Digital Commons Network^™

Summary Of Taxonomy Changes Ratified By The International Committee On Taxonomy Of Viruses (Ictv) From The Bacterial Viruses Subcommittee, 2025, Dann Turner, Evelien M. Adriaenssens, Rudolf I. Amann, Pavol Bardy, Nina Bartlau, Jakub Barylski, Stanislaw Błażejak, Majid Bouzari, Ariane Briegel, Yves Briers, Daniel Carrillo, Xia Chen, Dennis Classen, Ryan Cook, Marco A. Crisci, Arnaud Dechesne, Paulina Deptula, Bas E. Dutith, Bert Ely, Lars Fieseler, Et. Al.

Faculty Publications

This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy …

Assessment Of Dnase Activity By Ratiometric Fluorescence Resonance Energy Transfer, Candace L Minchew, Vladimir V Didenko

Faculty, Staff and Students Publications

The present protocol describes a simple and sensitive ratiometric Förster resonance energy transfer (FRET) assay for the detection and quantitative assessment of DNase activity. Ratiometric FRET measurements make use of the ratio of donor and acceptor emission signals. The assay detects single-stranded DNA breaks using a staple-shaped, dual-tagged 38-mer FRET oligoprobe, employed as a real-time DNA cleavage sensor. The main application of the described approach is the quantitative assessment of the effects of reaction conditions, such as pH, temperature, and buffer composition, on DNase activity. Due to its ability to detect even minor and slow DNA cleavage, the assay is …

U-Rich Elements Drive Pervasive Cryptic Splicing In 3′ Utr Massively Parallel Reporter Assays, Khoa Dao, Courtney F Jungers, Sergej Djuranovic, Anthony M Mustoe

Faculty, Staff and Students Publications

Untranslated RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich elements in 3' untranslated regions (3' UTRs) can drive upregulation or downregulation of mRNA expression depending on 3' UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3' UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent …

Advances In Key Technologies For The Management, Restoration, Development, And Utilization Of Coal Mining Subsidence Areas, Meng Zhuanghan, Wang Yutao, Tian Yanzhe

Coal Geology & Exploration

Background Coal mining subsidence areas, formed by the exploitation of coal resources, have emerged as severe challenges to the construction of ecological civilization and the sustainable development of the social economy in China. Their management, restoration, development, and utilization play a significant role in ecological security, food security, and energy transformation. Methods This study aims to address the unresolved and emerging issues in the management of coal mining subsidence areas. Based on the core concepts of management, restoration, development, and utilization, this study developed a dual-level zoning basis system combining theories and reality. Accordingly, coal mining subsidence areas in China …

Qualitative Thematic Analysis Of Crisis Communications From The Digital Pulpits Of Megachurches During Covid-19, Ralph Dustin Henderson

Doctoral Dissertations and Projects

The purpose of this qualitative thematic analysis multi-case study was to explore how secular crisis communication theories were adopted and modified by theological themes in U.S. megachurches during the first six weeks of the COVID-19 pandemic related lockdowns. Image Repair Theory (IRT), Discourse Renewal Theory (DRT), and Rhetorical Arena Theory (RAT) were examined alongside Christian themes (Theodicy, Radical Love, Physical Care, and Nontraditional Stakeholder Scope). Thematic analysis of sermon transcripts from 18 megachurches showed that IRT modified: high-attribution tactics were minimal; denial (via IMRA theodicy) defended the Church Universal (CU); evasion justified Church Local (CL)actions; and offensiveness reduction (esp. Transcendence) …

Pre-Service Teachers’ Perceptions Of Creativity In Education, Merve Topak-Jamsran

Theses and Dissertations

This study examined the relationship between pre-service teachers’ self-reported creativity and their appreciation for students’ creative characteristics. The researcher replicated Kettler et al.'s (2018) "Teacher Perceptions of Creativity in the Classroom" study of in-service teachers. Specifically, the relationship among pre-service teachers’ creative self-efficacy, self-reported personal creativity, perceived importance of promoting creativity, and their preference for student characteristics in the classroom was investigated. Data were gathered using a web-based questionnaire e-mailed to pre-service teachers in educational preparation programs in a southern U.S. state. The study sample were 92 pre-service teachers who had completed at least one practicum or who were currently …

Twist And Snout: Head And Body Morphologies Determine Feeding Kinematics In Substrate-Biting Fishes, Tal Perevolotsky, Jacob M. Brotman-Krass, Yarden Ratner, Yael Avigad, Adam P. Summers, Cassandra M. Donatelli, Roi Holzman

Engineering Faculty Articles and Research

Synopsis

Across teleosts, feeding by biting substrate-attached prey has evolved multiple times and is associated with convergent morphologies that include a deep body and an elongated, tapered head. However, the functional role of these morphologies in substrate-biting fish is not established. Here, we tested the hypothesis that these morphologies function as control surfaces that affect feeding kinematics during biting. To test this hypothesis, we used simplified physical models of substrate-biting reef fish and examined the role of head, body, and fin morphology in determining feeding kinematics that facilitate the removal of substrate-attached prey. Models simulated the swift lateral movement of …

Long Term Outcomes Of Dermal Substrate Treated Burns And Wounds, Sarvesh Senguttunvan, Sigrid A. Blome-Eberwein Md

Research Scholars

No abstract provided.

Adaptive Bayesian Clinical Trials: The Past, Present, And Future Of Clinical Research, Donald A Berry

Faculty, Staff and Student Publications

Background/Objectives: Decision-analytic Bayesian approaches are ideally suited for designing clinical trials. They have been used increasingly over the last 30 years in developing medical devices and drugs. A prototype trial is a bandit problem in which treating participants is as important as treating patients in clinical practice after the trial.

Methods: This article chronicles the use of the Bayesian approach in clinical trials motivated by bandit problems. It provides a comprehensive historical and practical review of Bayesian adaptive trials, with a focus on bandit-inspired designs.

Results: The 20th century saw advances in Bayesian methodology involving computer simulation. In the …

Human Ipsc-Based Breast Cancer Model Identifies S100p-Dependent Cancer Stemness Induced By Brca1 Mutation, Jingxin Liu, Cai Zhao, Jiahao Chen, Pengguihang Zeng, Qingjian Li, Ranran Dai, Xingqiang Lai, Wenqian Song, Jianing Chen, Xixi Zhu, Xinyi Liu, Jun Sun, Jia Wang, Peihang Fang, Tengfei Wang, Wenjie Chen, Diana Guallar, Nan Cao, Jianli Zhao, Shicheng Su, Andy Peng Xiang, Yi Arial Zeng, Jie Li, Junchao Cai, Dung-Fang Lee, Jinxin Bei, Yongliang Huo, Hai Hu, Shengbao Suo, Dong-Feng Huang, Jin Bai, Junjun Ding

Faculty, Staff and Student Publications

Breast cancer is the most common malignancy in females and remains the leading cause of cancer-related deaths for women worldwide. The cellular and molecular basis of breast tumorigenesis is not completely understood partly due to the lack of human research models which simulate the development of breast cancer. Here, we developed a method for generating functional mammary-like cells (MCs) from human-induced pluripotent stem cells (iPSCs). The iPSC-MCs closely resemble human primary MCs at cellular, transcriptional, and functional levels. Using this method, a breast cancer model was generated using patient-derived iPSCs harboring germline

Il-6 Predicts Cdk4/6 Inhibitor Resistance, Identifying Stat3 As A Target In Hr + /Her2-Negative Metastatic Breast Cancer, Nicole M Kettner, Tuyen N Bui, Juliana Navarro-Yepes, Sanaz Ghotbaldini, Bethanie Quintela, Catherine K Luo, Nghi Lam, Xiayu Rao, Akshara Singareeka Raghavendra, Yan Wang, Nancy Azizian, T Kris Eckols, Moses Makokha Kasembeli, Kurt Evans, Min Yi, Hannah Wingate, Jing Wang, Aysegul A Sahin, Funda Meric-Bernstam, Kelly K Hunt, Senthil Damodaran, David J Tweardy, Debu Tripathy, Khandan Keyomarsi

Faculty, Staff and Student Publications

Resistance to CDK4/6 inhibitors (CDK4/6i) is a major challenge in treating hormone receptor-positive, HER2-negative metastatic breast cancer. This study aimed to identify a biomarker predictive of resistance that could also serve as a therapeutic target. Circulating IL-6 levels in 166 patients significantly increased at progression, making IL-6 a non-invasive biomarker to predict CDK4/6i resistance. Knockdown of IL-6 re-sensitized resistant cells to palbociclib and endocrine therapy, underscoring IL-6's critical role in maintaining resistance. Patient-derived xenograft models from patients who progressed within 3 months versus ≥6 months of palbociclib therapy revealed distinct transcriptomic profiles, with later progressors exhibiting IL-6/STAT3 activation, epithelial-to-mesenchymal transition, …

Creation Of Bacteria In Tongue Diagnosis Based On Fractal Methods, S. Pavithra, G. Jayalalitha

Baghdad Science Journal

Bacteria play a vital role in helping with digestion and protecting against harmful infections. However, the Gram-negative bacteria in Tongue will have some disadvantages in the human body. These can be diagnosed by employing the fractal concept. Bacteria's irregular shape and Complex nature can be quantified using fractal dimensions that exhibit self-similarity at different scales. The fractal measurement procedure deliberates the dissimilarity and surface complexity of the tongue-inclusive spot on the tongue. An image of the tongue is analyzed by the HarFa Fractal Method. The Sobel improved Box counting Method is employed to enumerate the outgrowth of Bacteria in Tongue. …

Replication Of Sensor-Based Categorization Of Upper-Limb Performance In Daily Life In People Post Stroke And Generalizability To Other Populations, Chelsea E Macpherson, Marghuretta D Bland, Christine Gordon, Allison E Miller, Caitlin Newman, Carey L Holleran, Christopher J Dy, Lindsay Peterson, Keith R Lohse, Catherine E Lang

2020-Current year OA Pubs

BACKGROUND: Wearable movement sensors can measure upper limb (UL) activity, but single variables may not capture the full picture. This study aimed to replicate prior work identifying five multivariate categories of UL activity performance in people with stroke and controls and expand those findings to other UL conditions.

METHODS: Demographic, self-report, and wearable sensor-based UL activity performance variables were collected from 324 participants (stroke

RESULTS: Two PCs explained 70-90% variance: PC1 (overall UL activity performance) and PC2 (preferred-limb use). A five-variable, five-cluster model was optimal across samples. In comparison to clusters, two PCs and individual accelerometry variables showed higher convergent …

U-Rich Elements Drive Pervasive Cryptic Splicing In 3' Utr Massively Parallel Reporter Assays, Khoa Dao, Courtney F Jungers, Sergej Djuranovic, Anthony M Mustoe

2020-Current year OA Pubs

Untranslated RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich elements in 3' untranslated regions (3' UTRs) can drive upregulation or downregulation of mRNA expression depending on 3' UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3' UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent …

Phase 1b/2 Study Evaluating Safety, Efficacy And Immune Effects Of Tlr9 Agonist Cavrotolimod With Anti-Pd-1 Antibodies Among Patients With Advanced Solid Tumors, Mohammed M Milhem, George Ansstas, Et Al.

2020-Current year OA Pubs

BACKGROUND: There is an unmet need for novel immunotherapies to overcome immune evasion in patients with advanced skin cancers resistant to programmed death (PD)-1 / PD-ligand 1 (PD-L1) blockade. Cavrotolimod is a novel spherical nucleic acid configuration of a toll-like receptor 9 agonist oligonucleotide, designed to trigger innate and adaptive immune responses to tumors.

PATIENTS AND METHODS: The safety, pharmacokinetics, pharmacodynamics and preliminary efficacy of intratumoral cavrotolimod, first dosed alone and then in combination with anti-PD-1 antibodies (pembrolizumab or cemiplimab), were assessed in a combined Phase 1b/2 dose escalation/dose expansion study in patients with advanced skin cancers, including melanoma, Merkel …

Inhibition Of The Caveolin-1 Pathway Promotes Apoptosis And Overcomes Pan-Tyrosine Kinase Inhibitor Resistance In Hepatocellular Carcinoma, Tasnuva D. Kabir, Samuel Beck, Lisa M. Stuart, Ji Li, Rui Hou, Peiwen Liu, Shelby Margolius, Claire Kim, Yu Suk Choi, Edward R. Bastow, Dianne J. Beveridge, Lisa Spalding, Ziyi Li, Florent Ginhoux, Pierce Chow, Michael Phillips, Andrew D. Redfern, George C. Yeoh, Alistair Forrest, Andrew J. Woo, Ankur Sharma, Jacob George, Geoffrey Mccaughan, Peter Leedman

Research outputs 2022 to 2026

Resistance to multi-tyrosine kinase inhibitors (TKI) is a major clinical concern in advanced hepatocellular carcinoma (HCC). Herein, we aimed to uncover the mechanisms underlying pan-TKI resistance and to identify potential therapeutic targets. We used multiple TKI-resistant HCC cell lines to identify caveolin-1 (CAV1) as a key driver of therapeutic resistance. CAV1 downregulation induced apoptosis, inhibited metastasis and restored TKI sensitivity in both inherent and acquired TKI-resistant HCC cells. Mechanistically, in acquired TKI-resistant cells aberrant CAV1/STAT3/P70S6K signalling is required for their survival, motility, and invasiveness. CAV1 inhibition reduced expression of dormancy regulators E-cadherin, RAC1 and p21, enhanced cancer stemness markers, and …

Creating Learning Bridges: Redesigning Homework Within The Framework Of Multiple Intelligences, Vasileios Zagkotas

Journal of Educational Research and Practice

The article explores the application of Howard Gardner’s theory of multiple intelligences to homework and the potential of this approach to enhance the educational experience. Through a pilot application in philological subjects in Greek secondary education, the article presents the Homework Toolkit for Cultivating Multiple Intelligences, which offers various activities adapted to different types of intelligence. The findings from the case study research indicated that applying multiple intelligence theory to homework design improved academic performance, responsibility, and student collaboration, while also enhancing critical thinking and creativity. The results indicate that designing homework based on multimodal learning can reform the learning …

The Human Condition, Hannah Arendt

Hannah Arendt Marginalia - All

[Chicago] University of Chicago Press [1958]

Call #: HM211. A7

contains marginalia, marginal lining, editing, endpaper notes and “Hannah’s corrections” see late edition (front page)

PDF Information: 36 pages – 3 MB

The Human Condition, Hannah Arendt

Hannah Arendt Marginalia - All

Garden City, N.Y., Doubleday, 1959

Call #: HM211 .A7 1959

contains marginalia

PDF Information: 8 pages – 291 KB

Anatomical And Palynological Studies On Turkish Primula Taxa (Primulaceae) And Their Taxonomic And Phylogenetic Significance, Deni̇z Ulukuş, Esengül Özkaymakoğlu, Rebecca Stubbs, Hüseyi̇n Baykal, Kami̇l Coşkunçelebi̇, Osman Tugay, Barbara Keller, Elena Conti, Ferhat Celep

Turkish Journal of Botany

Anatomical (scape, pedicel, leaf lamina, and leaf midrib) and pollen morphological features of 11 taxa belonging to the genus Primula subgen. Primula (P. vulgaris subsp. vulgaris, P. vulgaris subsp. rubra, and P.megaseifolia, P. meyeri,P. elatior subsp. pallasii, P. pseudoelatior, P. veris subsp. columnae, P. veris subsp. macrocalyx) and subgen. Aleurita (P. longipes, P. algida and P. auriculata) were examined using light and scanning electron microscopy to shed light on the existing taxonomic and phylogenetic relationships. The anatomical and palynological features of the majority of the taxa studied were revealed for the first time in this study. In anatomical studies, the …

How Effective Are Engineered And Non-Engineered Riparian Forest Restoration Projects In Providing Salmonid-Quality Habitat In The San Francisco Bay Area?, Alexander Ivanov

Master's Theses

Streams and their riparian zones in the San Francisco Bay Area have been degraded, severely harming salmonid populations in the region. Ecological restoration is a common approach to return stream function. Such restoration projects vary widely in intensity, from low-impact vegetation removal/planting to highly engineered projects involving structures and grading. This research investigated the effectiveness of streams restored using engineered versus non-engineered solutions in supporting salmonid habitat viability in San Francisco Bay Area streams. Fourteen streams, seven from each of the two types of restoration, were sampled in the wet and dry season in 2024, three times each season. Data …

Replicating Vignoles Et Al. Results On Multidimensional Self-Construal: Comparing The United States, East Asia, Southeast Asia, And Latin America, Jon Lorenz A. Lim

Master's Theses

Contemporary research on self-construal indicates that people define and perceive themselves either as independent or interdependent. Self-construal scales have become the most common method to quantitatively measure both types of self-construal across the United States, East Asia, Southeast Asia, and Latin America. Multidimensional measures of the self tend to be more accurate in defining the self than earlier dichotomous scales. In general, European Americans and Latin Americans perceived themselves as independent and East and Southeast Asians as interdependent. In the current study, undergraduate European American, East Asian American, Southeast Asian American, and Latin American students from San Jose State University …

Small Current, Big Potential: Bridging Mechanistic Insight Of The Sk Channel With Translational Promise, Yang Zheng, Miao Zhang, Nipavan Chiamvimonvat

Pharmacy Faculty Articles and Research

"Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia, with a lifetime risk of approximately 1 in 4 for adults aged 40 years and above. Despite advances in clinical management, AF remains a major public health concern. Its burden extends beyond symptoms; it quadruples the risk of heart failure and increases the likelihood of stroke fivefold – strokes that are often more severe and fatal than those unrelated to AF. In the United States alone, AF-associated healthcare costs exceed $26 billion annually, and the cost is projected to grow as the population ages (Ko et al., 2025). Regarding current treatments, …

A Genetically-Engineered Thyroid Gland Built For Selective Triiodothyronine Secretion, Cintia E. Citterio, Berenice Morales-Rodriguez, Xiao-Hui Liao, Catherine Vu, Rachel Nguyen, Jessie Tsai, Jennifer Le, Ibrahim Metawea, Ming Liu, David P. Olson, Samuel Refetoff, Peter Arvan

Pharmacy Faculty Articles and Research

Thyroid hormones (thyroxine, T₄, and triiodothyronine, T₃) are indispensable for sustaining vertebrate life, and their deficiency gives rise to a wide range of symptoms characteristic of hypothyroidism, affecting 5–10% of the world’s population. The precursor for thyroid hormone synthesis is thyroglobulin (Tg), a large iodoglycoprotein consisting of upstream regions I-II-III (responsible for synthesis of most T₄) and the C-terminal CholinEsterase-Like (ChEL) domain (responsible for synthesis of most T₃, which can also be generated extrathyroidally by T₄ deiodination). Using CRISPR/Cas9-mediated mutagenesis, we engineered a knock-in of secretory ChEL into the endogenous TG …

Scoring Goals With Autistic Children: Decision Making And Successful Implementation, Victoria Henbest, Brenda L. Beverly

APLL Lab Presentations

No abstract provided.

Anti-Nociceptive Properties Of Cardiopulmonary Baroreceptors In Patients With Chronic Back Pain, Yuto Iwakuma, Jennifer Liu, Davina A. Clonch, Megan E. Gangwish, Christopher M. Lam, Seth W. Holwerda

Student Publications

Introduction: Reduced pain perception following a persistent noxious stimulus during a study session (short-term habituation) is believed to be partially mediated by descending inhibitory mechanisms, although these mechanisms have not been fully elucidated. We examined the hypothesis that cardiopulmonary baroreceptor would significantly increase short-term habituation in chronic back pain (CBP) patients.

Methods: A short-term habituation protocol was utilized that involved 1-sec pulses (×10) at 105% heat pain threshold on the anterior forearm at 0.5 Hz. Cardiopulmonary baroreceptor unloading was performed via lower body negative pressure (LBNP) that reduces central venous pressure to elicit a reflex increase in sympathetic nerve activity. …

Quantifying The Economic Burden Of Cancer In California Using Advanced Analytics, Terence Casey Kelley

Walden Dissertations and Doctoral Studies

Cancer imposes a significant and multifaceted economic burden on California’s health care system and communities. Despite extensive national data, California-specific cost analyses have been outdated and limited. This study quantified California’s cancer-care burden through a quantitative, cross-sectional design grounded in the cost-of-illness framework and human-capital theory. A retrospective modeling approach used 2015–2023 data from the California Cancer Registry, National Cancer Institute, National Program of Cancer Registries, and California’s all-payer claims database. California’s economic burden from cancer was estimated using a meta-analysis of national cost data, which was then applied to state-specific cancer incidence, prevalence, and mortality through a multicriteria decision …

Effect Of Sodium Dodecyl Sulfate And Three Commercial Detergents On The Growth And Physiological Parameters Of The Filamentous Green Alga Cladophora Sp., Eduardo Ruíz-Hernández, Alma Socorro Sobrino-Figueroa, César Abelardo González Ramírez, José Roberto Villagómez-Ibarra

Turkish Journal of Botany

Surfactants are pollutants of environmental concern. Released in large volumes into aquatic environments, they have detrimental effects on the growth and physiological functions of living organisms. This study aimed to determine physiological effects of sodium dodecyl sulfate (SDS) and three commercial detergents on filamentous alga Cladophora sp. It followed the methodological guidelines of the Organisation for Economic Cooperation and Development (OECD) to test seven concentrations of SDS (0, 0.1, 1, 5, 10, 50, and 100 mg/L) and six concentrations of commercial detergents (0, 1, 15, 30, 45, and 60 mg/L) using three replicates in a fully randomized design. At the …

Genotoxicity Assessment Of Conventional And Cad/Cam Denture Base Materials, Alanood Aldubayan

Master's Theses (2009 -)

Aim: In prosthodontics, polymethyl methacrylate (PMMA) has been widely used. Their biocompatibility and potential genotoxicity remain a concern due to the residual monomer release. Computer-aided design and manufacturing (CAD/CAM) denture base materials have emerged and offered some improved mechanical and physical properties compared to the standard conventional heat-cured denture base material. However, their long-term biocompatibility remains unstudied. Therefore, this study evaluates the genotoxicity effects of conventional and CAD/CAM denture base materials on human gingival fibroblasts (HGFs). Methodology: Disk-shaped samples were fabricated of six denture base resins, including heat-cured PMMA, milled PMMA, and four 3D-printed resins. HGFs were exposed to the …

Navigating Environmental Changes: Placencia Peninsula Voices & Local Expertise (Report No. 10), Kris-An Hinds, Rebecca Zarger, Rory Mckenna, Linden Cheek, Natasha Gibson, Delcia Mcdougall, Monique Vernon, Maya Trotz

Strong Coasts Collection

The “Navigating Environmental Changes: Placencia Peninsula Voices & Local Expertise” event, hosted on July 24, 2024, at the Placencia Village Basketball Court, was a significant step in strengthening community-centered environmental research and action in Belize. Organized as part of the NSF-funded Strong Coasts Coastlines and People (CoPe) project, this two-part event was designed as a way to share research findings with the communities and partners who have been central to the project’s success.