Digital Commons Network^™

Cat: A Conditional Association Test For Microbiome Data Using A Permutation Approach, Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert R Jenq, Christine B Peterson

Faculty, Staff and Student Publications

In microbiome analysis, researchers often seek to identify taxonomic features associated with an outcome of interest. However, microbiome features are intercorrelated and linked by phylogenetic relationships, making it challenging to assess the association between an individual feature and an outcome. This paper proposes a novel conditional association test, CAT, that can account for other features and phylogenetic relatedness when testing the association between a feature and an outcome. CAT adopts a permutation approach, measuring the importance of a feature in predicting the outcome by permuting operational taxonomic unit/amplicon sequence variant counts belonging to that feature from the data and quantifying …

Pol Θ-Mediated End-Joining Uses Microhomologies Containing Mismatches, Yuzhen Li, Ngoc K Dang, Wei He, Mark Returan, Denisse Carvajal-Maldonado, Adele T Guerin, Han Xu, Bin Liu, Richard D Wood

Faculty, Staff and Student Publications

DNA polymerase theta (Pol θ) initiates repair of DNA double-strand breaks by pairing single strands at short "microhomologies". It is important to understand microhomology selection, as some cancer cells rely on Pol θ for survival. Here, we investigate end-joining by purified human Pol θ, employing DNA sequencing of products generated from oligonucleotide libraries having diverse 3' ends. Pol θ overwhelmingly selects short internal microhomologies found within 15 nucleotides of the terminus of single-stranded DNAs, restricting deletion size during end-joining. Significantly, we find that the selected microhomologies are usually interrupted by mismatches and that base pairing within 6 nucleotides of the …

Structural And Functional Characterization Of Creb-Binding Protein (Crebbp) As A Histone Propionyltransferase, Guiling Cui, Marie Ley, Ariel E Mechaly, Linh-Chi Bui, Christina Michail, Jérémy Berthelet, Julien Dairou, Haopeng Yang, Guillaume Chevreux, Gautier Moroy, Michael R Green, Ahmed Haouz, Fernando Rodrigues Lima

Faculty, Staff and Student Publications

In addition to histone acetylation, histone lysine propionylation (such as the H3K18Pr mark) has recently attracted significant attention as a common and abundant modification linking the cellular metabolic state and gene expression. CREB-binding protein (CREBBP) and EP300 are key histone acetyltransferases that play a critical role in gene expression through their catalytic activity. Although CREBBP and EP300 are homologous enzymes with high structural similarities, they exhibit both redundant and specific functions. Dissecting the shared and divergent properties of CREBBP and EP300 is thus important to understand their roles. However, despite the importance of CREBBP, most mechanistic and structural studies have …

Irradiation Of Prostate Cancer Alters Circulating Small Extracellular Vesicle Functions, Aejaz Sayeed, Vaughn Garcia, Cecilia E. Verrillo, Rachel M. Derita, Md Niamat Hossain, Shiv R. Krishn, Samuel Sey, Christopher D. Shields, Adrian D. Altieri, Qin Liu, Khalid Sossey-Alaoui, William K. Kelly, Lucia R. Languino

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

It is known that β1 integrins and a downstream signaling molecule c-Src are upregulated in prostate cancer (PrCa) tissues, are co-expressed in circulating small extracellular vesicles (sEVs) and contribute to cancer progression. Here, we demonstrate that sEVs from PrCa patients show robust expression of both β1 integrins and c-Src. The impact of irradiation, a widely used therapy for the treatment of PrCa, on circulating sEVs is however not fully understood. We show that sEVs isolated from the plasma of transgenic adenocarcinoma of mouse prostate (TRAMP) mice, stimulate migration and anchorage-independent growth of recipient cancer cells, but sEVs are not active …

Preferred Plants And Nectar Collecting Times For Honey Production, David Macfawn, Jennifer M.K. O'Keefe, Sophie Warny, Carol Wymer, June Rampy Ponder

Clemson Extension Publishing

This book addresses three important questions for South Carolina beekeepers – which plants are bees in South Carolina using for nectar forage, when bees collect nectar from those plants, and how can understanding nectar foraging habits inform beekeepers as they work to gather specific types of premium honey? In 2021, the South Carolina Beekeeper’s Association, led by David MacFawn, designed and implemented a statewide pollen study, the first in any state in over fifty years, to answer these questions. Informed by data gathered from 19 apiaries across the state, this book contains the results of that study, including large-scale melissopalynological …

Healthcare Administration Within Free Medical Clinics And The Impacts On The Sustainable Development Goals, Saneywongse Le Mar

Goal 3: Good Health and Well-Being

No abstract provided.

Macrophage Subsets In Cardiomyocyte Interaction And Infarct Repair In Heart Failure, Jolissa Davis-Mccrea, Yuhui Yang, Huilan Tan, Yajing Wang

Expo Student Presentations

2025 Summer Expo Poster Presentation

• Biological & Life Sciences
• Health Sciences & Health Professions

Commentary On Blaser's "Antibiotic Use And Its Consequences For The Normal Microbiome", Fred C. Tenover

AMR Commentary

If you have not read this eye-opening commentary by Dr. Martin Blaser about the negative impact of the widespread use of antibiotics in children, you should. The goal of giving antibiotics to children usually is to treat an infection — an earache, a respiratory tract infection, or perhaps a potentially deadly bloodstream infection. Those antibiotics, however, will often kill more than just the bacteria that are causing the infection. Humans have large quantities of “good bacteria” in our intestinal tracts, on our skin, and elsewhere on our body that play an important role in keeping us healthy.

Prior To Termination, The Rye Cover Crop Increased The Soil Methane Sink, Shailesh Pandit, Graig W. Reicks, Janet Moriles Miller, Deepak R. Joshi, Sharon A. Clay, David E. Clay

Agronomy, Horticulture and Plant Science Faculty Publications

Even though the impact of cover crops on soil moisture has been well documented, little work has investigated the resulting impact on methane emissions. Therefore, the objective was to determine the influence of a dormant seeded rye (Secale cereale) cover crop on soil temperatures, soil moisture, inorganic N, and total CH₄-C emission in a well-drained frigid soil from the start of growth in April/May through corn's (Zea mays) V4 growth stage. In this study, soil moisture, temperature, CH₄-C, and N₂O-N fluxes were measured near-continuously. The rye cover crop: (1) reduced …

Skin Bacteriome Structure And Batrachochytrium Dendrobatidis Prevalence Differs Amongst Two Sympatric Salamanders In The San Francisco Bay Area., Aria Norwood, Jadyn Jamora, Micuel Madison, Jamiee Nguyen, Azan Yousaf, Katya Morales, Emily Vu, Obed Hernández-Gómez

Natural Sciences and Mathematics | Student Professional Publications

Microbial surveys are becoming an important component of wildlife health research, especially in cases where environmental change and infectious diseases are serious issues. Amongst amphibians, Batrachochytrium spp. have the potential to be fatal pathogens that can impact the population health of numerous species. We assessed the skin bacteriome, prevalence of Batrachochytrium dendrobatidis (Bd) and body conditions of two salamander genera with different life histories: the California slender salamander (Batrachoseps attenuatus) and members of the Pacific newt species complex (Taricha torosa and Taricha granulosa; Taricha sp.). We used 16S rRNA V4 amplicon sequencing to characterise the bacterial communities. Taricha sp. had …

Creek-Friendly Practices For Hoas, Plaster Creek Stewards

Print Materials

This booklet is intended to be a comprehensive guide to encourage Homeowner Associations (HOAs) in nurturing and safeguarding their local waterways. Within these pages the challenges facing our water ecosystems will be addressed, with particular focus being placed on the Plaster Creek Watershed in West Michigan. This booklet will also emphasize the role HOAs can play in fostering environmental stewardship and healthier, more resilient creek systems. This booklet contains practical strategies, from rain gardens to native plantings, that not only enhance the beauty of your HOA but extends care to downstream neighbors and the creek.

Fisheries Science Update - Pilbara Fishing Competition Science 2020 To 2024 - July 2025, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

Key Points:

• Pilbara recreational fishing competitions are helping to track the sustainability of pelagic species like Spanish mackerel.
• Over 500 pelagic fish have been sampled at Pilbara fishing competitions over 5 years.
• This information goes towards DPIRD’s assessment of Spanish mackerel and monitoring the large pelagic resource in the North Coast Bioregion.

Alpha-Synuclein Null Mutation Exacerbates The Phenotype Of A Model Of Menkes Disease In Female Mice, Meganne Casey, Dan Zou, Renee Reijo Pera Phd, Tiffany Hensley-Mcbain, Deborah E. Cabin

Touro College of Osteopathic Medicine (Great Falls) Publications and Research

Human SNCA, which encodes a-synuclein protein (SNCA), was the first gene linked to familial Parkinson's disease (PD). Since the discovery of the genetic link of SNCA to Parkinson's nearly three decades ago, many studies have investigated the normal function of SNCA protein. However, understanding of the normal function of SNCA is complicated by the lack of a reliable mammalian model of PD; indeed, mice with homozygous null mutations in the Snca gene live a normal lifespan and have only subtle synaptic deficits. Here, we report the first genetic modifier (a sensitized mutation) of a murine Snca null …

Covid-19-Related Beliefs And Dietary Behaviors Of American Undergraduate Students Vary By Race Via The Lens Of The Health Belief Model, Doreen Liou, Jong Min Lee

Department of Nutrition and Food Studies Scholarship and Creative Works

The COVID-19 pandemic caused immense physical disruptions, affecting young adults in the U.S. The Health Belief Model is a social psychological framework that predicts the likelihood of adopting health behavior. The purpose of this research is to investigate COVID-19-related health beliefs and dietary behaviors among undergraduate students during the pandemic. Using convenience sampling, a cross-sectional survey was completed by 304 individuals at a New Jersey state university. Survey data included the frequency of COVID-19 prevention behaviors (e.g., wearing an indoor mask, handwashing), and consumption of fruit and vegetables. The Health Belief Model constructs measured perceived susceptibility to COVID-19, severity, benefits, …

Protein Supplementation, Plasma Branched-Chain Amino Acids, And Insulin Resistance In Postmenopausal Women: An Ancillary Study From The Supplemental Protein To Outsmart Osteoporosis Now (Spoon) Trial, Jessica Dauz Bihuniak, Alessandra Byer, Christine A. Simpson, Rebecca R. Sullivan, Josephine M. Dudzik, Karl L. Insogna, Jeannette M. Beasley

Department of Nutrition and Food Studies Scholarship and Creative Works

Background/Objectives: Studies have reported an increased risk of type 2 diabetes among people with higher protein intake. Moreover, branched-chain amino acids (BCAA) are reported to be positively associated with insulin resistance (IR). However, it is not understood whether elevated levels of BCAA are causal to IR development, or if higher BCAA are a marker of IR. The objective of this study was to examine the effects of long-term protein and carbohydrate supplementation on plasma BCAA levels, and the relationship between plasma BCAA and IR in postmenopausal women. Methods: Stored samples and data from 84 postmenopausal women who participated in a …

Effect Of Traditional Versus Fenceline Weaning On Lamb Stress, Emma N. Sutton

Animal Science Undergraduate Honors Theses

Stress is a significant factor affecting the health, behavior, and performance of sheep in production settings. Most lambs go through artificial weaning, and this is a stressful time in a lamb’s life. Stress can negatively affect growth rates, feed efficiency, and susceptibility to illness and parasites. The traditional and most common method of weaning is the abrupt separation of lambs from their dams. An alternative method of weaning, fenceline weaning, has been found to reduce stress in cattle and may also reduce stress in sheep. The objectives of this study were to evaluate body weights, fecal egg counts, and behavior …

Identification Of The Gd-Iga1 Autoantigen By New Monoclonal Finds Differential Nf-Kb Signaling, Hannah Adams, Taylor Person, Terri Rice, Colin Reily

Expo Student Presentations

2025 Summer Expo Poster Presentation

• Biological & Life Sciences

Comparing Extenders For Cryopreservation Of Sperm From The Sea Urchin, Lytechinus Variegatus, Gus Roveri, Katie Gibbs

Expo Student Presentations

2025 Summer Expo Poster Presentation

• Biological & Life Sciences

Dynamic Microbiome Responses To Structurally Diverse Anthocyanin-Rich Foods In A Western Diet Context, Mohammed F. Almatani, Giovanni Rompato, Eliza C. Stewart, Marcus Hayden, Jeremy Case, Samuel Rice, Korry J. Hintze, Abby D. Benninghoff

Animal, Dairy, and Veterinary Science Student Research

Background/Objectives: Anthocyanin (ACN)-rich foods are known to influence the gut microbiota composition, but the temporal dynamics and structural specificity of these effects remain poorly understood. This study investigated how distinct ACN-rich fruit supplements impact the gut microbiome over time in the context of a Western-style diet. We hypothesized that ACN-induced microbial shifts would occur rapidly, differ by ACN source, and require continued intake to persist. Methods: C57BL/6J mice were fed the total Western diet (TWD) supplemented with freeze-dried powders from bilberry (BB), tart cherry (TC), chokeberry (CB), elderberry (EB), black currant (BC), or black raspberry (BRB) for 0, 1, 3, …

Cdemapper: Enhancing National Institutes Of Health Common Data Element Use With Large Language Models, Yan Wang, Jimin Huang, Huan He, Vincent Zhang, Yujia Zhou, Xubing Hao, Pritham Ram, Lingfei Qian, Qianqian Xie, Ruey-Ling Weng, Fongci Lin, Yan Hu, Licong Cui, Xiaoqian Jiang, Hua Xu, Na Hong

Faculty, Staff and Student Publications

Objective: Common Data Elements (CDEs) standardize data collection and sharing across studies, enhancing data interoperability and improving research reproducibility. However, implementing CDEs presents challenges due to the broad range and variety of data elements. This study aims to develop a CDE mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs.

Methods: We propose CDEMapper, a large language model (LLM)-powered mapping tool designed to assist in mapping local data elements to NIH CDEs. CDEMapper has 3 core modules: (1) CDE indexing and embeddings. NIH CDEs were indexed and embedded to support semantic search; …

Evaluating Large Language Model Performance To Support The Diagnosis And Management Of Patients With Primary Immune Disorders, Nicholas L Rider, Yingya Li, Aaron T Chin, Daniel V Digiacomo, Cullen Dutmer, Jocelyn R Farmer, Kirk Roberts, Guergana Savova, Mei-Sing Ong

Faculty, Staff and Student Publications

Background: Generative artificial intelligence (GAI) is transforming health care in a variety of ways; however, the present utility of GAI for supporting clinicians who treat rare disease such as primary immune disorders (PIs) is not well studied. We evaluated the ability of 6 state-of-the-art large language models (LLMs) for providing clinical guidance about PIs.

Objective: To quantitatively and qualitatively measure the utility of current, open-source LLMs for diagnosing and providing helpful clinical decision support about PIs.

Methods: Five expert clinical immunologists each provided 5 real-world, anonymized PI case vignettes via multi-turn prompting to 6 LLMs (OpenAI GPT-4o, Llama-3.1-8B-Instruct, Llama-3.1-70B-Instruct, Mistral-7B-Instruct-v0.3, …

Wnt-Directed Cxcl12-Expressing Apical Papilla Progenitor Cells Drive Tooth Root Formation, Mizuki Nagata, Gaurav T Gadhvi, Taishi Komori, Yuki Arai, Hiroaki Manabe, Angel Ka Yan Chu, Ramandeep Kaur, Meer Ali, Yuntao Yang, Chiaki Tsutsumi-Arai, Yuta Nakai, Yuki Matsushita, Nicha Tokavanich, W Jim Zheng, Joshua D Welch, Noriaki Ono, Wanida Ono

Faculty, Staff and Student Publications

The tooth root is a critical component of the tooth anchored to surrounding alveolar bones. Tooth root formation is driven by cells in the apical papilla (AP) that generate new dentin-forming odontoblasts at the root-forming front. Mesenchymal stem cells have been isolated from AP for regenerative use; however, how AP cells physiologically coordinate tooth root formation remains undefined. We find that CXCL12+ cells emerge in AP under hypoxic environments at the onset of tooth root formation. Using Cxcl12-creER-based cell-lineage analysis, we further find that CXCL12+ AP cells contribute not only to odontoblasts but also to cementum-forming cementoblasts of the elongating …

Studying The Population Dynamics Of Nslab And Their Influence On Spores During Cheese Ripening, Rakesh Kaushik, Sanjeev Anand

Dairy Science and Food Science Faculty Publications: 2022 to Present

Cheese ripening involves microbial changes, with starter lactic acid bacteria (SLAB) initiat- ing fermentation and nonstarter lactic acid bacteria (NSLAB) driving flavor and texture development. However, heat-resistant spores of Clostridium and Bacillus can survive pas- teurization and cause spoilage during ripening. This study evaluated NSLAB dynamics in the presence of spores during cheese ripening. Cheddar cheese samples at pilot-scale level (110 L) with four treatments, namely control, with spores of B. licheniformis (T1), with spores of Cl. tyrobutyricum (T2), and both spores (T3) at 2.0 Log10 CFU/mL, were ripened at 7 ◦C for six months. SLAB declined from 8.0 to …

Alfred Russel Wallace Notes 37. What About Wallace On Vaccination . . . ?, Charles H. Smith

Faculty/Staff Personal Papers

Best known for his natural history studies on evolution and biogeography, Alfred Russel Wallace (1823−1913) had a significant second career as a social critic. One of his most controversial stances was his position on (smallpox) vaccination. Anti-vaxxers of the present frequently bring up his name as a resource for their side, but the situation is not so easily reducible to that.

Utilizing Pharmacogenomics To Improve Students' Self-Perception On The Interprofessional Competencies Of Roles And Responsibilities, And Teams And Teamwork, Amanda Brown, Moom R. Roosan, Robert Goldsteen, Scott D. Ochs, Reza Taheri

Pharmacy Faculty Articles and Research

Introduction

Pharmacogenomics (PGx) is an emerging discipline with the potential to revolutionize personalized medicine, but its successful implementation requires interprofessional collaboration. To address this need, a virtual interprofessional education (IPE) session was designed for student pharmacists and medical students to engage in a case-based learning experience.

Objective

The primary objective was to develop and implement an IPE activity focused on a patient case requiring PGx-guided dual antiplatelet therapy and to assess students' perceptions of two Interprofessional Education Collaborative (IPEC) Version 3 Core Competencies. A secondary objective was to identify key lessons from the session.

Methods

Pharmacist and physician faculty collaboratively …

Thriving Hives: Making Products With Honey - Skincare And Food Recipes, Brynn Meredith, Teresa Hunsaker, Andree' Walker Bravo

All Current Publications

While keeping bees is beneficial for many reasons, one of the most notable benefits is producing honey and wax, which have many practical uses. This fact sheet provides information on honey's properties and how to make creamed honey to control crystallization. It also provides instructions on how to make skincare and various food products using honey.

A Child With Severe Pneumonia Cannot Feed, Causing Malnutrition: Exploring Health Worker And Caregiver Perspectives And Practices For Mitigating Malnutrition Among Children With Severe Pneumonia, A Case Of Uganda, Damalie Nalwanga, Robert Opoka, Andrew Sentoogo Ssemata, Lawrence Kakooza, Andrew Kiggwe, Victor Musiime, Sarah Kiguli

Paediatrics and Child Health, East Africa

Background: Severe pneumonia remains the leading cause of morbidity and mortality among children worldwide. Severe pneumonia causes death during hospitalization, and survivors are prone to malnutrition after discharge from the hospital. The World Health Organization and United Nations International Children’s Fund recommend ‘continued’ feeding following a severe pneumonia illness without specific recommendations on nutritional support. This recommendation could influence health workers’ and caregivers’ nutritional practices. This study aimed to explore the perspectives and practices of health workers and caregivers for mitigating malnutrition among children with severe pneumonia.

Methods: We conducted a cross-sectional qualitative study between June and November 2021 among …

Effectiveness Of A Telephone-Delivered Walk With Ease Program On Arthritis-Related Symptoms, Function, And Activity: A Randomized Trial, Christine Pellegrini Ph.D., Sara Wilcox Phd, Yesil Kim, Scott Jamieson, Katherine Devivo, Daniel Heidtke

Faculty Publications

Objective

Walk With Ease (WWE) is a six-week arthritis-appropriate evidence-based physical activity program traditionally offered in a face-to-face format. Because many populations encounter participation barriers to in-person programs, WWE was modified for telephone delivery (WWE-T). The short- and long-term effects of this program on physical activity and arthritis-related outcomes were examined.

Methods

Participants (n = 267) with arthritis were randomized to WWE-T or a wait list control. WWE-T participants received two telephone calls per week (one group and one individual call) for six weeks. Group calls focused on arthritis education and social support. Individual calls focused on problem-solving and goal …

Bibliometric Analysis Of Congenital Toxoplasmosis: A Ten-Year (2013-2023) Review Of Research Publications, Festus Mulakoli, Horatius Musembi, Ann Kimani

School of Nursing & Midwifery, East Africa

Background:Toxoplasma gondii, an obligate intracellular protozoan, infects more than one-third of the global population and causes toxoplasmosis, which can lead to severe fetal complications in pregnant women. The global prevalence of latent toxoplasmosis in pregnant women is 33.8%, with regional variations and risk factors, including the consumption of undercooked meat, exposure to cat feces, and consumption of contaminated water. Pregnant women lack sufficient awareness of these risk factors, necessitating enhanced education, regular screening, and counseling during antenatal care for early detection and management.

Aim: This study performed a comprehensive bibliometric analysis of research on congenital toxoplasmosis published between 2013 …

Full Issue, Volume 13, Number 1, Donna J. Peterson, Scott Cummings, Elizabeth Gregory North

Journal of Human Sciences and Extension

No abstract provided.