Digital Commons Network^™

Effects Of Fine Sediment On The Productivity Of Stream Ecosystems In The Pacific Northwest, Veena I. Davis

University Honors Theses

Salmon are important to the culture, ecosystem and economy of the Pacific Northwest. However, populations have declined significantly since European colonization. Salmon require specific conditions for each life stage and are highly sensitive to environmental stressors. Excess fine sediment is a leading form of pollution as it degrades salmon spawning habitat and the benthos upon which their main food source, stream insects, live. To evaluate the effect of sediment pollution on food availability for salmon smolt, we conducted an experiment  estimating the amount of stream insect biomass and calories lost due to sediment pollution. We counted insects on substrate samples …

Mycelial Modeling: Teaching Biology Students Statistical Modeling With Mushrooms, Colette Wolf

University Honors Theses

This paper summarizes and describes the development of a set of learning materials that were created to educate students and professionals from other fields in statistical modeling techniques. These materials are primarily aimed at biology students, but are still intended to be useful for anyone who is interested in incorporating decision trees and random forest models into their personal research in the future. By directing the reader towards the JMP software, these materials navigate around the statistical knowledge base and coding implementation practices that otherwise would serve as a barrier to learning statistical modeling techniques, and instead focus on the …

Pharmacotherapeutic Interventions For Sensorineural Hearing Loss: A Scoping Review, Matthew Mavandi, Jack Hyler, Eric Lee, Ramanjot Singh, De Wet Swanepoel, Ashley M. Nassiri, Vinaya Manchaiah

Student Publications

Background/Objectives: Sensorineural hearing loss (SNHL) is a chronic condition with no established pharmacological treatment. Recent advances in drug-based therapies offer promising opportunities to prevent or treat SNHL. This scoping review summarizes the current landscape of pharmacotherapeutics for SNHL.

Methods: This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). A literature search of PubMed, Google Scholar, Embase, Scopus, and Web of Science was conducted in 2024 using keywords related to SNHL and pharmacotherapeutics. A review protocol was preregistered on the Open Science Framework. A systematic search of five …

Why Student Research Matters: A Graduate Student’S Perspective, Jessica L. Hensley

The Journal of Integrative Physiology

Research fundamentally changes how students engage with knowledge. Rather than memorizing established facts, students learn to question, analyze, and contribute to the body of knowledge within their field (1). This shift supports deeper understanding and promotes critical thinking skills by encouraging active construction of knowledge (1). It also exposes students to the process of engaging with scientific literature and integrating information within the context of their research (2).

In my experience, research requires individuals to confront uncertainty. Experiments do not always produce exact results, and methods can require modification. Through this process, students develop adaptability, persistence, and the ability to …

Literature Carries Philosophy’S Open Secret: On Derrida’S Reading Of Romeo And Juliet, Rajesh Sampath

Critical Humanities

This paper attempts a close reading of Derrida’s texts, particularly with a focus on his brief but significant reading of Shakespeare’s The Tragedy of Romeo and Juliet in “Aphorism Countertime” (originally published in French in 1986). We compare this short work with his more sustained engagement with the philosophy of death in Aporias (1993), which itself is an attempted critique of Heidegger’s Being and Time (1927); the latter is, arguably, the most influential work of twentieth-century continental European philosophy, particularly on issues of time, death, and authentic life. The paper tries to show that a fruitful engagement between philosophy and …

Endothelin-1 Drives Cox-2 And Prostaglandin E2 Expression In Osteoblasts Through Mapk/ Ap-1 Signaling During Periodontal Inflammation, I-Ta Lee

Articles in Press

No abstract provided.

Antimicrobial Susceptibility And Targeted Molecular Detection Of Methicillin Resistance Determinants In Staphylococcus Spp. Isolated From Broiler Bco Lesions, Woro Wulandari Kalanjati, Chrystalee Ailani Alvarez, Anh Dang Trieu Do, Adnan Ali Khalaf Alrubaye

School of Integrative Biological & Chemical Sciences Faculty Publications

Background/Objectives: Antimicrobial resistance (AMR) in Staphylococcus spp. associated with poultry production is an emerging concern with implications for animal and public health. This study aimed to characterize antimicrobial susceptibility patterns and detect targeted methicillin resistance determinants in Staphylococcus isolates recovered from broiler chickens affected by bacterial chondronecrosis with osteomyelitis (BCO). Methods: A total of 200 bacterial isolates were evaluated, of which 167 were confirmed as Staphylococcus spp. Species identification was performed using presumptive phenotypic characterization followed by 16S rRNA gene sequencing. Antimicrobial susceptibility was assessed using disk diffusion, while presumptive methicillin-resistant phenotypes were evaluated using oxacillin screening and CHROMagar MRSA. …

Trans-Regulation Of Heterochromatin Underlies Genetic Variation In 3d Genome Contacts In Mouse Embryonic Stem Cells., Haley J Fortin, Anna Z Struba, Arad Bustan, Christopher L. Baker

Faculty Research 2026

BACKGROUND: Genetic variation drives phenotypic diversity and disease susceptibility. Trans-acting genetic variation coordinates genome-wide chromatin changes, yet the molecular mechanisms underlying this distal regulation remain unclear. Here, we use the power of mouse genetics to investigate how genetic variation at trans-acting loci regulates three-dimensional (3D) chromatin interactions.

RESULTS: Using HiChIP to map chromatin contacts among regulatory elements in C57BL/6J and DBA/2J embryonic stem cells (ESCs), we identify 4,962 strain-differential interactions. Of these, 71% overlap chromatin accessibility quantitative trait loci (QTL), establishing that interaction variation is predominantly heritable. These differential interactions show coordinated changes in chromatin state and gene expression, with …

The Neuroprotective Effect Of Cdc42 Inhibition In The G93a Mutant Hsod1 Mouse Model Of Als, Andrea Koly

Undergraduate Theses, Capstones, and Recitals

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease characterized by the selective loss of upper and lower motor neurons, leading to muscle weakness, neuromuscular junction (NMJ) degeneration, paralysis, and eventual death due to respiratory failure. Despite extensive research, effective disease-modifying therapies remain limited, underscoring the need to identify novel molecular targets involved in ALS pathogenesis. Dysregulation of Rho family GTPases has been implicated in neurodegeneration, with Rac and Rho exerting opposing effects on neuronal survival; however, the role of the closely related GTPase Cdc42 remains poorly understood in ALS. In this study, the therapeutic potential of inhibiting …

Differential Roles Of Moesin And Vasp In Β-Catenin-Associated Networks During Zebrafish Heart Regeneration, Allen Rutman

Undergraduate Theses, Capstones, and Recitals

With cardiovascular disease remaining as the leading cause of mortality worldwide, it is largely due to the limited regenerative capacity of the human heart. However, zebrafish (Danio rerio) can fully regenerate cardiac tissue following injury, providing a valuable model for studying the mechanisms of heart repair. To investigate these mechanisms, we used proteomics methods in the past. Proximity labeling is a technique that identifies proteins based on their physical proximity to a protein of interest. It can be applied in organisms and in living cells (Roux et al., 2012; Cho et al., 2020). We used proximity labeling to characterize protein …

Gendered Justice: The Role Of Women’S Civil Society Organizations In Shaping Chile’S Truth Commissions, Frankie Stroud

Undergraduate Theses, Capstones, and Recitals

Scholarly literature has increasingly recognized that the inclusion of women and gender in formal transitional justice processes is essential for addressing the gendered nature of mass atrocities. This thesis seeks to contribute to the existing literature on how and why some transitional justice processes have come to address women and gender by specifically studying Chile’s Rettig Commission and Valech Commission. Several hypotheses have emerged from the literature for why the Valech Commission addressed gender to a greater extent, including that women’s civil society organizations, diffusion of international norms, and shifting domestic politics each played a role. Grounded in an anti-reductionist …

Bias, Structure, And Inference In Applied Network Analysis, Anna Vasenina

Dartmouth College Ph.D Dissertations

This dissertation develops mathematical and statistical methods for extracting reliable information from network data across biological applications, with an emphasis on understanding what observed network structure can and cannot resolve. The first study leverages protein–protein interaction network topology in the c-di-GMP signaling system of Pseudomonas fluorescens, showing that node centrality measures accurately classify protein domain types and that physical interaction structure contributes statistically significant predictive power for biofilm formation phenotypes across nearly 200 environments, while gene expression does not. The second study examines sampling bias in lemur-plant trophic interaction networks in Madagascar, demonstrating that differential detection of diurnal versus …

Fluorescence Cryotomography For Preclinical Validation: Applications In Gene Therapy And Fluorescence-Guided Surgery, Caleb Y. J. Kwon

Dartmouth College Ph.D Dissertations

Fluorescence imaging has become a powerful tool in biomedical research and clinical practice, offering molecular specificity and high sensitivity for visualizing biological processes in real time, However, the successful translation of novel fluorescent probes or medicines from preclinical development to clinical applications requires rigorous validation of their biodistribution and target specificity. Traditional methods for assessing performance, such as bulk excised organ analysis or two-dimensional histology, provide limited information as they cannot capture the complete, organism-wide distribution of these probes or medicines. This thesis aims to improve this analysis pipeline through the application and optimization of fluorescence cryotomography for quantitative, high-resolution …

Deciphering Small Sequence Differences In T Cell Receptor-Antigen Pairing, Yi Han, Yuqiu Yang, James Zhu, Farjana J Fattah, Mitchell S Von Itzstein, Minying Zhang, Casey Bermack, Peixin Jiang, Shailbala Singh, Yanhua Tian, Yifei Hu, Yafang Deng, Xiongbin Kang, Donghan M Yang, Jialiang Liu, Yaming Xue, Chaoying Liang, Indu Raman, Chengsong Zhu, Olivia Xiao, Jonathan E Dowell, Jade Homsi, Sawsan Rashdan, Ke Pan, Shengjie Yang, Mary E Gwin, David Hsiehchen, Yvonne Gloria-Mccutchen, Fangjiang Wu, John V Heymach, Don Gibbons, Junzhou Huang, Chao Cheng, Jianjun Zhang, Cassian Yee, Alexandre Reuben, David E Gerber, Tao Wang

Faculty, Staff and Students Publications

T cells have important functions in development and disease processes through T cell receptor (TCR)-dependent activities. Many tools were developed to predict the binding between TCRs and antigens. However, one of the uncertainties is whether such tools can decipher how small changes in the TCRs or antigenic peptides contribute to binding. We develop a deep learning model, pMTnet-omni, which not only predicts the binding vs. non-binding of TCRs towards pMHCs, but also distinguishes the stronger vs. weaker binding of TCRs similar in sequence. We leverage this capability to interpret the biological rules that govern TCR-antigen pairing. This also enables pMTnet-omni …

Platonic Affection, Philia, And Trans-Philosophy, Kai Parker

McNair Research Journal SJSU

In this article, I review the heteronormative social conventions of cisgender

men and women's abilities to build and maintain friendships vis-.vis

traditional Western gender roles. It divides the philosophical concept of

Plato’s “platonic love” as fully realized Eros from the basic social

interpretation of “platonic” relationships as connections devoid of sexual or

romantic feelings. Aristotle's definitions of friendship, divided into the three

categories of pleasure, utility, and virtue, are compared to friendships

cisgender men and women form with others of the same orientation. Men's

friendships are found to more often fall into friendships of utility and

pleasure, while women's friendships …

The Relationship Between Gender, Platonic Physical Affection, And Interpersonal Sensitivity, Mariam Malik

McNair Research Journal SJSU

Interpersonal sensitivity (IS), also known as emotional maturity or empathy,

is characterized by recognizing emotions and displaying empathy, which

are important social skills. Understanding the factors that are associated

with interpersonal sensitivity can provide the foundation for research

revolving around improving interpersonal sensitivity, and in turn,

improving social skills. Platonic physical affection (PPA), such as holding

hands and hugging, is a social variable often associated with those close to

one another (e.g., friends and family). However, the exhibition and

receptivity to this social variable may differ across cultures and genders.

This study aimed to see if there is a relationship …

Full Issue

McNair Research Journal SJSU

No abstract provided.

Refining A Flow Injection Analysis Method For Trace Concentrations Of Iron In Seawater, Brooke I. Stafford, Liam W. Hodgson, Noah S. Schuhmann, Elijah J. Vestal, Claire P. Till

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Iron is an essential micronutrient required for the growth of phytoplankton, the base of the oceanic food chain. Iron exists in the ocean in extremely low concentrations, limiting primary productivity in ~⅓ of the surface ocean, and can be affected by physical processes such as upwelling of water masses, and by biological and chemical processes within the water. In order to further our understanding of iron availability in the ocean, here we refine and improve our understanding of an analytical method to measure nanomolar iron in seawater. The method used is an adaptation of Lohan et al. (2006), a flow …

Exploring The Relationship Between Tree Dbh And Lichen Cover On Coast Redwood, Grace M. Personeus, Sierra Gittleman, Alisa A. Zarattini

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

We investigated the relationship between Diameter at Breast Height (DBH) and lichen cover on coast redwood (Sequoia sempervirens) to see if larger trees had higher percentages of cover. We measured cover using 10 cover classes on the southeastern and southwestern sides of trees in a secondary growth forest. We found a significant relationship between DBH and cover, yet no significant difference between the two sides measured. We suggest that further research with a larger sample size and more varied age classes will provide further insight into the relationship.

Allosteric And Uncompetitive Inhibition Of Yeast Alcohol Dehydrogenase Identified By Enzyme Kinetics, Dylan Jeremy Harrison, Jenny A. Cappuccio

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Enzyme kinetics is a powerful technique used to quantify the rate at which an enzyme converts a substrate into a product and to identify potential inhibitors. In this study, kinetic analysis was employed to assess the activity of yeast alcohol dehydrogenase (YADH) in the presence and absence of sweeteners commonly found in alcoholic beverages. YADH catalyzes the oxidation of ethanol to acetaldehyde using NAD⁺ as a cofactor; the reduction to NADH can be monitored spectrophotometrically at 340 nm. Based on structural similarities to the ribose moiety of NAD⁺, it was hypothesized that sucrose and sucralose could directly interact with the …

Full Issue, The Press At Cal Poly Humboldt

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

Survival Outcomes And Tumor Site Distribution By Molecular Subtype In Breast Cancer Patients Under 40, Muhammad Noorani, Shubhank Goyal, Sierra Viduarri, Aura Calderon, Christine Pham, Shweta Singh, Mutaaz Ahmed, Anupam Dhasmana, Swati Dhasmana, Murali Yallapu, Shubash Chauhan, Diane Nguyen, Sidketa Fofana, Sheema Khan

Research Symposium

Background: Screening guidelines for breast cancer typically begin at age 40, leaving younger women at risk for delayed detection. The survival outcomes and tumor site patterns by subtype in this younger population remain underexplored. Our analysis leverages comprehensive national data to fill this critical knowledge gap, offering one of the most detailed evaluations to date of molecular subtype distribution, prognostic disparities, and anatomical presentation in women under 40.

Methods: Using the SEER 18 registry, we identified 5,026 female patients diagnosed under age 40 with invasive breast cancer in 2018. This year was selected for the most recent data available on …

Expression And Functional Significance Of The G Protein–Coupled Estrogen Receptor (Gper) In Breast Cancer Subtypes, Sierra E. Vidaurri, Shweta Singh, Valerie E. Ledezma, Rajasekhar Baru, Emma Garza, Francisco Flores, Muhammad Noorani, Shubhank Goyal, Aura Calderon, Alexander Lim, Anupam Dhasmana, Swati Dhasmana, Murali Yallapu, Subhash Chauhan, Diane Nguyen, Sheema Khan

Research Symposium

Background: The G protein–coupled estrogen receptor (GPER) mediates rapid non-genomic estrogen signaling and has been implicated in breast cancer progression and aggressiveness. However, its expression patterns across molecular subtypes and its direct functional contribution to tumor behavior remain incompletely defined. The objective of this study was to comprehensively characterize GPER expression in breast cancer tissues and to functionally validate its role in regulating tumor cell proliferation and migration using genetic modulation approaches.

Methods: GPER expression was evaluated in breast cancer cell lines and patient tumor tissues using immunohistochemistry (IHC), Western blotting, and RT-PCR. Tumors were classified into Luminal A, Luminal …

Gper As A Therapeutic Target In Breast Cancer: Pharmacologic Inhibition And Microbiome Associations, Sierra E. Vidaurri, Shweta Singh, Valerie E. Ledezma, Rajesekhar Baru, Emma Garza, Francisco Flores, Muhammad Noorani, Shubhank Goyal, Aura Calderon, Alexander Lim, Anupam Dhasmana, Swati Dhasmana, Murali Yallapu, Subhash Chauhan, Diane Nguyen, Sheema Khan

Research Symposium

Background: The G protein–coupled estrogen receptor (GPER) mediates rapid estrogen signaling that promotes proliferation, migration, and therapeutic resistance in breast cancer, including in hormone receptor–negative subtypes. Notably, standard endocrine therapies may inadvertently activate GPER, highlighting the need for direct targeting of this pathway. The objectives of this study were to evaluate GPER as a therapeutic target using pharmacologic modulators and to determine how GPER-driven tumor behavior relates to tumor microbiome composition across breast cancer subtypes.

Methods: Breast cancer cell lines representing Luminal A (MCF7), Luminal B (BT474), HER2-enriched (SKBR3), and triple-negative (HCC38, MDA-MB-453, MDA-MB-231) subtypes were treated with Ormeloxifene (ORM). …

Oriented Electrospun Fibers Of Poly(Pro-Curcumin/Peg) Sequester Reactive Oxygen Species And Promote The Growth Of Schwann Cells, Jack W. Devlin, Payton R. O'Connor, Conrad H. Cheung, John T. Leman, Martin Oudega, Edmund F. Palermo, Ryan J. Gilbert

Chemical and Biochemical Engineering Faculty Research & Creative Works

In the biological injury microenvironment, pathologically elevated oxidative stress hinders healthy cell migration. Aligned electrospun fibers are used as tissue engineering scaffolds to support and guide the directionality of cell migration. The ability of cells in the central nervous system to sequester and quench reactive oxygen species is limited, and most electrospun fibers do not exert any antioxidant activity on contact. Thus, the challenge remains in designing a scaffold that can both guide cells to the injury site as well as sequester and quench excess free radicals, allowing cells to thrive and potentially regenerate. Curcumin is a well-known, potent antioxidant, …

An Extension To A. Goldshtein, Et Al, 2025, Manish Rami

Communication Sciences & Disorders Faculty Publications

This note extends the findings reported in “Onboard recordings reveal how bats maneuver under severe acoustic interference” available at:

Goldshtein, Aya, et al. “Onboard Recordings Reveal How Bats Maneuver under Severe Acoustic Interference.” Proceedings of the National Academy of Sciences, vol. 122, no. 14, Apr. 2025, p. e2407810122. pnas.org (Atypon), https://doi.org/10.1073/pnas.2407810122.

Decoupled Carbon Assimilation And Growth Responses To Aridity In Temperate Deciduous Oaks, Mukund Palat Rao, Arturo Pacheco-Solana, Rong Li, Bar Oryan, Johanna E. Jensen, Milagros Rodriguez-Caton, Steve L. Voelker, Et Al.

Michigan Tech Publications

The magnitude of the terrestrial carbon sink remains a key uncertainty in future climate projections, in part due to poorly understood links between carbon uptake and its allocation to woody biomass in vegetation. Here, in this study, we show that photosynthesis and aboveground growth occur asynchronously across diel to seasonal scales in eight North American oak species. Across 137 tree ring sites, current-year annual growth was insensitive to climate variability after midsummer despite 26 to 36% of annual gross primary productivity (GPP) occurring during this period. Hourly GPP flux and growth measurements at four sites spanning seven site years further …

Understanding Whole-Brain Dynamics Through Generative Modeling, Ruiqi Chen

Arts & Sciences Graduate Student Theses and Dissertations

A central goal in cognitive neuroscience is to map mental processes onto their physical substrates. Traditionally, this goal is pursued by associating different mental processes with spatially-based anatomic localization. On the contrary, much less is known about the temporal dynamics of neural activity, particularly at the scale of the whole brain. Research into whole-brain dynamics has been challenging primarily due to the lack of an analytic framework that can summarize such dynamics, expose the underlying mechanisms, and associate the mechanisms with cognitive processes. In this dissertation, I describe my doctorate research aimed at building such a framework and deploying it …

The Palm Farm Next-Door: Land Concessions, Livelihoods, And Nutrition In Plantation-Adjacent Communities, Julia Entwistle

Electronic Theses and Dissertations

Large-scale land concessions have reshaped agrarian landscapes globally, yet their implications for community land tenure, livelihoods, and nutrition remain unevenly understood. This dissertation examines how plantation agriculture and foreign investment have transformed land access, labor relations, and food systems in Liberia, a country with one of the highest proportions of land under concession globally. Guided by a political ecology framework, the study employs a mixed-methods design integrating policy analysis, in-depth interviews, and household surveys across two palm oil concession sites. The findings show that ambiguous land policies historically facilitated dispossession, while recent legal reforms have enabled communities to strategically mobilize …

2026-06-12 Agenda Booklet, Morehead State University. Board Of Regents.

Morehead State Board of Regents Agenda Books and Meeting Minutes

Agenda booklet for the Board of Regents meeting of June 12, 2026, held in Prestonsburg, which includes the meeting minutes of the meeting held on March 27, 2026.