Digital Commons Network^™

January 15, 2025, Faculty, Illinois Wesleyan University

2024-2025

No abstract provided.

Active Learning Of Enhancers And Silencers In The Developing Neural Retina, Ryan Z Friedman, Avinash Ramu, Sara Lichtarge, Yawei Wu, Lloyd Tripp, Daniel Lyon, Connie A Myers, David M Granas, Maria Gause, Joseph C Corbo, Barak A Cohen, Michael A White

2020-Current year OA Pubs

Deep learning is a promising strategy for modeling cis-regulatory elements. However, models trained on genomic sequences often fail to explain why the same transcription factor can activate or repress transcription in different contexts. To address this limitation, we developed an active learning approach to train models that distinguish between enhancers and silencers composed of binding sites for the photoreceptor transcription factor cone-rod homeobox (CRX). After training the model on nearly all bound CRX sites from the genome, we coupled synthetic biology with uncertainty sampling to generate additional rounds of informative training data. This allowed us to iteratively train models on …

Foxr2 Targets Lhx6+/Dlx+ Neural Lineages To Drive Central Nervous System Neuroblastoma, Selin Jessa, Antonella De Cola, Bhavyaa Chandarana, Michael Mcnicholas, Steven Hébert, Adam Ptack, Damien Faury, Jessica W Tsai, Andrey Korshunov, Timothy N Phoenix, Benjamin Ellezam, David T W Jones, Michael D Taylor, Pratiti Bandopadhayay, Manav Pathania, Nada Jabado, Claudia L Kleinman

Faculty, Staff and Students Publications

Central nervous system neuroblastoma with forkhead box R2 (FOXR2) activation (NB-FOXR2) is a high-grade tumor of the brain hemispheres and a newly identified molecular entity. Tumors express dual neuronal and glial markers, leading to frequent misdiagnoses, and limited information exists on the role of FOXR2 in their genesis. To identify their cellular origins, we profiled the transcriptomes of NB-FOXR2 tumors at the bulk and single-cell levels and integrated these profiles with large single-cell references of the normal brain. NB-FOXR2 tumors mapped to LHX6+/DLX+ lineages derived from the medial ganglionic eminence, a progenitor domain in the ventral telencephalon. In vivo prenatal …

Dna Methylation Profile In Buffy Coat Identifies Methylation Differences Between Cirrhosis With And Without Hepatocellular Carcinoma, Hyeyeun Lim, Hashem B El-Serag, Michelle Luster, Megan L Grove, Jinyoung Byun, Yuri Jung, Younghun Han, Eric Boerwinkle, Christopher I Amos, Aaron P Thrift

Faculty, Staff and Students Publications

Background/Objectives: Cirrhosis is the precursor to most cases of hepatocellular carcinoma (HCC). Understanding the mechanisms leading to the transition from cirrhosis to HCC and identifying key biomarkers is crucial to developing effective screening strategies and reducing HCC-related mortality. DNA methylation is associated with gene inactivation and plays an important role in physiological and pathological processes; however, its role in cirrhosis progression to HCC is unknown.

Methods: We performed genome-wide DNA methylation profiling using Illumina Infinium MethylationEPI BeadChip in pre-diagnostic samples from 22 cirrhosis patients who subsequently developed HCC and 22 cirrhosis patients who remained HCC-free during an average 4-year follow-up. …

Communication And Successful Aging: Challenging The Dominant Cultural Narrative Of Decline, Jennifer E. Ohs, Jill Yamasaki

Communication Research Trends

No abstract provided.

Communicating Aggression, Paola Pascual-Ferrá

Communication Research Trends

No abstract provided.

Rural Devotion, Emma Johnson

Diamond Line Undergraduate Literary Magazine

No abstract provided.

Understanding Consumer Perception And Behavior Toward Biodegradable Plastic Products Based On The Moa Model, Nayeon Baek, Hyemi Lee

Asia Marketing Journal

This study investigated the factors influencing consumers' switching intentions to biodegradable plastic products. Applying a modified Motivation-Opportunity-Ability (MOA) framework, we analyzed the impact of factors such as environmental concern, novelty seeking, negative attitude, perceived consumer effectiveness, green consumer availability, and environmental knowledge on switching intention, while also examining the moderating effect of perceived greenwashing. Results showed that environmental concern, perceived consumer effectiveness, and negative attitude from the motivation dimension, and environmental knowledge from the ability dimension, had significant effects on switching intentions. Furthermore, it was found that the level of perceived greenwashing moderated the effects of environmental concern, perceived consumer …

Ferrate(Vi) Transformation Of Nitrogen In Secondary Wastewater Effluent: Implications For Water And Nutrient Management, Qiufeng Lin, Zepei Tang, Hussein I. Abdel Shafy, Yang Deng

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Ferrate(VI) is a promising chemical agent for wastewater treatment. While targeting various contaminants, it can inevitably react with different water matrix constituents such as nitrogen (N) species. However, the reactions of ferrate(VI) with wastewater N compounds remain poorly understood. This study explores ferrate(VI)-mediated transformations of different N species in a secondary wastewater effluent. Ferrate(VI) oxidation minimally abated total dissolved nitrogen (TDN), while oxidizing dissolved organic nitrogen (DON) into dissolved inorganic nitrogen (DIN), primarily nitrate nitrogen (NO3--N), without noticeably altering ammonia nitrogen (NH3-N) levels. Consequently, ferrate(VI) treatment increased the fraction of bioavailable, soil-leachable NO3--N while lowering the portion of less bioaccessible …

Introducing "Identification Probability" For Automated And Transferable Assessment Of Metabolite Identification Confidence In Metabolomics And Related Studies., Thomas O Metz, Christine H Chang, Vasuk Gautam, Afia Anjum, Siyang Tian, Fei Wang, Sean M Colby, Jamie R Nunez, Madison R Blumer, Arthur S Edison, Oliver Fiehn, Dean P Jones, Shuzhao Li, Edward T Morgan, Gary J Patti, Dylan H Ross, Madelyn R Shapiro, Antony J Williams, David S Wishart

Faculty Research 2025

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate …

University Of Dayton Awarded $660k For Choose Ohio First Scholarships, University Of Dayton

News Releases

The Choose Ohio First program awarded the University of Dayton nearly $660,000 to recruit and graduate students in science, technology, engineering and math (STEM) fields.

Sensitive And Robust Biosensing Using Plasmonic Enhancement Of Fluorescence By Rapid Thermal Annealed Silver Nanostructures, Shuangming Li, Venkat R. Bhethanabotla

USF Patents

Chips and metallic nanostructure biosensors comprising a dielectric substrate and discontinuous and disordered metallic nanostructures of flat island shapes thereon are disclosed herein. Also disclosed are methods of making and using the same.

Drug For Treating Tinnitus, Joseph P. Walton, Luisa Lynn Scott

USF Patents

Compounds, pharmaceutical compositions, and methods for treating tinnitus in a subject in need thereof. The methods include administering a therapeutically effective amount of a compound having a structure represented by Formula I as described herein. The compounds and compositions are administered transdermally or orally, preferably via a sustained release mechanism. The compounds and compositions reduce at least one behavioral correlate of tinnitus and/or at least one neurophysiological correlate of tinnitus. The compounds and compositions reduce hyperactivity in the auditory system.

Methods For Optimizing A Transmittance And/Or A Self-Cleaning Property Of A Substrate Using A Self-Cleaning Coating, Dharendra Yogi Goswami, Mohammed Khaleel M. Alhussain

USF Patents

Described herein relates to methods for optimizing a transmittance and/or a self-cleaning property of a substrate using a self-cleaning coating. As such, the substrate may be treated using a photocatalytic reaction of titanium dioxide (hereinafter “TiO2”)-based solution via a light treatment. The substrate may be treated using a combination including but not limited to wet chemicals, dry-cleaning, and/or mechanical polishing. Additionally, the substrate may then be overlayed with a self-cleaning coating, such that the transmittance and the self-cleaning properties of the substrate may be optimized. Furthermore, the methods for optimizing the transmittance and/or the self-cleaning functionality of the substrate may …

Gotta Take My Avatar Shopping: Impacts Of Interactive Virtual Shopping In Esport, Yongjin Hwang, Keshav Gupta

Faculty Publications

Purpose

Esports game developers are incorporating interactive virtual shopping (IVS) experiences into their products to facilitate consumer–brand interactions. Despite the potential influence of IVS, existing research lacks an understanding of its impact on consumers’ overall affect– particularly game enjoyment, a critical factor in sustaining engagement with esports products – and on attitudinal change toward brands in the real world.

Design/methodology/approach

An experiment was designed to examine the impact of shopping in the virtually interactive esports marketplace on game enjoyment. Mediating effects of positive change in brand attitude, perceived realism and character attachment and the moderating effect of self-avatar gender congruity …

Usage Statistics: Project Counter R5 Tr_J1 Report Fy2024 - Journal Requests (Excluding Oa_Gold) By Title, Andrée J. Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report TR_J1 for the University of Rhode Island for the period from July 1, 2023 - June 30, 2024. The TR_J1 report is defined as "Journal Requests (Excluding OA_Gold)." This report presents an annual total only and only includes those platforms successfully configured for automated harvesting via SUSHI.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

Total Item Requests - 805,131

Unique Item Requests - 602,267

Usage Statistics: Project Counter R5 Dr_D1 Report Fy2024 - Database Search And Item Usage, Andrée J. Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report DR_D1 for the University of Rhode Island for the period from July 1, 2023 - June 30, 2024. The DR_D1 report is defined as "Database Search and Item Usage." This report presents an annual total only and only includes those platforms successfully configured for automated harvesting via SUSHI.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

Searches Automated - 30,626

Searches Federated - 918

Searches Regular - 1,049,169

Total Item Investigations - 554,019

Total Item Requests - 235,329

Usage Statistics: Project Counter R5 Tr_B1 Report Fy2024 - Book Requests (Excluding Oa_Gold) By Title, Andrée J. Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report TR_B1 for the University of Rhode Island for the period from July 1, 2023 - June 30, 2024. The TR_B1 report is defined as "Book Requests (Excluding OA_Gold)." This report presents an annual total only and only includes those platforms successfully configured for automated harvesting via SUSHI.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

Total Item Requests - 130,532

Unique Title Requests - 54,592

Venoms And Extracellular Vesicles: A New Frontier In Venom Biology, Auwal A. Bala, Naoual Oukkache, Elda E. Sánchez, Montamas Suntravat, Jacob Galan

School of Medicine Publications

Extracellular vesicles (EVs) are nanoparticle-sized vesicles secreted by nearly all cell types under normal physiological conditions. In toxicological research, EVs have emerged as a crucial link between public health and multi-omics approaches, offering insights into cellular responses to disease-causing injury agents such as environmental and biological toxins, contaminants, and drugs. Notably, EVs present a unique opportunity to deepen our understanding of the pathophysiology of envenomation by natural toxins. Recent advancements in isolating and purifying EV cargo, mass spectrometry techniques, and bioinformatics have positioned EVs as potential biomarkers that could elucidate biological signaling pathways and provide valuable information on the relationship …

Cardiometabolic Multimorbidity And Dementia Onset Among Middle-Aged And Older Adults: Differences By Race/Ethnicity., Siting Chen, Ana R. Quiñones, Corey L. Nagel, Nicholas J. Bishop, Heather G. Allore, Jason T. Newsom, Jeffrey Kaye, Anda Botoseneanu

Psychology Faculty Publications and Presentations

Racial/ethnic minoritized groups in the U.S. have higher prevalence of cardiometabolic multimorbidity and experience higher risk of dementia. This study evaluates the relationship between cardiometabolic multimorbidity and dementia onset according to racial/ethnic group in a nationally representative cohort of U.S. middle-aged and older adults.

Professor Franklin's Annotated Bibliography Of Young Adult Literature, 2023-24, John Franklin

Open Educational Resources - English and Modern Languages

Designed to be a useful, time-saving source of primary reading material, Professor Franklin’s Annotated Bibliography of Young Adult Literature, 2023—24 includes his notes and reading recommendations for 218 authors, editors and illustrators; 209 titles; and 60,638 pages of reading.

Pathogenesis, Diagnosis, And Examination Of Corynebacterium Diphtheriae, Ika Ningsih, Muhammad Iqbal Safrullah

Indonesian Journal of Medical Chemistry and Bioinformatics

Corynebacterium diphtheriae is a rod-shaped bacterium, Gram-positive (purple), growth requires the presence of oxygen or can live with oxygen or without oxygen, nonmotile, non-capsular, non-sporing, catalase positive. Most species ferment carbohydrates such as fructose, galactose, glucose, maltose, and mannose and produce an exotoxin called diphtheria toxin (DT) which can cause diphtheria, a respiratory infection characterized by sore throat and the production of a thick layer / gray pseudomembrane and generally affects children aged 15 years and under and is very vulnerable in people who are not immunized and in low immune systems. Diphtheria is a dangerous and life-threatening disease if …

Spatial Distribution Of Tumor Cells In Clear Cell Renal Cell Carcinoma Is Associated With Metastasis And A Matrisome Gene Expression Signature, Prahlad Bhat, Pheroze Tamboli, Kanishka Sircar, Kasthuri Kannan

Faculty, Staff and Student Publications

Background/Objectives: Predicting the behavior of clear cell renal cell carcinoma (ccRCC) is challenging using standard-of-care histopathologic examination. Indeed, pathologic RCC tumor grading, based on nuclear morphology, performs poorly in predicting outcomes of patients with International Society of Urological Pathology/World Health Organization grade 2 and 3 tumors, which account for most ccRCCs.

Methods: We applied spatial point process modeling of H&E-stained images of patients with grade 2 and grade 3 ccRCCs (n = 72) to find optimum separation into two groups.

Results: One group was associated with greater spatial randomness and clinical metastasis (p < 0.01). Notably, spatial analysis outperformed standard pathologic grading in predicting clinical metastasis. Moreover, cell-to-cell interaction distances in the metastasis-associated group were significantly greater than those in the other patient group and were also greater than expected by the random distribution of cells. Differential gene expression between the two spatially defined groups of patients revealed a matrisome signature, consistent with the extracellular matrix's crucial role in tumor invasion. The top differentially expressed genes (with a fold change > 3) stratified a larger, multi-institutional …

Anti-Ctla-4 Generates Greater Memory Response Than Anti-Pd-1 Via Tcf-1, Stephen Mok, Huey Liu, Didem Ağaç Çobanoğlu, Nana-Ama A S Anang, James J Mancuso, E John Wherry, James P Allison

Faculty, Staff and Student Publications

The effects of T cell differentiation arising from immune checkpoint inhibition targeting cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) on the immunological memory response remain unclear. Our investigation into the effects of anti-CTLA-4 and anti-PD-1 on memory T cell formation in mice reveals that memory T cells generated by anti-CTLA-4 exhibit greater expansion, cytokine production, and antitumor activity than those from anti-PD-1. Notably, anti-CTLA-4 preserves more T cell factor-1 (TCF-1)+ T cells during priming, while anti-PD-1 leads to more thymocyte selection-associated high mobility group box (TOX)+ T cells. Experiments using conditional

The Southwest Climate Adaptation Science Center (Sw Casc), Michelle Baker

Funded Research Records

No abstract provided.

A Framework For A Sustainable Archaeology Field School In South Florida, Alanna L. Lecher, Katharine G. Napora, Sara Ayers-Rigsby, Malachi Fenn, Melissa Lehman, Peter De Witt, John Sullivan

Faculty and Staff Publications & Presentations

Entry into the profession of archaeology generally requires the completion of an archaeological field school, which teaches proper field, laboratory, and curation methodologies. Archaeology as a discipline has been making strides towards integrating cross-disciplinary methods to increase the depth and breadth of the subject and enhancing inclusivity. These efforts have been mirrored in the approaches of some archaeological field schools, but not necessarily in a systematic fashion. This paper presents a cohesive framework for an archaeological field school that integrates cross-disciplinary training and inclusivity by model of the United Nations Sustainable Development Goals (UN SDGs), specifically SDGs 11: Sustainable Cities …

A Pilot And Feasibility Study Investigating The Abundance And Activity Of Nitrate-Reducing Bacteria In Women With Pre-Eclampsia, Lisa Du Toit, Ifeoma Offiah, Alvaro Redondo-Rio, Tanya Kahawita, Michele Kiernan, Yen Ming Lin, Louise A. Belfield, Gemma Montagut, Alicia Benavente, Tomas Nicholas, Amazon Doble, Renske Dikkers, Robert Freeman, Toni Gabaldón, Zoe Brookes, Raul Bescos Garcia

Peninsula Dental School

BackgroundOral health may influence blood pressure control by modulating the abundance and activity of nitrate-reducing bacteria, which are essential for enhancing nitrite and nitric oxide (NO) bioavailability. This study aimed to investigate the oral health and microbiome composition of women with pre-eclampsia (PET) compared to healthy controls (CN).MethodsTen PET and eleven CN women participated in this study, respectively. An oral health examination was conducted in all the participants. Saliva and blood samples were collected for analysis of the oral microbiome and NO biomarkers.ResultsHigher plaque levels were observed in the PET group compared to the CN group (P = 0.038). The …

Fostering Undergraduate Research A Practice-Based Approach, Muireann Okeeffe, Tim Kovar, Robert Tully, Ruth Harris, Sue Norton, Emma Obrien, Deirdre Mcgrath Mcgrath, Rachelle O'Brien, Evin Mccarthy, Liam Mcglynn, Ceri Almrott, Connell Vaughan, Aija Freimane, Con Kennedy, Jesús Urda, Pearl O’Rourke, Clare Bell, Deirdre Kennedy, Sinead Mcdonald, Robbie O Connor

Compendium

This Compendium has its origins in the Undergraduate Practice-Based Research Community of Practice (CoP) established as an outcome to a Faculty of Arts & Humanities Teaching and Learning symposium that highlighted the importance of practice-based learning, including research, at undergraduate level.

The examples in this Compendium describe research that is focused on active-learning goals that help in creating a richer learning experience for students, assisting them to become more capable and effective learners across a range of disciplines in the Arts and Humanities.

Thirteen cross-disciplinary case studies are presented in this compendium that seek to both contribute to this …

Impaired Hydrogen Sulfide Biosynthesis Underlies Eccentric Contraction-Induced Force Loss In Dystrophin-Deficient Skeletal Muscle, W Michael Southern, Erynn E Johnson, Elizabeth K Fasbender, Katherine S Fallon, Courtney L Cavazos, Dawn A Lowe, George G Rodney, James M Ervasti

Faculty, Staff and Students Publications

Eccentric contraction-induced (ECC-induced) force loss is a hallmark of murine dystrophin-deficient (mdx) skeletal muscle that is used to assess efficacy of potential therapies for Duchenne muscular dystrophy. While virtually all key proteins involved in muscle contraction have been implicated in ECC force loss, a unifying mechanism that orchestrates force loss across such diverse molecular targets has not been identified. We showed that correcting defective hydrogen sulfide (H2S) signaling in mdx muscle prevented ECC force loss. We also showed that the cysteine proteome of skeletal muscle functioned as a redox buffer in WT and mdx muscle during ECCs, but that buffer …

The Effectiveness Of Augmented Reality Technology (Metaverse) On Mathematics Achievement Among Students With Learning Difficulties, Somaia Al-Nawaiseh

Jordan Journal of Applied Science-Humanities Series

The study aimed to assess the effectiveness of using augmented reality (Metaverse) technology on the academic achievement in mathematics among fifth-grade students with learning difficulties in the Southern Al-Mazar district. An experimental approach was employed, utilizing an application based on augmented reality to teach a mathematics unit, along with an achievement test to evaluate the treatment's effects. A purposive sample of 60 male and female students with learning difficulties was used. After implementing the measurement tools during the academic year 2022/2023, where validity and reliability were verified through appropriate methods, statistically significant differences were observed between the means of the …