Globally-Distributed Microbial Eukaryotes Exhibit Endemism At Deep-Sea Hydrothermal Vents, Sarah K. Hu, Amy R. Smith, Rika E. Anderson, Sean P. Sylva, Michael Setzer, Maria Steadmon, Kiana L. Frank, Eric W. Chan, Darlene S. S. Lim, John A. Breier

School of Earth, Environmental, & Marine Sciences Faculty Publications

Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from four geographically- and geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. The four vent fields include Axial Seamount at the Juan de Fuca Ridge, Sea Cliff and Apollo at the Gorda Ridge, all in the NE Pacific Ocean, and Piccard and Von Damm at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify …

Characterization Of Patients With Type 2 Diabetes Admitted For Acute Heart Failure During The Covid-19 Pandemic, Paola Delahoz, Karen Corrales, Justin P. Cagulada, Jessica Cardona, Jasmin Qyyum, Venessa Rodriguez, Catherina Chang Martinez

Nursing & Health Sciences Research Journal

Background: Cardiomyopathy (CMP) and heart failure (HF) are serious health conditions that impact millions of Americans, including people with Type 2 Diabetes (T2DM). The COVID-19 pandemic presented disruptions, yet it is unclear how it affected those living with T2DM and HF. This study aimed to describe the demographic and clinical characteristics of patients with T2DM and CMP who were hospitalized with acute heart failure (aHF) during the COVID-19 pandemic. Methods: Retrospective study of 288 adults with aHF between May 2020 to June 2021. Descriptive statistics were used to summarize the characteristics of adults hospitalized at a non-profit community hospital in …

Exploring The Potential Of Tesla Valve For Filtering And Sorting Microscale Active Swimmers: A Computational Study, Ariel Rogers, Zhiyao He, Yong Wang

Physics Faculty Publications and Presentations

It is well-known that a Tesla valve allows fluids to flow unidirectionally without moving parts; however, how Tesla valves interact with active matters and the potential applications of Tesla valves in biology remain largely unexplored. Here, we present a computational study on the potential use of Tesla valves for filtering and sorting microscale active swimmers such as bacteria. We investigated the behavior of microscale swimmers passing through the Tesla valve at different linear and angular velocities using numerical simulations and quantified the diodicity of the Tesla valve for active swimmers. Our results demonstrate that the Tesla valve can effectively filter …

Sensory Input To Cortex Encoded On Low-Dimensional Periphery-Correlated Subspaces, Andrea K. Barreiro, Antonio J. Fontenele, Cheng Ly, Prashant Chama Raju, Shree Hari Gautam, Woodrow L. Shew

Physics Faculty Publications and Presentations

As information about the world is conveyed from the sensory periphery to central neural circuits, it mixes with complex ongoing cortical activity. How do neural populations keep track of sensory signals, separating them from noisy ongoing activity? Here, we show that sensory signals are encoded more reliably in certain low-dimensional subspaces. These coding subspaces are defined by correlations between neural activity in the primary sensory cortex and upstream sensory brain regions; the most correlated dimensions were best for decoding. We analytically show that these correlation-based coding subspaces improve, reaching optimal limits (without an ideal observer), as noise correlations between cortex …

Atypical Meningiomas With Multiple Extracranial Metastases: A Case Description, Yipei Song, Mengyao Hu, Xiwen Wang, Qiming Fang, Xuan Xiao, Lianggeng Gong

Faculty, Staff and Student Publications

No abstract provided.

How Beavers (Castor Canadensis) Affect Habitat Availability For Two Native Oregon Turtles: Actinemys Marmorata And Chrysemys Picta Bellii, Rodé Krige

University Honors Theses

Oregon is home to two native freshwater turtle species: the northwestern pond turtle and the western painted turtle. Both turtles are Oregon conservation strategy species with a status rating of sensitive, indicating declining populations. Oregon's decline in these turtle's populations is thought to be predominantly due to loss and degradation of habitat that results from development and urbanization. Beavers' ability to dam streams and create ponds may be creating habitat usable by turtles, but the relationship is under-studied. This study assessed water temperature, basking habitat, and overall turtle habitat suitability at beaver-dammed and control ponds in Portland, Oregon. Average basking …

A Capstone Journey In Enterprise Software Consulting For Microsoft: How An Interdisciplinary Philosophy Fosters Critical Thinking And Promotes Cross-Functional Teamwork, Jacob Mccall

University Honors Theses

This capstone review thesis explores the application of strategic innovation and enterprise software with a Portland State University (PSU) School of Business Administration (SBA) interdisciplinary team consulting for Microsoft. Faced with improving pitch meetings with a new target audience of Chief Marketing Officers (CMOs), Microsoft's West Coast enterprise software sales team sought consultation from the PSU SBA 2023 Business Honors cohort. This text reflects on the precursors responsible for the consulting project’s success, including the university’s guiding principles, interdisciplinary philosophy, and applicable business practices. The final solution includes insights into CMO types, needs development, a marketing enterprise software visual sales …

The Effects Of Salt Marsh Restoration On The Hydrology Of Salt Marsh Channels, Isis Kontas

University Honors Theses

Salt marshes produce many ecosystem services, from water purification to protection from hurricanes. Despite their benefits, salt marshes have been impacted negatively by human activities. There are many salt marsh restoration projects that intend to bring back all ecological functions and services. Quantifiable measurements are needed to evaluate the effectiveness of such restoration efforts. Earlier work by Reagan Thomas demonstrated what happens to the hydrology of salt marsh channels when they are adjacent to restored salt marshes. This study builds on Thomas’ work and uses the sinuosity of channels as a quantitative, representative metric of salt marsh hydrology restoration effectiveness. …

Economic Analysis Of Population-Based Next Generation Sequencing For Breast Cancer, Sapphire Curelaru

University Honors Theses

Breast cancer develops due to accumulated DNA replication insults which causes cancer to uncontrollably proliferate. An individual's predisposition to developing cancer, as well as the composition of a tumor, can be sequenced using genetic tests. Myriad's BRACAnalysis CDx^® seems to be the most utilized genetic test. However, Next Generation Sequencing (NGS) seems to be a better genetic test for breast cancer when compared to Myriad's BRACAnalysisCDx^® in terms of return-time, accuracy, efficiency, and healthcare cost. By using Next Generation Sequencing tests, stakeholders can save money on genetic testing which can be invested in more genetic tests. Payers can …

The Association Between Inflammatory Bowel Disease And All-Cause And Cause-Specific Mortality In The Uk Biobank, Fangyu Li, Yesenia Ramirez, Yukiko Yano, Carrie R Daniel, Shreela V Sharma, Eric L Brown, Ruosha Li, Baharak Moshiree, Erikka Loftfield, Qing Lan, Rashmi Sinha, Maki Inoue-Choi, Emily Vogtmann

Faculty, Staff and Student Publications

PURPOSE: Inflammatory bowel disease (IBD) has a rising global prevalence. However, the understanding of its impact on mortality remains inconsistent so we explored the association between IBD and all-cause and cause-specific mortality.

METHODS: This study included 502,369 participants from the UK Biobank, a large, population-based, prospective cohort study with mortality data through 2022. IBD was defined by baseline self-report or from primary care or hospital admission data. We estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause and cause-specific mortality in multivariable Cox proportional hazards regression models.

RESULTS: A total of 5799 (1.2%) participants had a history of …

Development Of Novel Methods To Study Host-Microbe Interactions In The Larval Zebrafish Gastrointestinal Tract, Anh K. Trinh Nguyen

Dissertations and Theses (Open Access)

The dynamic nature and inaccessible location of the intestine pose significant challenges to the study of intestinal physiology and pathology. Zebrafish larvae, possessing optical transparency and genetic tractability, offer an accessible and clinically relevant model for investigating dynamic events in the intestine via time-lapse imaging. In the first part of this work, I discuss our efforts to optimize the parameters of a foodborne infection assay using paramecia as a vehicle. This method provides an effective, high-throughput alternative to infection via immersion or oral gavage, and replicates the most common route of transmission of gastrointestinal (GI) infection in humans. The foodborne …

Telomeric Regulation Of Chromosomal Instability In Colorectal Cancer, Kyle Labella, Kyle A Labella

Dissertations and Theses (Open Access)

Telomere dysfunction drives chromosomal instability (CIN) during the transition from benign adenoma to malignant adenocarcinoma. While CIN provides a mutator mechanism for cancer-relevant genomic events, its role in shaping tumor biology during carcinogenesis is not well understood. Here, we explored the molecular and biological impact of telomere dysfunction and associated CIN in vivo in a faithful model of CRC. In vivo lineage tracing revealed that CIN increased neoplastic cell competition and clonal expansion through accelerated differentiation of neighboring stem cells, resulting in increased number of adenomas and decreased survival in CIN-high Apc^min mice. Mechanistically, CIN represses EZH2 leading to …

Role Of The Immune System In The Modulation Of The Mmr-Deficient Intestinal Stem Cell Niche, Shepard Conner

Dissertations and Theses (Open Access)

Mismatch Repair (MMR) is a crucial DNA repair system to maintain genomic integrity in cells that is integrated by specific genes including MLH1, MSH2, MSH6, and PMS2. These genes play a critical role in repairing errors that occur in base pairing by stabilizing the genetic material. When the MMR system fails to correct those errors, MMR deficiency occurs where monoallelic mutations in the MMR genes result in a condition known as Lynch Syndrome (LS). LS makes up approximately 3% of all colorectal cancer (CRC) and is regarded as a hereditary form of CRC, which progresses from MMR-deficient …

Development Of A Remote Dosimetric Audit Framework For Carbon Therapy, Paige Taylor

Dissertations and Theses (Open Access)

Carbon ion therapy is available at over a dozen institutions around the world and is being employed for treatment of cancer. The increased biological effect of carbon compared to conventional photon-based radiotherapy holds promise for the therapeutic benefit in historically radioresistant tumors. While ion chamber dosimetry has been used for day-to-day clinical measurements of absorbed dose, there are few options for remote dosimetry. The availability of such tools would support the development of a robust remote audit program for carbon ion therapy.

The Imaging and Radiation Oncology Core (IROC) conducts remote audits of photon and proton therapy. These audits are …

Downregulation Of Mir-10a-5p As A Potential Therapeutic Target To Improve The Detrimental Effects Of Post-Stroke Social Isolation, Patrick Mooz

Dissertations and Theses (Open Access)

Introduction

Social isolation is detrimental to health. Isolation and loneliness are linked to all-cause mortality and accelerated disease progression in patients with cancer, dementia, and vascular disease. The number of individuals that live alone is increasing in our society, especially in the elderly, and loneliness and isolation represent a profound growing public health challenge. Previous studies have found that the detrimental effects of social isolation can be recapitulated in animal models. Mice that are socially isolated (SI) prior to an experimental stroke have larger infarcts and significantly worse outcomes. Importantly, animals that remain pair housed (PH) when an experimental stroke …

A Signal To Divide: Apoptotic Extracellular Vesicles As Carriers Of Mitogenic And Immunogenic Signals, Safia Essien, Safia Essien

Dissertations and Theses (Open Access)

Efficient replacement of dead cells in epithelial tissue is crucial for maintaining barrier function and tissue homeostasis. Apoptotic cells can signal to neighboring cells to stimulate proliferation and compensate for cell loss and maintain overall cell numbers in normal physiology and cancer. While dying cells can transmit instructive cues to neighboring cells, the molecular mechanisms that induce cell division are not well understood. Recent evidence suggests that apoptotic bodies (ABs) or apoptotic extracellular vesicles (AEVs) mediate cell-to-cell communication and carry diverse biologically active cellular cargo which can influence cell proliferation. This dissertation visualizes and characterizes AEVs in larval zebrafish and …

A Novel Ngs Assay To Detect Any Kmt2a Fusion Transcript At Low Levels, Ghayas Issa

Dissertations and Theses (Open Access)

Measurable residual disease (MRD) detection is associated with cancer relapse. Leukemias with rearrangement of the lysine methyltransferase 2 A gene (KMT2Ar) have an adverse prognosis with more than 80 possible fusion partner genes (FPG) identified. With the advent of effective targeted therapies for KMT2Ar leukemia such as menin inhibitors, there is an unmet need for sensitive assays to detect these various fusions. Standard next-generation sequencing (NGS) methods cannot accurately detect genetic alterations at low frequencies because of inherent technical errors and the need for high sequencing depth. Blocker Displacement Amplification (BDA) technology enables selective detection of such rare …

Single Cell Proteogenomics Analysis Of Aml Samples Treated With Decitabine And Venetoclax Reveals Divergent Treatment Escape Mechanisms, Yi June Kim

Dissertations and Theses (Open Access)

Venetoclax is a small molecule inhibitor targeting BCL-2. Since its approval, the combination therapy of hypomethylating agents and Venetoclax (HMA+Ven) has become a standard of care for acute myeloid leukemia (AML) patients unfit for intensive chemotherapy. Nonetheless, clinical challenges persist as patients either do not respond or eventually relapse, and the underlying mechanisms of these outcomes are not yet fully understood. Prior studies have identified genetic factors (TP53 and RTK/RAS pathway mutations) and phenotypic factors (monocytic differentiation) to be associated with resistance. In this light, we hypothesized that integrative assessment of genetic and phenotypic factors could further elucidate the unknown …

Opening The Black Box Of Family-Based Treatments: An Artificial Intelligence Framework To Examine Therapeutic Alliance And Therapist Empathy, Phillippe B Cunningham, Jordon Gilmore, Sylvie Naar, Stephanie D Preston, Catherine F Eubanks, Nina Christina Hubig, Jerome Mcclendon, Samiran Ghosh, Stacy Ryan-Pettes

Faculty, Staff and Student Publications

The evidence-based treatment (EBT) movement has primarily focused on core intervention content or treatment fidelity and has largely ignored practitioner skills to manage interpersonal process issues that emerge during treatment, especially with difficult-to-treat adolescents (delinquent, substance-using, medical non-adherence) and those of color. A chief complaint of "real world" practitioners about manualized treatments is the lack of correspondence between following a manual and managing microsocial interpersonal processes (e.g. negative affect) that arise in treating "real world clients." Although family-based EBTs share core similarities (e.g. focus on family interactions, emphasis on practitioner engagement, family involvement), most of these treatments do not have …

A Double-Robust Test For High-Dimensional Gene Coexpression Networks Conditioning On Clinical Information, Maomao Ding, Ruosha Li, Jin Qin, Jing Ning

Faculty, Staff and Student Publications

It has been increasingly appealing to evaluate whether expression levels of two genes in a gene coexpression network are still dependent given samples' clinical information, in which the conditional independence test plays an essential role. For enhanced robustness regarding model assumptions, we propose a class of double-robust tests for evaluating the dependence of bivariate outcomes after controlling for known clinical information. Although the proposed test relies on the marginal density functions of bivariate outcomes given clinical information, the test remains valid as long as one of the density functions is correctly specified. Because of the closed-form variance formula, the proposed …

Analyzing Extracellular Vesicles For Disease Monitoring In Metastatic Colorectal Cancer Patients, Vahid Bahrambeigi

Dissertations and Theses (Open Access)

Colorectal cancer (CRC) is the second leading cause of cancer deaths in the United States. Metastases are the main cause of cancer-related death, and the most frequent metastatic sites in patients with CRCs are liver and lung. To confirm the diagnosis of metastatic CRC (mCRCs) and to classify mCRCs, tumor biopsy of a suspected metastasis is often required. The consensus molecular subtype (CMS) classification which is based on gene expression profiles of CRC tumor specimens, is a predictive factor for treatment outcomes of standard chemotherapies for mCRCs. The practicality of repeated tumor biopsies for disease monitoring in mCRC patients is …

Genomic Characterization Of Adolescent And Young Adult Cancers: Investigation Of Ewing Sarcoma Susceptibility And Chornobyl Thyroid Tumors, Olivia Lee

Dissertations and Theses (Open Access)

Adolescent and young adult (AYA) cancers, diagnosed between the ages of 15 and 39, can exhibit distinctive genetic and molecular characteristics. Reported epidemiologic findings and treatment outcomes based on pediatric and adult cancer studies are often not suitable for application to the AYA population, underscoring the need for more thorough genomic research. Advances in sequencing technologies have enabled comprehensive analyses of complex genomic characteristics of AYA cancers, crucial for understanding the underlying biology of these malignancies. Here, I have utilized advanced sequencing techniques and integrated analytic approaches to describe important genomic features in two different AYA cancer types: Ewing Sarcoma …

Oncogenic Kras And Telomere Biology In Crc Progression, Ronald Depinho

Dissertations and Theses (Open Access)

While colorectal cancer (CRC) patients diagnosed with localized stage disease (as defined by SEER) have a 5-year survival rate of 90%, this rate plunges to 14% for patients diagnosed with metastatic CRC. Consequently, there is an immediate imperative to elucidate the mechanisms that drive the transition to advanced CRC.

Human CRCs carrying oncogenic mutations in the KRAS oncogene, henceforth referred to as KRAS*, exhibit a 25% higher propensity for developing liver metastases. Similarly, in our CRC mouse model, engineered with an inducible Kras* transgene and conditional null alleles of Apc and Tp53 (referred to as iKAP), KRAS* has been …

Synthesis Of Glucomannan-Xylan Composite Biofilms: Characterization And Applications For Food Packaging, Kholoud Al-Ajlouni

Dissertations

Scientists are most concerned about the need for green alternatives for efficient food packaging polymers to replace petroleum-based packaging products. The waste of corn cobs and the roots of the konjac plant contain hemicellulose, xylan and glucomannan respectively, and can be used to produce biofilms for food packaging.

The aim of these studies is to formulate biofilms from glucomannan-xylan blends that compete with petroleum-based plastic wrap. The biofilms must be strong, smooth, transparent, have a water vapor barrier, have the required mechanical properties and be cheap. Biofilms from glucomannan were stiff, lacked mechanical properties, and absorbed moisture. Therefore, it reacts …

The Effect Of Nitroglycerin In Testicular Histopathology, Reproductive Hormones And Testicular Oxidative Stress In Adolescent Rats, Volkan Koşal, Çağlar Okulmuş, Yılmaz Koçak, Ömer Faruk Keleş, Nesrin Ceylan, Yıldıray Başbuğan

Mansoura Veterinary Medical Journal

Background: Nitroglycerin (NTG) exerts a vasodilation effect by acting on vascular smooth muscles. The exact impact of vasodilation on the testes is not fully understood. Objectives: This study aimed to investigate the effects of NTG on the testes before the onset of spermatogenesis and reproductive activity in adolescent rats. Methods: An Average of 45 days male Albino Wistar rats were used. Two groups were formed: an adolescent control group and an adolescent NTG group (10 mg/kg, 5 d). Results: At the end of the study, testicular oxidative stress (malondialdehyde /MDA, catalase/ CAT, advanced oxidation protein products /AOPP, and nitric oxide/ …

Comparing City Park Perspectives: Users Vs Organizers, Kalli Hull

Undergraduate Honors Capstone Projects

Green spaces and parks are an essential aspect of a healthy community. Incorporating parks into the landscape of a city can benefit the community. Understanding the relationship between park management and park users is important for creating the most effective use of space and accessibility. This project looks at the comprehensive viewpoints of both park managers and park users through a series of interviews and reviews of previous research and literature. Logan City, Utah is used as the location of interest for collecting and determining outcomes. This project displays the key findings of the priorities and viewpoints of both park …

Instrumentality: How We Develop Relationships With Objects And People, Nathaniel Bee

Undergraduate Honors Capstone Projects

There are many different types of relationships a person will have throughout their life, each being given varying levels of authenticity, weight, and care. One’s attention is primarily placed upon the meaningful relationships in one’s life, but often deeper consideration of one’s “lesser” relationships is neglected. Networking and professional relationships are often impersonal. Family members will often lie to each other in favor of avoiding conflict. The emotional labor of service workers often goes underappreciated and undercompensated. Careers in the political sphere revolve heavily around maintaining a positive public image, and there are well-observed disparities between politicians’ stated values and …

Assessing Chondrocyte Viability Of Articular Cartilage Using Label-Free Imaging Methods, Hongming Fan

All Dissertations

ABSTRACT

Articular cartilage covers the ends of bones, providing a protective layer that can endure forces during movement. Chondrocytes, the only cell type found in articular cartilage, produce collagen fibers and proteoglycans that maintain the extracellular matrix (ECM). Cartilage damage impairs chondrocytes and their ability to maintain tissue stability. There are various factors that can cause cell death, which can be broadly classified into two categories: programmed cell death (apoptosis) and non-programmed cell death (necrosis). The consequences of cell death can have significant impacts on the extracellular matrix (ECM). The ECM is a complex network of proteins and carbohydrates that …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

An In Vitro Platform To Characterize Myocardial Wound Remodeling, Jonathan Heywood

All Dissertations

Heart Failure, sometimes called Congestive Heart Failure, is a collection of pathological disruptions in which the heart is unable to pump blood properly. It affects over 6 million people in the United States, with the cost-per-patient at approximately $30,000 and the total cost estimated to be $160 billion by 2030. There is no single cause of heart failure, as it can manifest as a varying array of diseases, disorders, and syndromes. However, many of these underlying diseases result specifically from dysregulation of mechanically active cells called cardiac fibroblasts, which play a critical role in the remodeling of the extracellular matrix …