Digital Commons Network^™

Systematic Analysis Of Nonsense Variants Uncovers Peptide Release Rate As A Novel Modifier Of Nonsense-Mediated Mrna Decay, Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortázar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Zeynep H Coban-Akdemir, Sujatha Jagannathan

Faculty, Staff and Student Publications

The phenotypic impact of nonsense variants is determined by nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). Despite the clinical importance of nonsense variants, transcript-specific and context-dependent variations in NMD activity remain poorly understood. Here, we show that the amino acid preceding the PTC strongly influences NMD activity. Glycine codons promote robust NMD efficiency and show striking enrichment before PTCs but are depleted before normal termination codons. Glycine-PTC enrichment is particularly pronounced in genes tolerant to loss-of-function variants, suggesting efficient elimination of truncated proteins from nonessential genes. We further demonstrate that the peptide release rate during …

Wdr2 Regulates The Orphan Kinesin Kin-G To Promote Hook Complex And Golgi Biogenesis In Trypanosoma Brucei, Qing Zhou, Huiqing Hu, Ziyin Li

Faculty, Staff and Student Publications

The flagellum in Trypanosoma brucei plays crucial roles in cell locomotion, cell morphogenesis, and cell division, and its inheritance depends on the faithful duplication of multiple flagellum-associated structures. One of such cytoskeletal structures is a hairpin-like structure termed the hook complex, composed of a fishhook-like structure and a centrin arm structure, whose cellular functions remain poorly understood. We recently identified KIN-G, an orphan kinesin that promotes hook complex and Golgi biogenesis. Here we report a WD40 repeat-containing protein named WD40 Repeat-containing protein 2 (WDR2), which interacts with and regulates KIN-G. WDR2 co-localizes with KIN-G at the centrin arm, and knockdown …

From Novice To Expert: Preparing Your Peer Review, Diana M Proctor, Rachy Abraham, Shannon Esher Righi

Faculty, Staff and Student Publications

Peer review is the process by which the quality of scholarly work is assessed prior to being published, presented, or funded. The consequences of flawed research entering the public domain in the "post-truth" era highlight the need to improve peer review quality, which we believe can be achieved by standardizing training. Here, we aim to enhance the quality of published literature by presenting a systematic guide to train new reviewers (and aid experienced ones) in the art of peer reviewing the rigor of scientific manuscripts.

Computational And Imaging Approaches For Precision Characterization Of Bone, Cartilage, And Synovial Biomolecules., Rahul Kumar, Kyle Sporn, Vibhav Prabhakar, Ahab Alnemri, Akshay Khanna, Phani Paladugu, Chirag Gowda, Louis Clarkson, Nasif Zaman, Alireza Tavakkoli

Department of Medicine Faculty Papers

Abstract

Background/Objectives: Degenerative joint diseases (DJDs) involve intricate molecular disruptions within bone, cartilage, and synovial tissues, often preceding overt radiographic changes. These tissues exhibit complex biomolecular architectures and their degeneration leads to microstructural disorganization and inflammation that are challenging to detect with conventional imaging techniques. This review aims to synthesize recent advances in imaging, computational modeling, and sequencing technologies that enable high-resolution, non-invasive characterization of joint tissue health. Methods: We examined advanced modalities including high-resolution MRI (e.g., T1ρ, sodium MRI), quantitative and dual-energy CT (qCT, DECT), and ultrasound elastography, integrating them with radiomics, deep learning, and multi-scale modeling approaches. We …

Intracranial Directed Connectivity Links Subregions Of The Prefrontal Cortex To Major Depression, John Myers, Jiayang Xiao, Raissa K Mathura, Ben Shofty, Victoria Gates, Joshua Adkinson, Anusha B Allawala, Adrish Anand, Ron Gadot, Ricardo Najera, Hernan G Rey, Sanjay J Mathew, Kelly Bijanki, Garrett Banks, Andrew Watrous, Eleonora Bartoli, Sarah R Heilbronner, Nicole Provenza, Wayne K Goodman, Nader Pouratian, Benjamin Y Hayden, Sameer A Sheth

Staff and Researcher Publications

Research on the neural basis of major depressive disorder suggests that it is fundamentally a disease of cortical disinhibition, where breakdowns of inhibitory neuronal systems lead to diminished emotion regulation and intrusive rumination. Subregions of the prefrontal cortex are thought to be sources of this disinhibition. However, due to limited opportunities for intracranial recordings from humans with major depression, this hypothesis has not been directly tested. Here, we use intracranial recordings from the dorsolateral prefrontal, orbitofrontal, and anterior cingulate cortices from patients with major depression to measure daily fluctuations in self-reported depression symptom severity. Results indicate that directed connectivity within …

Single-Cell Profiling Of Bone Metastasis Ecosystems From Multiple Cancer Types Reveals Convergent And Divergent Mechanisms Of Bone Colonization, Fengshuo Liu, Yunfeng Ding, Zhan Xu, Xiaoxin Hao, Tianhong Pan, George Miles, Siyue Wang, Yi-Hsuan Wu, Jun Liu, Igor L Bado, Weijie Zhang, Ling Wu, Yang Gao, Liqun Yu, David G Edwards, Hilda L Chan, Sergio Aguirre, Michael Warren Dieffenbach, Elina Chen, Yichao Shen, Dane Hoffman, Luis Becerra Dominguez, Charlotte Helena Rivas, Xiang Chen, Hai Wang, Zbigniew Gugala, Robert L Satcher, Xiang H-F Zhang

Faculty, Staff and Students Publications

Bone is a common site for metastasis of solid cancers. The diversity of histological and molecular characteristics of bone metastases (BMs) remains poorly studied. Here, we performed single-cell RNA sequencing on 42 BMs from eight cancer types, identifying three distinct ecosystem archetypes, each characterized by an enrichment of specific immune cells: macrophages/osteoclasts, regulatory/exhausted T cells, or monocytes. We validated these archetypes by immunostaining on tissue sections and bioinformatic analysis of bulk RNA sequencing/microarray data from 158 BMs across more than 10 cancer types. Interestingly, we found only a modest correlation between the BM archetypes and the tissues of origin; BMs …

Inferring Chromosome Segregation Error Stage And Crossover In Trisomic Disorders With Application To Down Syndrome, Zhenhua Li, Wenjian Yang, Gang Wu, Ti-Cheng Chang, Zhongshan Cheng, Meenakshi Devidas, Mary Shago, Andrew J Carroll, Nyla A Heerema, Julie M Gastier-Foster, Brent L Wood, Lauren Sanclemente, Elizabeth A Raetz, Stephen P Hunger, Mignon L Loh, Eleanor Feingold, Tracie C Rosser, Emily G Allen, Stephanie L Sherman, Karen R Rabin, Philip J Lupo, Jun J Yang

Faculty, Staff and Students Publications

Errors in chromosome segregation during gametogenesis, such as nondisjunction (NDJ) errors, have severe consequences in human reproduction, and a better understanding of their etiology is of fundamental interest in genetics. Mapping NDJ errors to meiotic/mitotic stages typically requires proband-parent comparison, limiting its applicability. Herein, we develop Mis-segregation Error Identification through Hidden Markov Models (MeiHMM), a method for inferring NDJ error stage and crossover events based on only genomic data of trisomic probands. Guided by triallelic genotype/haplotype configurations, MeiHMM discerns the allelic origin at each locus, which informs NDJ error during gamete formation, without identifying the parental origin of the trisomy. …

Genome Report: Whole-Genome Assembly Of The Relapsing Fever Tick Ornithodoros Turicata Dugès (Acari: Argasidae), Mackenzie Tietjen, Amanda R Stahlke, David Luecke, Perot Saelao, Sheina B Sim, Scott M Geib, Brian E Scheffler, Anna K Childers, Alexander R Kneubehl, Pete D Teel, Job E Lopez

Faculty, Staff and Students Publications

The soft tick family Argasidae contains vectors of medical and veterinary importance, but few molecular resources are available compared to hard ticks (Ixodidae). One example is Ornithodoros turicata, a recognized vector of Borrelia turicatae, causal agent of human relapsing fever, and a putative vector of African swine fever virus. To address the current lack of molecular resources for the Argasidae, we generated a chromosome-level genome assembly for O. turicata using PacBio sequencing in conjunction with an Illumina Hi-C library. The resulting reference genome has a total of 1.1 Gb in length and was assembled into 10 chromosomes and 368 unplaced …

Distinct Systemic Impacts Of Aβ42 And Tau Revealed By Whole-Organism Snrna-Seq, Ye-Jin Park, Tzu-Chiao Lu, Tyler Jackson, Lindsey D Goodman, Lindsey Ran, Jiaye Chen, Chung-Yi Liang, Erin Harrison, Christina Ko, Xi Chen, Baiping Wang, Ao-Lin Hsu, Elizabeth Ochoa, Kevin F Bieniek, Shinya Yamamoto, Yi Zhu, Hui Zheng, Yanyan Qi, Hugo J Bellen, Hongjie Li

Faculty, Staff and Students Publications

Both neuronal and peripheral tissues become disrupted in Alzheimer's disease (AD). However, a comprehensive understanding of how AD impacts different tissues across the whole organism is lacking. Using Drosophila, we generated an AD Fly Cell Atlas (AD-FCA) based on whole-organism single-nucleus transcriptomes of 219 cell types from flies expressing AD-associated proteins, either human amyloid-β 42 peptide (Aβ42) or Tau, in neurons. We found that Aβ42 primarily affects the nervous system, including sensory neurons, while Tau induces accelerated aging in peripheral tissues. We identified a neuronal cluster enriched in Aβ42 flies, which has high lactate dehydrogenase (LDH) expression. This LDH-high cluster …

Clinically Important Endpoints In Individuals With Leukodystrophy: A Multisite Study, Emma R Kotes, Sarah Woidill, Russell D'Aiello, Amina Khan, Jacob Mccann, Mark Ramos, Francesco Gavazzi, Stephanie Keller, Keith Van Haren, Ali Fatemi, Florian Eichler, Joshua Bonkowsky, Jamie Fraser, Lisa Emrick, Omar Sherbini, Ashley Hackett, Jeilo Gauna, Dandre Amos, Jordan Goodman, Amena Smith Fine, Amanda Nagy, Seungil Lee, Nicole Page, Johanna Schmidt, Amy Pizzino, Kayla Muirhead, Mariko Bennett, Amy Waldman, Justine Shults, Laura Adang, Robert Grundmeier, Adeline Vanderver

Faculty, Staff and Students Publications

Importance: Leukodystrophies are a diverse group of rare disorders that disrupt central myelination. These disorders present with a broad spectrum of neurologic severity and are associated with a range of potential secondary complications, such as scoliosis and failure of independent feeding.

Objective: we explore real-world data of leukodystrophy complications to inform future evidence-based care guidelines across these rare diseases.

Design: In a cross-sectional observational study, we use a leukodystrophy-specific research consortium and the availability of electronic health records (EHR) to capture a cross-section of real-world data.

Setting: Subjects were identified using EHR data from five hospital systems with established expertise …

Wendell Philips Center Dedication Program, Callison College

Callison College and School of International Studies

No abstract provided.

Callison And Raymond College Course Offerings, Callison College

Callison College and School of International Studies

No abstract provided.

Callison College Promotional Book: Bangalore, Callison College

Callison College and School of International Studies

No abstract provided.

America, China, Japan: A Fresh Perspective, Callison College

Callison College and School of International Studies

No abstract provided.

Full Issue - Excelsior 17/2, Excelsior Journal

Excelsior: Leadership in Teaching and Learning

No abstract provided.

Integrating Digital Escape Room Design Into Teacher Education: Cultivating Instructional Creativity In Preservice Teachers, Gina L. Solano, Wen Wen

Excelsior: Leadership in Teaching and Learning

This action research documents how a teacher education program incorporates game-based learning to engage pre-service teachers (PSTs) in developing their instructional creativity. In this project, game-based learning goes beyond playing games; Instead, it allows PSTs to design their own game-a digital escape room created using a website with embedded clues, digital locks, and online challenges. This paper showcases an impressive level of creativity through the variety and complexity of PSTs’ clues, the creative graphics and layout of their websites, and their cleverly written scenarios and context for the game. Moreover, PSTs reflect on their design processes, considering the affordances and …

The Impact Of Mental Health Support On Academic Achievement, David Ersig, Tyrone Bynoe

Excelsior: Leadership in Teaching and Learning

Mental health concerns are becoming more pressing in American culture. There is an increasing call for mental health issues to be prioritized in policy discussions involving need, strategy, and funding. Addressing the cultural stigma and various barriers surrounding treatment and support for mental health issues are concerns that have infiltrated our school system; these concerns have exerted increased pressure on educators to provide effective and efficient mental health support mechanisms. There is growing recognition and observation that improving students’ mental health will help to remove barriers or hinderances to learning and achievement. With the increased pressure schools already face regarding …

Critical Literacy Approaches To Teaching Canonical Texts: Analyzing Race In To Kill A Mockingbird In Rural, Predominately White Classrooms, Ashley Graegin, Margery Gardner

Excelsior: Leadership in Teaching and Learning

In the 21st century, U.S. legislation continues to push for teacher censorship and seemingly depoliticized curriculums that ignore systemic issues regarding race, gender, sexuality, and other social justice topics. With the understanding that texts can never be politically neutral, English language arts (ELA) teachers must adopt critical approaches to teach required, and often hegemonic texts, and help students cultivate criticality and critical race consciousness. In this study, we aim to explore strategies that can be used to promote critical readings of canonical texts and how the topic of racial oppression can be broached in rural, predominantly White secondary English classrooms. …

Design Of A Simplified Biomimetic Autonomous Entertainment Robot, Jessica E. Morris, Shanny May Ruiz, Morgan Snyder, Hannah Guild, Gabriel Cardona-Tous

Graduate Scholarship and Creative Works

The advancement of technology has paved the way for robots with the purpose of entertainment to become more popular. However, the exploration of biomimetic actions as a factor of entertainment is majorly limited to the mimicry of young domesticated animals such as puppies and kittens, with some notable exceptions. However, there is a wide range of possibilities for robotics that mimic animals marketed as pets, outside of the common examples. This work seeks to explore the opportunity for autonomous systems with entertainment driven and expressive actions in the family of Testudines (turtles and tortoises), an undomesticated species, but still often …

The Impact Of The Translated Frankenstein Story On The Child›S Psyche And Thinking, Riham Halawani

Al Jinan الجنان

In this study, the researcher explored the impact of Frankenstein’s translated story on children. Choosing a topic or idea in translating children’s stories is likely to cause children to not respond to it and therefore not read it. It is therefore imperative for the translator to consider the elements of the story in the translation process, including the subject and idea, characters, environment, and style. Accordingly, the researcher sought to highlight the psychological and intellectual effects that this translated story has on children and its reflection on society. The researcher also mentioned the technique used in translating the proper names …

The Extent Of The Effectiveness Of Electronic Management In The Educational Process From The Point Of View Of Students Of Northern Border University, Tahani Al-Anazi

Al Jinan الجنان

The study aims to identify the conceptual framework of electronic management in contemporary educational thought, including the features of the educational process at the Northern Border University in the Kingdom of Saudi Arabia in order to determine the definition of the reality of the educational process in the light of the use of electronic management. The researcher used the descriptive analytical approach in order to obtain specific results, using the data collection tool (questionnaire) for a stratified random sample of university students amounting to 1343 students. The study resulted in that students can use all activities electronically, with some weaknesses …

مستوى مقروئية نصوص مقرر (الفلسفة والعلوم الإنسانية) للصف الثالث الثانوي في الجمهورية العربية السورية. Readability Level Of Texts In The (Philosophy And Humanities) Curriculum For The Third Secondary Grade In The Syrian Arab Republic, أمين شيخ محمد

Association of Arab Universities Journal for Education and Psychology

هدف البحث إلى تحديد مستوى مقروئية نصوص مقرر (الفلسفة والعلوم الإنسانية) للصف الثالث الثانوي في الجمهورية العربية السورية، ومعرفـة الفـروق المعنوية بين درجات تطبيقهم تبعاً لمتغيرات النوع الاجتماعي، والمحافظة، ونوع الموضوع. اعتمد البحث المنهج الوصفي التحليلي، وتكونت عينة البحث من (274) طالباً وطالبة من مدارس مديريتي تربية دمشق وريفها، واستخدم اختبار كلوز مقروئية نصوص عينة البحث التي تكونت من (7) نصوص موزعة على موضوعات الفلسفة وعلم النفس وعلم الاجتماع.

وقد أظهرت نتائج البحث: أن مستوى مقروئية نصوص مقرر (الفلسفة والعلوم الإنسانية) للصف الثالث الثانوي في الجمهورية العربية السورية كان ضمن المستوى الإحباطي، كما أظهرت نتائج البحث وجود فرق دال إحصائياً …

The Hoynes Code, Notre Dame Law School

Hoynes Code

A COMPILATION OF FACULTY RESOLUTIONS AND ADMINISTRATIVE REGULATIONS GOVERNING NOTRE DAME LAW SCHOOL

This code governs legal education at the University of Notre Dame in all programs and in all locations. Requirements for the LL.M. and J.S.D. degrees are included in the appendices.

Impact Of Telehealth On Outcomes In Daily Practice, Shannon Stuebs

Theses and Dissertations

While telepsychology has existed in various forms for years and has been researched since the 1960s (Abrams, 2020), it was not until the COVID-19 pandemic that telepsychology started to be widely used. Prior to the COVID-19 pandemic, one study found that psychologists conducted only around 7% of their work via telepsychology, a number that jumped to over 85% in response to COVID-19 (Pierce, Perrin, Tyler, et al., 2020). While there has been a significant increase in the research exploring the efficacy of telehealth since the start of the pandemic (Lin et al., 2022), further research regarding long-term impacts and specific …

Mitigation Behaviors Of Homeowners And Renters In The Wildland Urban Interface, Aishwarya Borate, Omar Pérez Figueroa, Douglas Houston, Christopher Ihinegbu, Ariane Jong-Levinger, Jochen E. Schubert, Brett F. Sanders

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Residential development within the wildland-urban interface (WUI) has greatly expanded in the United States since the 1990s, amplifying wildfire risk by placing people and structures in greater proximity to flammable vegetation. Household wildfire mitigation actions can vary substantially by cost, knowledge required, and perceived effectiveness, but few studies have examined them separately and how their adoption varies by housing tenure in the context of wildfires. To address this gap, we surveyed residents living in WUI areas within Southern California near recent burn scars in the Santa Ana and San Bernardino Mountain ranges. Drawing on the Protection Motivation Theory and the …

Under Pressure: Performance Loads And Recovery In Ncaa Division I Women’S Soccer During Fixture Congestion, Jade X. Dawson, Fabiano T. Amorim

Health, Exercise, and Sports Sciences ETDs

Soccer places high physiological demands on athletes, and match congestion—playing more than two games per week—is a growing concern at the NCAA Division I level. Limited recovery time between matches can impair performance and increase injury risk, prompting widespread use of recovery strategies. However, research on their effectiveness remains inconclusive, and most existing studies focus on male athletes, leaving a gap in evidence specific to female players. This review and observational study aim to evaluate non-nutritional recovery strategies in NCAA Division I women’s soccer and examine how recovery duration influences performance.

Match load data were collected from eleven female athletes …

Breastfeeding Continuation At One Month Postpartum Among Women In Treatment For Opioid Use Disorder Who Initiated Breastfeeding: Prevalence And Determinants, Julia Eisenberg, Meghan Gannon, Kim Mclaughlin, Diane J. Abatemarco, Vanessa L. Short

Abington Jefferson Health Papers

Objective: To describe breastfeeding behaviors and determinants in the 1-month postdelivery period among women in treatment for opioid use disorder.

Study Design: Participants completed one questionnaire during pregnancy and one questionnaire at 1 month postpartum. Those who reported on the postpartum questionnaire that they had initiated breast- feeding were included in this analysis (N = 31). Infant feeding practices, receipt of lactation support, and demographic, psychosocial, and infant birth characteristics were compared between those who breastfed for at least 1 month and those who did not.

Results: In all, 45% of the participants were breastfeeding at 1 month post delivery. …

The Role Of Self-Reported Health Ratings In Identifying Hospitalization Risk Among Older Adults: An Integrated Review And Secondary Analyses Of Medicare Claims Data, Mary B. Prybylo

MUSC Theses and Dissertations

Purpose: This study examined how Self-Reported Health (ratings), a person’s own evaluation of their overall health, relates to hospital admissions and emergency department utilization. It further assessed the extent to which demographic characteristics, Risk Adjustment Factor (RAF) scores (used to estimate healthcare expenditures based on clinical complexity), and the number of chronic conditions influence SRH rating and the likelihood of hospitalization.

Problem and Aim: The growing population of older adults places greater demands on healthcare services, leading to increased financial strain and a need for improved care strategies. Primary care teams, particularly those managing older adults, require effective assessment …

Livestock Poultry Health Committee Minutes, Clemson University Board Of Trustees, 2025 July 8, Clemson University Board Of Trustees

Minutes

No abstract provided.

Adaptation And Standardization Of Two Arabic Communicative Development Inventories For Children Aged 8 To 30 Months And 30 To 48 Months In Egypt, Jordan And Palestine, Alshaimaa Abdelwahab, Caroline Floccia, Samuel Forbes, Zakiyah Alsiddiqi, Khalid Al-Shdifat, Cristina Mckean, Thair Odeh, Anastasia Trebacz, Ghada Khattab

School of Psychology

PURPOSE: Assessing early language skills through parental report is a cost-effective way to screen for language delays when resources are scarce. A pan-Arabic lexeme approach was tested by extending the Egyptian adaptation of the MacArthur-Bates Communicative Development Inventory (CDI) to Jordan and Palestine in infants aged 8-30 months (Arabic CDI Toddler). We also developed a version for children aged 30-48 months (Arabic CDI Child) in the three countries. A fair representation of the population in terms of geographical spread, maternal education, and environmental context was obtained through stratified sampling. METHOD: The Arabic CDI Toddler, containing a 100-word list with dialect …