Digital Commons Network^™

Large-Scale Crispr Screening In Primary Human 3d Gastric Organoids Enables Comprehensive Dissection Of Gene-Drug Interactions, Yuan-Hung Lo, Hudson T Horn, Mo-Fan Huang, Wei-Chieh Yu, Chia-Mei Young, Qing Liu, Madeline Tomaske, Martina Towers, Antonia Dominguez, Michael C Bassik, Dung-Fang Lee, Lei S Qi, Jonathan S Weissman, Jin Chen, Calvin J Kuo

Faculty, Staff and Student Publications

Understanding how genes influence drug responses is critical for advancing personalized cancer treatments. However, identifying these gene-drug interactions in a physiologically relevant human system remains a challenge, as it requires a model that reflects the complexity and heterogeneity among individuals. Here we show that large-scale CRISPR-based genetic screens, including knockout, interference (CRISPRi), activation (CRISPRa), and single-cell approaches, can be applied in primary human 3D gastric organoids to systematically identify genes that affect sensitivity to cisplatin. Our screens uncover genes that modulate cisplatin response. By combining CRISPR perturbations with single-cell transcriptomics, we resolve how genetic alterations interact with cisplatin at the …

Iterative Intraoperative 3t Mri (Imri)-Guided Brachytherapy: A Prospective Study On Enhancing Implantation Precision And Dosimetric Gains In Advanced Gynecologic Cancers, Shrikiriti S Rajan, Matthew S Ning, Megan Jacobson, Samantha J Simiele, Teresa Bruno, Ramez Kouzy, Kyoko Yoshida-Court, Tatiana Cisneros-Napravnik, Henry Yu, Jason Stafford, Yusung Kim, Geena Mathew, Rauda Alicia Cordova, Maliah Domingo, Anuja Jhingran, Lilie L Lin, Melissa Joyner, Travis T Sims, Lauren Colbert, Aradhana M Venkatesan, Ann Klopp

Faculty, Staff and Student Publications

Purpose: To report on primary outcomes and dosimetric results of a prospective clinical trial and protocol for use of iterative intraoperative magnetic resonance imaging (iMRI) in gynecologic brachytherapy.

Methods: Patients with locally advanced cervical or vaginal cancer (FIGO stages IB2 - IVA, and stage II-IVA, respectively) undergoing pulsed dose rate (PDR) brachytherapy were enrolled in a prospective clinical trial (NCT03634267) using iterative 3T iMRI during brachytherapy implant placement. Applicator and optional interstitial needles were placed under iMRI guidance in a 3T clinical MRI scanner. Imaging, dosimetry and clinical outcomes (local control (LC), recurrence-free survival (RFS), overall survival (OS)), …

Genome Sequences Of Eight Fusobacterium Watanabei Sp Isolates, Martha A Zepeda-Rivera, Falk Ponath, Kaitlyn N Lewis, Rutika P Gavate, Floyd E Dewhirst, Junko Tomida, Yoshiaki Kawamura, Kaori Tanaka, Susan Bullman, Christopher D Johnston

Faculty, Staff and Student Publications

We report draft genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database indicates that F. watanabei genomes are part of the "Fusobacterium nucleatum_J" group.

An Investigation Of The Association Of Gdf9-C.260g>A Polymorphism With Lamb Live Weight In The Akkaraman Breed, Şeyma Kökkaya, Fadi̇me Daldaban, Davut Bayram, Mehmet Ulaş Çinar, Korhan Arslan, Bi̇lal Akyüz

Turkish Journal of Veterinary & Animal Sciences

In this study, the relationship between the Growth Differentiation Factor-9 (GDF9) gene polymorphism and birth weight, as well as weights on days 30, 60, 90, was investigated in Akkaraman lambs, one of the indigenous sheep breeds of Türkiye. For this purpose, a total of 314 lambs were genotyped by PCR-RFLP method for the single nucleotide polymorphism (SNP) c.260G>A in the GDF9 gene. While GG and GA genotypes were observed in the studied breed, the AA genotype was not observed. The results showed that Akkaraman lambs were in Hardy–Weinberg (H–W) equilibrium for the GDF9-c.260G>A polymorphism (p < 0.05). In this study, a significant association was observed between GDF9-HhaI polymorphism and 30th day weight and 60th day weight in Akkaraman lambs. When the animals were analyzed according to birth type, it was observed that this factor was associated with birth weight, as well as weights on days 30, 60, and 90. It is suggested that the c.260G>A coded SNP …

Cover And Contents

Turkish Journal of Veterinary & Animal Sciences

No abstract provided.

Growth Curve And Serum Calcium And Magnesium Concentrations In Duck Breeders (Anas Boschas) From Hatching To The Prelaying Period Reared Under Subtropical Conditions, Vanessa Peripolli, Fabiano Dahlke, Ellen Karen Dos Santos, Maila Palmeira, Stelamaris Dezen, Robert Lenock, Elizabeth Schwegler, Juahil Martins De Oliveira Júnior, Ivan Bianchi, Paula Gabriela Da Silva Pires, Betina Raquel Cunha Dos Santos, Andressa Fernanda Campos, Fabiana Moreira

Turkish Journal of Veterinary & Animal Sciences

Optimizing duck production requires understanding growth variability and monitoring serum calcium and magnesium levelsas health indicators. This study aimed to analyze the growth curve, mortality, and serum calcium (Ca) and magnesium (Mg) levels in White Mallard ducks from hatching to the prelaying period in subtropical conditions. A total of 1100 females and 270 males were raised for 146 days. At hatch, day 6 (D6), D13, D23, D34, D50, D64, D80, D94, D111, and D146, ducks were weighed separately to assess body weight (BW). Blood samples were collected at hatch, D50, D94, and D146 to determine serum calcium and magnesium levels. …

The Morphologic Structure Of Some Wing Muscles In The Common Pheasant (Phasianus Colchicus), Beste Demi̇rci̇, Murat Erdem Gülti̇ken

Turkish Journal of Veterinary & Animal Sciences

Avians use significant amounts of energy during flight that is supplied by muscles. The Common Pheasant, a member of the Phasianidae family, can fly swiftly over short distances and flies to evade predators. Pheasant species are terrestrial and have a global distribution. This investigation aimed to analyze the anatomical structure of skeletal muscles in pheasants. A cohort of 20 adult pheasants consisting of an equal number of females and males (10 each) was used. Dissections were performed on 5 females and 5 male pheasants for macroscopic evaluation. The remaining samples underwent immunohistochemical staining using an antimyoglobin antibody to measure the …

A Morphological Study On Acanthocephalan Species From Wild Birds In Northern Türkiye, Mehmet Öztürk, Şi̇nasi̇ Umur

Turkish Journal of Veterinary & Animal Sciences

The phylum Acanthocephala contains approximately 1300 acanthocephalan species. So far, only nine acanthocephalan species of wild birds have been reported in Türkiye. To study the context of acanthocephalan diversity in wild birds in Türkiye, we examined 193 birds from 69 species belonging to 16 orders. Acanthocephalans were found in seven bird species: Centrorhynchus aluconis in Buteo buteo and Buteo rufinus, Centrorhynchus spinosus in Buteo buteo and Strix aluco, Mediorhynchus papillosus in Iduna icterina, Mediorhynchus tenuis in Luscinia svecica, Plagiorhynchus cylindraceus in Erithacus rubecula and Turdus merula, Polymorphus contortus in Anas platyrhynchos, and Sphaerirostris turdi in Turdus merula. Except for Plagiorhynchus …

Improving Particle-Phase Nitrate Measurement In Pm2.5 Filter Sampling: Evaluation Of A Denuder–Nylon Filter Modification In The Spartan Network, Wenyu Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Accurate measurement of PM_2.5 composition is of global importance. Evaporation-induced mass loss introduces potential bias in filter-based PM_2.5 measurements, with ammonium nitrate volatilization from Teflon filters being a major contributor to negative mass artifacts. Previous studies have demonstrated that using an acid gas denuder in combination with nylon filters can help recover the nitrate mass. This study evaluates design modifications to the AirPhoton sampling station setup within the globally distributed Surface Particulate Matter Network (SPARTAN) incorporating an additional acid gas denuder upstream and a nylon filter downstream of the existing Teflon filter.

Two co-located AirPhoton Sampling stations were …

Co-Targeting Bcl-Xl With Mcl-1 Induces Lethal Mitochondrial Dysfunction In Diffuse Mesothelioma, Yuan Xu, Cristian G Medina, Deborah R Surman, Lacey E Dobrolecki, Monica Vilchis, Maheshwari Ramineni, Susan G Hilsenbeck, Yanming Li, Naren Li, Siqi Wu, Jaylon C Aggison, Xi Chen, Yi Zhu, Ying H Shen, R Taylor Ripley

Faculty, Staff and Students Publications

Diffuse mesothelioma (DM) is a rare but highly aggressive and treatment resistant neoplasm with low survival rates. Effective therapeutic strategies are limited, and resistance to treatment is a major obstacle. Myeloid Cell Leukemia (MCL)-1 and B-cell leukemia (BCL)-xL are anti-apoptotic B-cell lymphoma 2 (Bcl-2) family proteins that block cell-intrinsic apoptosis through interactions on the mitochondrial outer membrane which contribute to therapeutic resistance.

We investigated whether B-cell homology domain (BH)-3 profiles were consistent between intra-patient fresh tumor sample, patient-derived cells (PDC), and patient-derived xenografts (PDX) by BH3 profiling; we observed striking consistency which enabled cross model comparisons. Next, we co-targeted BCL-xl …

August 14, 2025, James Madison University

The Breeze, 2020-

The Breeze is the student newspaper of James Madison University in Harrisonburg, Virginia.

Planetary Health: At The Crossroads Of Cvd Prevention, Tasveer Khawaja, Sanjay Rajagopalan

Faculty Scholarship

Purpose of Review: To highlight important recent findings demonstrating the interconnectedness of planetary and human health with a focus on cardiovascular disease. Recent Findings: Data continue to demonstrate a clear interconnectedness between the health of the planet and human health, with cardiovascular disease as an important outcome. The central roles of air pollution, non-optimal temperatures, water/waste management, and food/biodiversity are highlighted. We also highlight the clear opportunity for healthcare organizations to facilitate change that will yield positive environmental and patient outcomes. Summary: The undeniable interconnectedness of the health of the planet and human health serves as a call to action …

Re: Butte Mine Flooding Site Cd, Cv 02-35 Bu-Rfc, 2025 Second Quarter Report, Mark Thompson, Dave Griffis

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Butte Priority Soils Operable Unit Revised Draft Final Reclamation Improvement Sites Field Sampling And Investigation Plan (Fsp): Bres No. 45 – Garfield Response To Agency Comments Received June 28, 2024, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Staff Education To Improve Knowledge And Adherence To Diabetic Foot Ulcer Screening Protocols Using The Brief Diabetic Foot Ulceration Risk Checklist Tool, Sandrine Happi

Walden Dissertations and Doctoral Studies

This doctoral project implemented a structured nurse education module on the Brief Diabetic Foot Ulceration Risk Checklist to improve knowledge and adherence to diabetic foot ulcer screening, supporting preventive care, clinical consistency, and equitable patient outcomes in primary care. The practice-focused question guiding the project was whether providing structured education on the BDFURC would improve nurses’ knowledge and adherence to DFU screening protocols within 12 weeks. The goal was to equip nurses with standardized screening tools to support the early identification of high-risk patients and reduce the burden of DFU-related outcomes. The project involved 12 nursing staff and used a …

A Qualitative Study Exploring The Prenatal Care Experiences Of Pregnant And Postpartum Women In Arochukwu, Nigeria, Esther Ejim

Walden Dissertations and Doctoral Studies

This basic qualitative research study explored the perceptions and lived experiences of pregnant and postpartum women in Arochukwu, Abia State, Nigeria, where access to quality prenatal and maternal healthcare is limited. Nigeria records the highest maternal and infant mortality rates in sub-Saharan Africa, largely due to weak healthcare systems, poverty, and entrenched sociocultural norms. Grounded in the Health Belief Model (HBM) and guided by the lens of social constructivism, the study explored how health beliefs, perceived risks, benefits, barriers, and cues to action shaped women’s healthcare decisions. Using semistructured, open-ended interviews with 13 purposefully selected women, the study captured how …

Using The Epic (Exposure, Persuasion, Identification, And Commitment) To Develop A Measure Of Student Buy-In To Laboratory Learning Goals, Elizabeth Blanche Vaughan, A. Montoya-Cowan, Jack Barbera

Chemistry Faculty Publications and Presentations

Buy-in has been described as the series of judgements students make when deciding to engage with a pedagogical practice. Buy-in to pedagogical practices is known to have a meaningful impact on students’ engagement in learning environments, making it a construct of interest for researchers and practitioners. This study develops a measure of student buy-in to faculty defined laboratory learning goals by adapting an existing measure which operationalizes the construct in terms of Exposure, Persuasion, Identification, and Commitment (EPIC). The adapted measure presented in this study, deemed the EPIC-LaG (Laboratory Goals), was developed using learning goals for general and organic chemistry …

Proteomics-Based Aging Clocks In Midlife Or Late-Life And Their Associated Risk Of Dementia, Sanaz Sedaghat, Saeun Park, Rob F Walker, Shuo Wang, Jialing Liu, Timothy M Hughes, Behnam Sabayan, Weihong Tang, Josef Coresh, James S Pankow, Keenan A Walker, Ramon Casanova, Ruth Dubin, Rajat Deo, Jerome I Rotter, Alexis C Wood, Peter Ganz, Pamela L Lutsey, Weihua Guan, Anna Prizment

Children’s Nutrition Research Center Staff Publications

Background: Biological age can be quantified by composite proteomic scores, called proteomics-based aging clocks (PACs). We investigated whether a discrepancy between chronological and biological age in midlife and late-life is associated with cognition and dementia risk.

Methods: We used two longitudinal population-based studies: the Atherosclerosis Risk in Communities (ARIC) Study and the Multi-Ethnic Study of Atherosclerosis (MESA). PACs were created in ARIC at midlife (mean age: 58 years, 57% female, n = 11,758) and late-life (mean age: 77 years, 56% female, n = 4934) using elastic net regression models in two-thirds of dementia-free participants and validated in the remaining one-third …

Validity Of Body Composition Estimates In Women Assessed By A Multifrequency Bioelectrical Impedance Device, Mitchell Evan Zaplatosch, Juliana F. Meireles, Janeen S. Amason, Sadaf Dabeer, Brian M. Kliszczewicz, Gerald Mangine, Valene G. Barry, Barbara A. Gower, Katherine H. Ingram

Faculty Articles

Background: Multifrequency bioelectrical impedance devices such as the InBody 770 (IB770) offer faster measurements and lower costs compared with other body composition assessments. This study validated measures from IB770 against the deuterium oxide dilution technique (D2O) and DXA and compared a four-compartment (4C) model using total body water (TBW) derived from IB770 compared with D2O. Methods: A total of 55 adult females (mean ± SD, age: 21.1 ± 2.6 years) completed IB770 and DXA scans and the D2O protocol. Lin’s concordance correlation coefficients (CCCs), Bland–Altman analyses, and other equivalence tests evaluated agreement between IB770 and the criterion for measures of …

Phenotypic Evaluation Of F10 Soybean Generations From Grobogan X Slamet Cross For Large Seed Size Selection, Ponendi Hidayat, Nurtiati, Zulfa Ulinnuha, Adellansyah

Jurnal Kultivasi

Soybeans are an important crop with high nutritional value and diverse uses. Current consumer and industry preference is for soybean varieties with large seeds and high productivity. To meet these demands, one effective approach is through hybridization. This study aims to evaluate the phenotype of F10 soybean line from a cross between Grobogan and Slamet for large-seeded and high-yield. The study was conducted in the screenhouse and Plant Breeding and Biotechnology Laboratory, Faculty of Agriculture, Jenderal Soedirman University. The experiment used a Randomized Complete Block Design (RCBD) with three replications, testing genotypes from Slamet x Grobogan crosses and three check …

Effect Of Eco-Enzyme Application On Soil Nutrient And Plant Productivity Of Green Mustard-Peanut In Inceptisol, Idris Abd Rachman, Buhari Umasugi, Krishna Aji, Nurul Fahira A Hakim, Adnan Sofyan, Asrul Dedy Ali Hasan

Jurnal Kultivasi

Appropriate land management has a long-term impact on soil performance and is believed to improve soil fertility. This study investigated the effect of eco-enzymes on soil nutrients and plant productivity of green mustard-peanut in inceptisol. The research was conducted from February to April 2025. The experiment used a randomized block design (RBD) consisting of 5 treatments and replicated 3 times, so that there were 15 units, including N0 = without Eco-enzyme, N1 = Eco-enzyme 2cc/L. N2= Eco-enzyme 4cc/L, N3= Eco-enzyme 6cc/L, and N4= Eco-enzyme 8cc/L. The commodities used were green mustard (Brassica juncea L) and peanut (Arachis hypogaea Linn). Soil …

Rna Gene Expression-Based Liquid Biopsies For Diagnosing Hepatocellular Carcinoma, Balvinder Bobbie Saarsal, Ila Chauhan, Jeevan Divakaran, Shizue Mito

School of Medicine Publications

The incidence of non-alcoholic steatohepatitis, a significant risk factor for hepatocellular carcinoma (HCC), is on the rise, highlighting the urgent need for improved diagnostic biomarkers. To date, no systematic analysis has evaluated international studies using liquid samples to assess the utilization of RNA species as biomarkers for HCC. Liquid biopsies based on RNA expression offer more specific and sensitive diagnostic biomarkers for HCC than alpha-fetoprotein (AFP). The inclusion criteria mandated English-language articles, freely available full texts, and primary research published between January 1, 2019, and May 15, 2024. Quantitative analysis was performed using the area under the receiver operating characteristic …

Maya Migrants And Psychotherapy: Recommendations And A Case Study From Comunidad Sol In Canton, Ohio, Robin Chancer, Gerónimo Ramírez, Ernesto Ajanel Calel, María Ixcoy Mejía

Maya America: Journal of Essays, Commentary, and Analysis

This article approaches the question: How can non-Indigenous mental health practitioners work appropriately with Maya K’iche’ and Ixil communities in the United States? The authors are three Maya leaders and one non-Indigenous psychotherapist, the four of whom have worked together for several years. Psychological treatment rooted in Euro-American paradigms can be minimally helpful—if not harmful—to many Indigenous communities (Dudgeon & Bray, 2016). Traditional approaches such as cognitive-behavior therapy continue the colonial preoccupation with individual pathology and the separation of mind, body, spirit, and nature. The authors suggest that more appropriate approaches would include acknowledging structural oppression and centering the K’iche’ …

Book Review: Un Maya Migrante: Un Viaje Sin Retorno/A Maya Migrant: A Journey Of No Return, Christián González Reyes

Maya America: Journal of Essays, Commentary, and Analysis

By Gaspar Pedro González Yax Te’ Books, 2021. 262 pp

Integration Of Modern Treatments With The Cosmology Of Health Contributes Integrally To Physical, Emotional And Community Wellbeing, An K'A'Ch Guzmán Marcos

Maya America: Journal of Essays, Commentary, and Analysis

An K'a'ch Guzmán Marcos, an Ixil health care worker in the Ixil region, Guatemala, describes how cosmology forms an integral part of the people's identity. She describes the importance of cosmic health to the lives of the people, and the increasingly successful efforts of Ixil workers to build bridges of understanding with the biomedical medical profession.

Artificial Intelligence Algorithm Predicts Response To Immune Checkpoint Inhibitors, Faisal Fa'ak, Nicolas Coudray, George Jour, Milad Ibrahim, Irineu Illa-Bochaca, Shi Qiu, Adalberto Claudio Quiros, Ke Yuan, Douglas B Johnson, David L Rimm, Jeffrey S Weber, Aristotelis Tsirigos, Iman Osman

2020-Current year OA Pubs

PURPOSE: Cancer treatment has been revolutionized by immune checkpoint inhibitors (ICI). However, a subset of patients do not respond and/or they experience significant adverse events. Attempts to integrate reliable biomarkers of ICI response as part of standard care have been hampered by limited generalizability. We previously reported our supervised machine learning (ML) model in a retrospective cohort of metastatic melanoma.

EXPERIMENTAL DESIGN: In this study, we expanded our testing to include larger cohorts of patients with melanoma accrued at several sites, including patients enrolled in clinical trials in both adjuvant and metastatic settings. We examined pretreatment hematoxylin and eosin slides …

The Genetic Architecture Of Cervical Length Is Shared With Spontaneous Preterm Birth Risk, Hope M Wolf, Bradley T Webb, Jerome F Strauss 3rd, Adi L Tarca, Roberto Romero, Sonia S Hassan, Shawn J Latendresse, Tinnakorn Chaiworapongsa, Stanley Berry, Nardhy Gomez-Lopez, Piya Chaemsaithong, Timothy P York

2020-Current year OA Pubs

BACKGROUND: Sonographic cervical length is a powerful predictor of maternal risk for spontaneous preterm birth (sPTB). Twin and family studies have established a maternal genetic heritability for sPTB ranging from 13 to 20%, however, there is no corresponding estimate for the heritability of mid-trimester cervical length, or an understanding of how genetic factors contribute to cervical changes across pregnancy.

METHODS: This study was based on a prospective longitudinal cohort of (N = 5,160) Black/African American women who underwent serial sonographic examination of the uterine cervix during pregnancy and were genotyped via next-generation low-pass whole genome sequencing.

RESULTS: Bivariate genetic correlations …

A Fluorescence Lifetime-Based Flim-Timer For Measuring The Protein Turnover Of Transcription Factor Nrf2 In Live Cells, Dina Dikovskaya, Claudia Bento-Pereira, Kanade Shiga, Andrea Corno, Maureen Higgins, Rachel Toth, Adrian T. Saurin, Albena T. Dinkova-Kostova

Peninsula Medical School

Measuring protein turnover in cells has been greatly assisted by fluorescent timers (FT). However, FT quantification requires relatively high fluorescence intensity samples, prohibiting their use for proteins with low or non-uniform expression like transcription factor Nrf2, the master regulator of redox homeostasis. To visualise changes in stability/turnover of Nrf2, we constructed a genetically encoded tag combining sfGFP and mCherry and used intensity-independent Fluorescence Lifetime Imaging (FLIM) to measure Förster Resonance Energy Transfer (FRET) within the tag (named FLIM-timer). We show that the ability of mCherry to act as a FRET-acceptor develops as the protein matures, allowing the use of FLIM-FRET …

One Tracer, Dual Platforms: Unlocking Versatility Of Fluorescent Probes In Tr-Fret And Nanobret Target Engagement Assays, Erika Y Monroy, Xin Yu, Dong Lu, Xiaoli Qi, Jin Wang

Faculty, Staff and Students Publications

Target engagement assays are essential for drug discovery, utilizing Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) and Nano Bioluminescence Resonance Energy Transfer (NanoBRET) as complementary methods for biochemical and cellular evaluation. Traditional platforms require distinct fluorescent tracers, increasing costs and complexity. This study systematically evaluates the cross-platform performance of T2-BODIPY-FL and T2-BODIPY-589, tracers developed for receptor-interacting protein kinase 1 (RIPK1) target engagement in TR-FRET and NanoBRET applications, respectively. Our results demonstrate both tracers effectively bridge biochemical and cellular assays, providing reliable measurements. T2-BODIPY-589 demonstrates superior performance in NanoBRET (Z’ up to 0.80) and acceptable functionality in TR-FRET (Z’=0.53). Conversely, T2-BODIPY-FL performs …

Baby Open Brains: An Open-Source Dataset Of Infant Brain Segmentations, Eric Feczko, Dimitrios Alexopoulos, Christopher D Smyser, Et Al.

2020-Current year OA Pubs

Reproducibility of neuroimaging research on infant brain development remains limited due to highly variable processing approaches. Progress towards reproducible pipelines is limited by a lack of benchmarks such as gold-standard brain segmentations. These segmentations are limited by the difficulty of infant brain segmentations, which require extensive neuroanatomical knowledge and are time-consuming in nature. Addressing this, we constructed the Baby Open Brains (BOBs) Dataset, an open source resource of manually curated and expert reviewed infant brain segmentations. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic …