills crucial gaps and offers nuanced insights into the prevalence of scabies in Basra prevalence, the cross-sectional …

Oms 4 Early List Of Papers, Tim Lenz

OMS Early List of Papers

The June 10th list for OMS 4, compiled by Tim Lenz.

Navigating The Convergence Of Global Competitiveness And Sustainable Development: A Multi-Level Analysis, Arman Canatay, Leonel Prieto, Muhammad Ruhul Amin

Business Administration Faculty Research

Sustainable Development (SD) involves multiple factors and different perspectives that are critical to individuals, organizations, regions, countries, and the world. Even though relationships among Global Competitiveness, the Macroeconomic Environment, and SD dimensions, encompassing 17 Sustainable Development Goals (SDGs), are critical, for national and global policymaking, many of these relationships have not been studied systematically nor at different aggregation levels. Therefore, this study examines the relationships among the Global Competitiveness pillars (e.g., Institutions, Infrastructure, Education, Technology, Business Sophistication, and Innovation) and the Macroeconomic Environment and the SD dimensions (Social, Economic, and Environmental) using various models. Additionally, this study examined three country …

Variable Natural Language Translator For Video Games, Gabriel Bernini, Cole Propach

Computer Science and Engineering Senior Theses

In the field of video games, developers work to immerse players in a variety of ways. In one genre of video games, 2D exploration, or Metroidvania as its colloquially known, developers try to immerse players by letting them explore large worlds with the hope to overcome isolation. Often these worlds are sparse or dead worlds where the player is alone, but by exploring more of the world familiarity with the space is achieved and this isolation can be overcome. We hope to innovate in this genre by utilizing a new way to simulate and overcome this isolation, through language learning. …

Neural Engineering In Action: Exploring Muscle Movement Through Data And Design, Dr. Ashwin Mohan, Dr. Sowmya Anjur, Mrs. Namrata Pandya, Matthew Stroud, Dr. David Bergin Emeritus, Dr. Satish Nair

2025

No abstract provided.

High-Salt Tumor Microenvironment: Not As Bad As It Sounds, Not As Good As It Seems, Umer Ali, Venkataswarup Tiriveedhi

Biology Faculty Research

Recent evidence suggests a high-sodium microenvironment in breast tumors. However, the exact role of this high-sodium microenvironment on tumorigenesis is unknown. Salt (sodium chloride, NaCl) is a well-known inflammatory molecule playing a significant role in various chronic ailments like cardiovascular and autoimmune diseases. Importantly, chronic inflammation is recognized as one of the major hallmarks of carcinogenesis. Breast cancer cell culture-based studies demonstrated that high-salt (HS) treatment (Δ35–50 mM NaCl) induced cancer cell proliferation. However, preclinical murine research showed reduced tumor progression kinetics in mice fed a short-term HS diet (4% NaCl diet, 0–2 weeks prior to the injection of tumor …

Human Gut Commensal Alistipes Timonensis Modulates The Host Lipidome And Delivers Anti-Inflammatory Outer Membrane Vesicles To Suppress Colitis In An Il10-Deficient Mouse Model, Ethan Older, Mary K. Mitchell, Andrew Campbell, Xiaoying Lian, Michael Madden, Yuzhen Wang, Lauren E. Van De Wal, Thelma Zaw, Brandon N. Vanderveen, Rodney Tatum, E. Angela Murphy, Yan-Hua Chen, Daping Fang, Melissa Ellermann, Jie Li

Faculty Publications

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the …

Legal Geographies Of Mapuche-Williche Ancestral Waters: Real Estate Development And Contested Jurisdiction In Riparian Areas, Adamari Benavidez

Geography Undergraduate Senior Theses

In the Wallmapu (ancestral Mapuche territory) of southern Chile, river and lakefront real estate development is often promoted by state institutions and developers as conservation or eco-tourism. However, these inmobiliaria projects are part of a longer trajectory of settler colonial jurisdiction, historically materialized through the dispossession of Mapuche-Williche territory. In the Maihue–Ranco subwatershed, this encroaching development are sparking increasing conflict with Mapuche-Williche lof (community), as developers and residents engage in extralegal practices—diverting waterways, denying access to lakefronts, surveilling mobility—that are fundamentally incompatible with Mapuche territorial order (Azmapu).

In this thesis I ask: (i) What spatial and legal strategies …

Ocean Acidification Decreases Molting But Not Survival Of Antarctic Amphipods Djerboa Furcipes, Gondogeneia Antarctica, And Prostebbingia Gracilis, Hannah E. Oswalt, Margaret O. Amsler, Charles D. Amsler, Julie Schram, James B. Mclintock, Paul A. Baker

Faculty, Staff, and Students

Ocean acidification refers to a decrease in the pH of the world’s oceans from the oceanic uptake of human-derived atmospheric CO2. Low pH is known to decrease the calcification and survival of many calcifying invertebrates. Shallow, hard bottom communities along the Western Antarctic Peninsula often have incredibly large numbers of invertebrate mesograzers that shelter on and are mutualists with the dominant brown macroalgae. The common amphipod species Djerboa furcipes, Gondogeneia antarctica, and Prostebbingia gracilis were collected from the immediate vicinity of Palmer Station, Antarctica (64°46′S, 64°03′W) in January–February 2023 and maintained under three different pH treatments simulating ambient conditions (approximately …

Redeeming The Amazon: Development Discourses And Imaginaries In Manaus, Brazil, Beatriz Da Silva Falcao

Geography Undergraduate Senior Theses

In 1957, the Brazilian government approved Law No.1310, establishing a free port in the city of Manaus, the capital of the state of Amazonas. Politicians at the time argued that such a project was essential to help mitigate the unfortunate economic circumstances the state faced due to its geographical isolation. Ten years later, the military dictatorship that ruled Brazil expanded that mission through Decree No.288, thus creating what is now known as the Zona Franca de Manaus (ZFM, Free Trade Zone, or FTZ), an area with a series of fiscal incentives to foment industrialization in the Amazon region. The Zona …