Digital Commons Network^™

Integrative Multi-Omics Profiling Identifies Infiltrative Hepatocellular Carcinoma As An Immunotherapy-Resistant Subtype With Distinct Molecular Features, Won Suk Lee, Seonjeong Woo, Sung Hwan Lee, Gae Hoon Jo, Ilhwan Kim, Hyeyeong Kim, Chansik An, Sanghoon Jung, Gwangil Kim, Haeyoun Kang, Beodeul Kang, Jung Sun Kim, Ho Yeong Lim, Incheon Kang, Hannah Yang, So Jung Kong, Dahyeon Son, Dong Jun Shin, Woo Young Kwon, Da-Yeon Lee, Ju-Seog Lee, Junho Park, Youngsoo Kim, Sohyun Hwang, Chan Kim, Hong Jae Chon

Faculty, Staff and Student Publications

Background/aims: Hepatocellular carcinoma (HCC) exhibits substantial morphological and biological heterogeneity. Clinical and molecular relevance of the infiltrative subtype remains poorly defined in the context of cancer immunotherapy. We aimed to evaluate the prognostic impact and molecular features of infiltrative HCC in patients treated with first-line atezolizumab plus bevacizumab (Ate/Bev).

Methods: We included 307 patients with advanced HCC treated with Ate/Bev and classified them into four gross morphological types based on imaging. Multi-omics profiling was conducted on tumor samples. Type IV infiltrative signature was derived and externally validated using five independent HCC cohorts, including IMbrave150.

Results: Infiltrative morphology, encompassing pure and …

Engineering Mutation Clones In Mammalian Cells With Crispr/Cas9, Zijun Huo, Jian Tu, Rachel Shoemaker, Dung-Fang Lee, Ruiying Zhao

Faculty, Staff and Student Publications

CRISPR, Clustered Regularly Interspaced Short Palindromic Repeat, as a powerful genome engineering system, has been widely accepted and employed in gene editing of a vast range of cell types. Compared to zinc finger nucleases (ZFNs) or transcription activator-like effector nucleases (TALENs), CRISPR shows a less complicated process and higher efficiency. With the development of different CRISPR systems, it can be used not only to knock out a gene but also to make precise modifications, activate or repress target genes with epigenetic modifications, and even for genome wide screening. Here we will describe the procedure of generating a stable cell line …

Organized Sports-Based Interventions And Motor Outcomes In Children Diagnosed With Autism Spectrum Disorder: A Systematic Review, Kailash Ram, Maeren Hill, Caitlyn Stewart, Kaitlin P. Hardy Md, Sonia Khurana

Rehabilitation Sciences Faculty Publications

Aim

To evaluate the effectiveness of organized sports-based interventions on motor outcomes in children with autism spectrum disorder (ASD).

Method

Four databases were searched from inception to November 2025 for randomized controlled trials (RCTs) and non-randomized controlled trials (NRCTs) reporting motor outcomes of organized sports-based interventions in children with ASD. Risk of bias was evaluated using ROB-2 (Cochrane Risk of Bias Tool, Version Two) for RCTs and ROBINS-I (Risk Of Bias In Non-randomized Studies - of Interventions) for NRCTs.

Results

Eleven studies (six RCTs, five NRCTs) were included and categorized as martial arts (n = 5), aquatic training (n = …

Poly(A) Probe Hcr Rna-Fish Specifically Marks Pyriform Nurse Cells In The Brown Anole Lizard Ovary, Zoe B Griffin, Bonnie K Kircher, Richard R Behringer

Faculty, Staff and Student Publications

Hybridization chain reaction RNA-fluorescent in situ hybridization (HCR RNA-FISH) is a powerful and increasingly used method for visualizing gene expression in cells and tissues. A probe set against polyadenylated RNA (poly(A)) is often used as a positive control for RNA integrity and staining quality. While optimizing this technique in the ovary of the brown anole lizard (Anolis sagrei), we found that the poly(A) probe produced a strikingly specific and intense signal in pyriform cells, a specialized lizard-specific nurse cell type. This staining pattern was found in both whole-mount samples and paraffin sections, suggesting that poly(A) signal intensity can serve as …

Uncertainty-Guided Test-Time Optimization For Personalizing Segmentation Models In Longitudinal Medical Imaging, Jaehee Chun, Austin Castelo, Mckell Woodland, Caleb O'Connor, Mais Al Taie, Mohamed Eltaher, Aashish Gupta, Bilel Daoud, Shanli Ding, Jeddy Bennett, Anirban Maitra, Matthew A Firpo, Kimberly Kirkwood, Eugene J Koay, Kristy K Brock

Faculty, Staff and Student Publications

Background: Accurate and consistent image segmentation across longitudinal scans is essential in many clinical applications, including surveillance, treatment monitoring, and adaptive interventions. While personalized model adaptation using patient-specific prior scans has shown promise, current approaches typically rely on fixed training durations and lack mechanisms to determine optimal stopping points on a per-patient basis, particularly in the absence of validation labels.

Purpose: We propose an uncertainty-guided test-time optimization (TTO) framework that dynamically adjusts the personalization duration for each patient using a validation-free stopping criterion based on predictive uncertainty.

Methods: Our framework personalizes a generalized segmentation model using patient-specific prior imaging and …

Contralateral Breast Cancer After Radiotherapy And Hormone Therapy In Two Cohorts Of Us Breast Cancer Survivors, Lene H S Veiga, Gretchen L Gierach, Susan A Smith, Rebecca M Howell, Matthew M Mille, Monjoy Saha, Rochelle E Curtis, Cody Ramin, Clara Bodelon, Heather Spencer Feigelson, Erin J Aiello Bowles, Diana S M Buist, Sheila Weinmann, Jacqueline B Vo, Choonsik Lee, Amy Berrington De Gonzalez

Faculty, Staff and Student Publications

Background: Radiotherapy increases contralateral breast cancer risk, while hormone therapy reduces it; their combined effects are unclear.

Methods: Data from two US retrospective cohort studies of 5-year breast cancer survivors (stage I-III, ages 20-84), Kaiser Permanente (KP, 1990-2012) and SEER (1990-2013), were analysed. Contralateral breast radiation doses were estimated for the KP cohort. Multivariable Poisson regression estimated relative risks (RRs) and excess relative risks per Gray (ERR/Gy), stratified by hormone therapy use.

Results: KP cohort (n = 9053) included 353 contralateral breast cancer cases (73% ER+); SEER cohort (n = 244,834) included 10,470 cases (72% ER+). Among women with ER+ …

Host Modulation Therapy In Periodontitis: From Established Therapies To Emerging Technologies, Aonjittra Phanrungsuwan, Jiaqi Huang, Neeraja Dharmaraj, Alejandra Cobos Perez, Omid Veiseh, Simon Young, Chun-Teh Lee

Faculty, Staff and Student Publications

Periodontitis is a biofilm-induced chronic inflammatory disease, characterized by gingival inflammation and alveolar bone loss. According to a national survey, approximately half of the U.S. adults are affected by periodontal disease. To effectively prevent and treat periodontitis, it is essential to address its underlying causes. The primary etiological factors include polymicrobial synergy and dysbiosis of the oral microbiota, and a dysregulated immune response. The standard therapeutic approach, mechanical removal of biofilm through debridement, sometimes demonstrates limited efficacy, particularly in cases of severe periodontitis, which may require adjunctive or additional therapy. Emerging evidence indicates that periodontal tissue destruction is initiated by …

Integrating Multi-Method Monitoring To Characterize Seasonal Habitat Use Of Green Sturgeon (Acipenser Medirostris) In Humboldt County, California, Olivia S. Boeberitz

Cal Poly Humboldt theses and projects

Green sturgeon (Acipenser medirostris) are a long-lived, anadromous, iteroparous species that spawns in large West Coast North American rivers but ranges widely in the coastal ocean. For coastal California Native American Tribes, green sturgeon are a vital part of their cultural heritage and traditions, and central to their food security. Two genetically distinct population segments (DPSs) of green sturgeon are recognized in the United States, Canada, and Mexico; the southern DPS is listed as “threatened” under the Endangered Species Act and the northern DPS is considered of “conservation concern.” Although green sturgeon are known to use large estuaries …

Factors Influencing Tree Vigor And Structural Failure Along Powerline Corridors In Northern California: A Multi-Species Analysis, David Justin Dorval

Cal Poly Humboldt theses and projects

Tree failures (e.g., stem breakage, uprooting, or branch drop) can pose significant risks to public safety, particularly along powerline corridors for the risk of power outages and wildfire ignitions. In California, tree-related powerline failures have led to severe ecological and human costs in recent years. Despite extensive research on tree failure in urban environments and post-disturbance contexts, comparatively little empirical work has examined where powerlines intersect largely unmanaged stands. This study evaluates tree failure trends across multiple forest types in Northern California by examining how tree-level characteristics influence recent growth and failure occurrence in regionally dominant tree species. Specifically, the …

Baker Cypress (Hesperocyparis Bakeri) In A Changing Fire Landscape: Characterizing Fire Refugia And Guiding Post-Fire Reforestation, Olivia Lorraine Moskowitz

Cal Poly Humboldt theses and projects

Increasing wildfire frequency threatens serotinous, fire-obligate species that depend on sufficient fire-free intervals to develop seed banks for reproduction. These species require fire intense enough to trigger seed release and create favorable substrate and light levels for regeneration, yet consecutive fires that reburn populations before they reach maturity can cause local population contraction or extirpation. Understanding the environmental drivers of natural regeneration and mature tree survival, as well as when and how active reforestation should supplement natural recovery, is critical for managing fire-adapted species under altered fire regimes.

This thesis uses Baker cypress (Hesperocyparis bakeri [Jeps.] Bartel), a rare …

Do California Rangeland Healthy Soil Practices Offer Co-Benefits For Grassland Birds?, Ximena O. Gil

Cal Poly Humboldt theses and projects

Rangelands are important landscapes in California that support a robust cattle industry and serve as vital grassland habitat for birds. Climate change is projected to impact rangelands, leading to economic and ecological deterioration. In California, the Healthy Soils Program (HSP) incentivizes climate-smart solutions to increase working land resiliency. While the HSP targets soil and range health for livestock, it may also benefit birds. We surveyed rangeland operators to examine whether the implementation and duration of specific range management practices, such as range seeding, prescribed grazing, and silvopasture, are associated with bird community responses, using avian point count data from Point …

Aquatic Habitat Use By Western Toads And American Bullfrogs In California’S Central Valley: Effects Of Local Habitat Characteristics And Landscape Composition, Kaitlyn Breana Hernandez

Cal Poly Humboldt theses and projects

Drastic losses of historic wetland habitat in the California Central Valley have caused widespread population declines and extirpations of aquatic breeding amphibians. Efforts to restore wetland habitat have included private land, which represents 70% of land tenure in the Central Valley. Management of these restored wetlands is focused on waterfowl with the assumption that they will provide habitat for native herpetofauna. This study used combined surveys to test the assumption that restored wetlands on private land provide habitat for native amphibians with the western toad (Anaxyrus boreas) as a case study. The objectives were to use environmental DNA …

Early Successional Response To Stream Daylighting In Redwood National And State Parks, Orick, California, Rylee Rawson

Cal Poly Humboldt theses and projects

In-channel stream restoration projects can act as both disturbance and recovery mechanisms, disrupting existing conditions to reestablish the hydrologic and ecological processes that sustain stream ecosystems. These interventions initiate successional trajectories in which channel form and biological communities reorganize over time. In Redwood National and State Parks (California, USA), the Redwoods Rising initiative restores buried headwater channels by recontouring legacy logging roads and daylighting streams buried by Humboldt crossings. Using the National Park Service Klamath Network wadable stream monitoring protocol, I evaluated nine restored reaches spanning one to five years post-restoration, alongside old-growth reference reaches and available pre-treatment data. I …

Forest Management Options For The Wildland Urban Interface: Comparative Analysis Of Stand Development, Economics, And Forest Carbon Over 100 Years In Sierra Nevada Ponderosa Pine, Kassandra A. Mcdaniel

Cal Poly Humboldt theses and projects

This thesis presents a simulation study of various forest stand treatments and their long-term effects on ponderosa pine-dominated forests in the Sierra Nevada Mountain Range of the western USA. The goal was to create recommendations for forest management in the wildland urban interface (WUI) of the Tahoe National Forest and other locations with similar conditions. This study simulates current United States Forest Service (USFS) - Truckee Ranger District silvicultural treatment alternatives repeated over a 100-year period using the USFS Forest Vegetation Simulator (FVS). Proposed treatment alternatives include restoration, resilience, transition, conservation, and no management. Treatments are to be compared in …

Coho Salmon (Oncorhynchus Kisutch) Response To Habitat Restoration Through Space And Time: Monitoring Growth, Survival, And Movement In A Restored Habitat Network, Carter Perez Adamson

Cal Poly Humboldt theses and projects

Despite the decline of coho salmon (Oncorhynchus kisutch), Prairie Creek, a tributary of Redwood Creek in northern California, remains a coho salmon stronghold. The restoration of juvenile coho rearing habitat was identified as a recovery objective in this watershed by the National Marine Fisheries Service. Among the restoration projects addressing this objective are an ongoing project on Prairie Creek and its tributary Skunk Cabbage Creek, and a prior effort on Strawberry Creek (a tributary of Redwood Creek’s estuary). Standard monitoring methods for assessing project success have limitations and may be improved by measuring salmon use of restored habitats …

Relational Approaches To Fire Resilience: Designing A Living Shaded Fuel Break With Indigenous Knowledge Systems, Natalee Nicole Lopes

Cal Poly Humboldt theses and projects

Escalating wildfire severity across California reflects not only changing climatic conditions but also the cumulative impacts of colonial land management systems that have disrupted Indigenous fire stewardship and altered forest structure and function. This project examines how wildfire mitigation infrastructure, specifically linear fuel treatments, such as fuel breaks, can be reimagined through Indigenous relational frameworks of care-based land stewardship. Grounded in Happy Camp (Athithúfvuunupma), California, within the ancestral homelands of the Karuk Tribe along the mid-Klamath River, this research is carried out in collaboration with Karuk knowledge holders, centering Indigenous knowledge systems and priorities.

Using a mixed-methods approach that integrates …

Regeneration And Fuel Loading With Varying Overstory Retention In Redwood Stands 10 Years After Transformation To Multiaged Management, Jud Fisher

Cal Poly Humboldt theses and projects

Forest managers using retention forestry in western forests need information on regeneration dynamics and fuel development to design stands that are both productive and fire resilient. This study analyzes 10-year remeasurement data from the Redwood Multiaged Experiment in Jackson Demonstration State Forest, California, comparing regeneration and fuel responses across group selection (GS), aggregated (HA), and dispersed (LD, HD) retention treatments. Target relative density (RD) of the residual stand was zero in GS, 13% in LD, and 21% in HA and HD. Measurements included sprout growth and size of redwood and tanoak, seedling and sprout density, and surface fuel loading.

Redwood …

Succession And Alpine Plant Habitat Of A Recently Deglaciated Foreland In The Trinity Alps, California, Sebastian Evans

Cal Poly Humboldt theses and projects

The recent extinction of the Salmon Glacier in the Trinity Alps, California, provides a rare opportunity to examine post-glacial succession in a region of high endemism experiencing climatic stress. Using a chronosequence spanning ~150 years since deglaciation, I investigated (1) vegetation successional trajectories in the foreland, (2) whether the foreland functions as a climate refugium for alpine specialists, and (3) whether facilitative interactions between the dominant vascular plant (DVP) and bryophytes occur and persist through succession. I surveyed 100 plots across 11 transects within the foreland and 40 randomized plots in adjacent ecosystems. Successional patterns and refugial potential were analyzed …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

Effects Of Coaching Interventions On Burnout And Mental Health Outcomes Among Collegiate Athletes: A Meta-Analysis, Natalie Mitchell

Cal Poly Humboldt theses and projects

This meta-analysis examined the effects of coaching interventions on burnout and mental health outcomes among collegiate athletes. Following PRISMA guidelines, literature published from 1980 onward was searched across SPORTDiscus, PsycINFO, PsycARTICLES, PubMed/MEDLINE, Web of Science, and ProQuest Theses & Dissertations. Studies were included if they assessed burnout, psychological well-being, or related mental health outcomes in collegiate athletes and investigated a coaching intervention. Twelve interventional studies met the inclusion criteria. Across studies, coaching interventions varied in structure, duration, sport context, and cultural setting, with most emphasizing intrapersonal strategies and emotional or mental health outcomes. Meta-analytic results indicated small, non-significant effects favoring …

Urban Trees In The Urban Hydrology Cycle, Jorge R. Vera

Theses, Dissertations and Capstones

In urban forestry, trees provide numerous economic, ecological, and aesthetic benefits to the surrounding community. One of their key roles is intercepting stormwater runoff, reducing flooding risk, and improving water quality. Chapter 1 of this thesis characterized the ecological and economic contributions of urban trees on the Marshall University campus and provides guidance on their management and conservation in the future. Chapter 2 examined how urban tree species modify the urban hydrology cycle by altering the volume and timing of precipitation delivery. In Chapter 1, we inventoried 114 acres of Marshall University's main campus in Huntington, WV, from June 28 …

Are There Enough Bees? Assessing Pollen Limitation In Native Eastern Washington Prairie Forbs, Alejandro Torres

EWU Masters Thesis Collection

Prairie ecosystems in eastern Washington have been severely degraded due to agricultural intensification, urbanization, and habitat fragmentation, leaving less than 0.1% of native prairie intact. As a result, these ecosystems have become some of the most endangered in the United States. One group of essential pollinators is the bees, which facilitate plant reproduction and contribute to the long-term persistence of restored plant communities. However, despite the presence of at least 257 native bee species in the region, the impacts of habitat fragmentation and restoration on pollinator activity and plant-pollinator networks remain poorly understood. For this study, we worked across Eastern …

Moth Assemblages Of Fort Leonard Wood, Missouri, Kimberly Anne Steese

Masters Theses

"Moths (Lepidoptera) are ecologically important insects that function as herbivores, pollinators, prey resources, and indicators of ecosystem integrity. Despite their ecological significance, moth communities in the Missouri Ozarks remain poorly documented, particularly within military-managed landscapes. This thesis examined patterns of moth diversity, assemblage structure, and environmental drivers at Fort Leonard Wood (FLW), Missouri, while also assessing the distribution and genetic diversity of species within the genus Papaipema.

Field surveys were conducted from 2019 through 2021 across prairie, savanna, forest, and restoration habitats at FLW using UV bucket traps, sheet trapping, and targeted larval surveys. Across all sampling efforts, 29,116 individual …

Assessing The Effects Of Theta Transcranial Alternating Current Stimulation During Working Memory Performance On Theta-Gamma Phase Amplitude Coupling In Healthy Adults, Samantha M. Zimmer

UNF Graduate Theses and Dissertations

Transcranial alternating current stimulation (tACS) is an emerging form of noninvasive brain stimulation with substantial effects on behavior and brain function due to its ability to entrain endogenous neural oscillations. Working memory is a cognitive process that involves holding onto information that is no longer present in the environment and manipulating or reorganizing information for immediate use. Theta oscillations are critical for the functionality of the frontoparietal network and are involved in strengthening communication and coordination between frontal and parietal brain regions, especially during working memory processing. TACS applied at the theta frequency, targets theta oscillations, strengthens network communications, and …

Real-Time Immersive Wildfire Simulation: A Game Engine Approach, Jake Bova

Graduate Student Theses, Dissertations, & Professional Papers

Wildfires are growing in frequency, size, and severity, placing escalating demands on firefighting resources and putting lives, property, and ecosystems at risk. Accurate prediction of fire behavior is critical to suppression planning, evacuation decisions, and firefighter training, yet the operational models that fire managers rely upon face a persistent tradeoff. High-fidelity physics-based models capture fire–atmosphere interactions faithfully but are computationally expensive, often running far slower than real time on CPU hardware, while faster empirical models sacrifice the dynamic coupling between a fire and the wind field it generates. Furthermore, most existing tools produce abstract, two-dimensional outputs that offer limited visual …

The Importance Of The Proline Residue In The Ldiapa Motif Of Cholera Toxin, Akash Bharathan

Honors Undergraduate Theses

Cholera is currently on its seventh global pandemic, disproportionately affecting developing countries. Vibrio cholerae, the bacterial etiologic agent, is able to cause infection by adhering to intestinal epithelial cells and secreting cholera toxin (CT), an AB-type exotoxin that dysregulates signaling pathways. Previous research by the Teter lab has shown that Hsp90, a host cytosolic chaperone, is required for CT to enter the cytosol where it produces toxic effects. Hsp90 binds to CT at two specific motifs, RPPDEI and LDIAPA. The prolines in the RPPDEI motif are essential for binding, but the proline in the LDIAPA has yet to be …

Aquatic Invasive Species Survey And Treatment On Lake Umatilla And Lake Celilo 2024-2025 Report, Jacob Rose, Gabriel E. Campbell

Center for Lakes and Reservoirs Publications and Presentations

Flowering Rush (Butomus umbellatus) is an invasive aquatic plant in the Pacific Northwest that threatens salmon habitat. The Center for Lakes and Reservoirs staff surveyed for this and other aquatic species from 2024 and 2025 in the Columbia River in Lake Umatilla and Lake Celilo. This document summarizes their survey efforts including their protocols, data, and small-scale removal efforts.

A Note On The Novel Passive Sampling In Environmental Dna (Edna) Collection Technique To Detect Yellow Mud Turtle (Kinosternon Flavescens): Field And Laboratory Approaches In Turtle Edna, Sakib Tahmid Rishan, Richard J. Kline, Md. Saydur Rahman

School of Integrative Biological & Chemical Sciences Faculty Publications

Environmental DNA (eDNA) is a powerful and sensitive method for monitoring aquatic and terrestrial organisms, offering insights into their distribution. Usually, eDNA is collected using a filter membrane through water filtration. However, the passive eDNA method can simplify sampling and broaden its scope, offering new insights for ecological surveillance. This study examined the efficacy of six different membrane filters in detecting the yellow mud turtle (Kinosternon flavescens) through a novel passive eDNA method. After being immersed in water for 12 h, only the mixed cellulose ester (MCE) membrane filter consistently demonstrated specific polymerase chain reaction (PCR) amplification using …

Single-Cell Transciptomic Analysis Reveals Age-Related Remodeling Of Brain Endothelial Cells, Hai Duc Nguyen, Summer Siddiqui, Diana G. Bohannon, Robert V. Blair, Hong-Wen Deng, Alexandre Prat, Woong-Ki Kim

Microbiology & Molecular Cell Biology Faculty Publications

Blood–brain barrier (BBB) integrity naturally declines with age. Brain endothelial cells (ECs) and pericytes (PCs) form the BBB, and aging impairs tight junctions, likely via altered PC-to-EC signaling. However, the molecular mechanisms underlying this impairment remain unclear. Using single-cell RNA sequencing, we profiled 68,316 brain ECs expressing 15,564 genes from young and old mice. Unsupervised clustering and annotation revealed five distinct EC subtypes—Capillary EC1, Capillary EC2, Arterial EC, Venous EC1, and Venous EC2—defined by marker genes Mfsd2a, Plvap, Bmx, Nr2f2, and Vcam1, respectively. Aging shifted EC subtype distribution, with reduced Capillary EC1 (45% vs. 57%) and increased Arterial …

Dietitian-Led Nutrition Care Across The Cellular Therapy Continuum Supports Weight And Strength Recovery, Ashley Pagano Ms, Rdn, Ldn, Samantha Okerson Rdn, Erin Levine Rd, Cso, Ldn, Deanna Yerg Ms, Rdn, Ldn

Clinical Nutrition Service

No abstract provided.