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Volumetric Imaging Of Cellular Dynamics Using Light-Sheet Microscopy: From Subcellular Structures To Whole Organisms, Md Nasful Huda Prince

Optical Science and Engineering ETDs

Advancing biomedical imaging requires platforms that combine high-resolution, speed, and stability across biological scales. This dissertation presents three innovations designed to address limitations of conventional light-sheet and oblique plane imaging. First, we introduce Reflected Inline Detection in Epi-Oblique Plane Microscopy (RIDE-OPM), a compact and drift-resistant system that eliminates a tertiary detection path while maintaining alignment flexibility, enabling robust long-term live imaging. Second, we present a high-speed Axially Swept Light-Sheet Microscopy (ASLM) platform for cleared tissues, using dual foci and synchronized sweeping to achieve isotropic sub-micron resolution at up to 40 frames-per-second, a fourfold improvement over standard ASLM. Integrated with a …

Silicon Is The Next Frontier In Plant Synthetic Biology, Aniruddha Acharya, Kaitlin Hopkins, Tatum Simms

Faculty Publications - Biological Sciences

Silicon has a striking similarity to carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable to macronutrients. Silicon is used extensively in artificial intelligence, nanotechnology, and the digital revolution, and thus can serve as an informational molecule such as nucleic acids. The diverse potential of silicon to bond with different chemical species is analogous to carbon; thus, it can serve as a structural candidate similar to proteins. The discovery …

Unci Maka’S Gift: An Outdoor Science Adventure For The First Graders, Arlene A. Abao, Larry M. Browning, Matt Miller, Jiyul Chang, Srinivas Janaswamy, Jessica Larson, Lydia Yellow Hawk, Michael Prate, Madhav P. Nepal

iLEARN Teaching Resources

In this super-fun lesson, kids are going outside to explore the schoolyard! They will look for all sorts of amazing plants, also called flora. They will use a special tablet to help us learn their names and then draw pictures of them. They will also dig a little to see the soil and learn why it's so important for plants to grow big and strong. And guess what? They’ll even look for little animals like ants or butterflies, also called fauna, that live near the plants, because everything in nature works together! They'll also hear cool stories about how people …

Culturally Responsive Teaching: Identifying Conifers Through Science And Tradition, Madhav P. Nepal

iLEARN Teaching Resources

This lesson on plant taxonomy introduces students to the scientific system used to name, classify, and identify plant species, with a focus on conifer trees found in local environments. Students explore how observable traits—such as needle shape, cone structure, and bark texture—are used to group plants into categories that reflect their evolutionary relationships. Through a hands-on tree-walk activity, students use a simplified dichotomous key to identify at least five conifer species on or near school grounds. They then use digital plant ID tools to confirm their findings and compare traditional and modern identification methods. The lesson also emphasizes the hierarchical …

Partial Cystectomy For Muscle-Invasive Bladder Cancer, Peter S Palencia, Nethusan Sivanesan, Syed Rahman, Fady Ghali, David Hesse, John Colberg, Ashwin Sridhar, John D Kelly, Byron H Lee, Ashish M Kamat, Wei-Shen Tan

Faculty, Staff and Student Publications

Partial cystectomy is a surgical bladder-sparing option for selected patients with muscle-invasive bladder cancer (MIBC), urachal adenocarcinoma and diverticular bladder tumors. Partial cystectomy hold several advantages. It allows for definite pathology and accurate staging while avoiding side effects from radiation therapy and preserves the option for salvage radical therapy (radical cystectomy or radical radiotherapy). Patients should have a CT urogram, prostatic urethral biopsy and mapping biopsies or blue light cystoscopy to rule out multifocal disease or CIS. Small solitary MIBC patients without carcinoma in situ in an area of the bladder where resection can be performed with negative margin would …

Bcl-2/Bcl-Xl Dual Inhibition Triggers Gasdermin D-Mediated Pyroptosis In Mantle Cell Lymphoma, Yijing Li, Joseph Mcintosh, Vivian Jiang, Fangfang Yan, Jovanny Vargas, Yuxuan Che, Wei Wang, Ching-Fei Li, Yue Fei, Celeste Lee, Lei Nie, Yixin Yao, Michael Wang, Heng-Huan Lee, Yang Liu

Faculty, Staff and Student Publications

No abstract provided.

Restoration At The Intersection Of Science And Outreach-The Working Woods Learning Forest, Katharine L. Stuble, David J. Burke, Samuel C. Harbol, Chad Knisely, Jessica Miller Mecaskey, Alexa S. Wagner, Michael Watson, Kevin E. Mueller

Biological, Geological, and Environmental Faculty Publications

Botanical gardens and arboreta have enormous (if often under-realized) potential to increase understanding of restoration as a predictive science while simultaneously serving as platforms promoting large-scale restoration by public and private stakeholders. Public gardens often have deep histories of both research and outreach and, increasingly, engagement in restoration efforts. As a team of researchers and practitioners, we share our experiences using a forest management manipulation at the Holden Arboretum for both research and outreach. Forest management is a key tool for enhancing biodiversity and ecosystem services in young forests. Known as the Working Woods Learning Forest, this restoration simultaneously serves …

Quantile Index Predictors Using R Package Hyper.Gam, Tingting Zhan, Misung Yi, Inna Chervoneva

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

MOTIVATION: Evaluation of single-cell protein expression from immunohistochemistry images is used increasingly in biomedical research. Many proteins are used solely for phenotyping cells in the tumor microenvironment. Other proteins with meaningfully quantitative expression levels provide so-called functional protein biomarkers. There is still a limited number of methods and software tools available for utilizing the entire distributions of single-cell expression levels.

RESULTS: We present the R package hyper.gam, providing a supervised learning framework for deriving biomarkers based on single-cell distribution quantiles. The single-cell data are first converted into sample quantile functions, which are then used as predictors in scalar-on-function regression models …

Rna Sequencing And Immunohistochemistry Jointly Improve Tumor Biomarker Interpretation, Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K Lennerz, Funda Meric-Bernstam, Alexander Bagaev

Faculty, Staff and Student Publications

This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers-ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20-were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman's correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to …

Sex, Stress And Hormones : The Role Of Modifiable Risk Factors In The Kinetics Of Alzheimer’S Disease, Hannah Marie Edwards

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s Disease (AD) is a neurodegenerative disease hallmarked by the presence of amyloid- plaques and tau tangles in the brain. The process of the disease begins decades prior to the onset of symptoms and is thought to be driven first by a buildup of amyloid- peptide in the extracellular space, triggering a cascade of pathology and symptomology culminating in loss of cerebral volume and cognitive impairment. Women are diagnosed with AD at a rate 2/3 higher than their male counterparts, even when controlling for age. While most driving factors of the disease are thought to be genetic, roughly 40% of …

Breeding Season Bird Use Of And Non-Native Plants Found In Food Plots In The Southern Appalachian Mountains, Nathan A. Klaus, Kirk Stodola

Georgia Journal of Science

Traditional agricultural style food plots, or wildlife openings, are widely used for wildlife management and hunting opportunities on public and private lands in the Southeastern United States. These habitats are often cited as beneficial for game and nongame wildlife, but there are few published studies examining nongame bird use of food plots in recent decades. Modern concerns about the ecological costs of food plots, particularly fragmentation and invasive non-native species, warrant a new examination of this practice. We conducted avian surveys during the breeding season of 2008 at 39 sites composed of three different treatments: traditional food plots, novel food …

Tides, Tourists, And Tails: Exploring Human-Wildlife Overlap On The Homer Spit, Alaska, Serena Seiler

Masters Theses & Specialist Projects

Coastal areas present unique challenges for human-wildlife coexistence due to their shared use by people and marine species. The Homer Spit in Homer, AK (59.6481° N, 151.5299° W) is a projection of land into Kachemak Bay on which lodging, restaurants, campgrounds, RV parks, fishing, and a variety of coastal activities exist or occur, especially during the summer months. Two of the most popular nearshore marine mammals that attract visitors are sea otters (Enhydra lutris) and harbor seals (Phoca vitulina). These two species spend time swimming, foraging, and resting around the Spit, potentially resulting in co occurrences with humans. Using a …

Product Evaluation Plan For Under-Desk Treadmills, Alison Larocca

Waldo Library Student Exhibits

No abstract provided.

Fisheries Research Report No. 350: Recreational Vessel Retrievals In Western Australia - 2009 To 2024, Stephen C. Bradshaw, Claire B. Smallwood, Stuart J. Blight, Troy Matthews, Karina L. Ryan

Fisheries Research Reports

This report provides a time series (2009 – 2024) of the total number of recreational vessel (powerboat) retrievals at a spatial (boat ramp) and temporal (annual, month, hour) resolution for 32 boat ramps distributed from Wyndham to Esperance. This time series has been developed using a workflow that outlines each step, from acquiring raw video data to producing a completed time series of vessel retrievals. As part of this workflow, modelling was undertaken to impute counts of vessel retrieval for sites and hours for which data had not been read, or for which there were significant outages. Features within the …

Demographic Characteristics And Selected Personality Traits Of Women In Competitive Bodybuilding, Chloe A. Zeeuw

Master's Theses

This study investigated demographic characteristics and measures of personality (dimensions of performance perfectionism and five-factor model characteristics) in women in competitive bodybuilding between 18-25 years old. A total of 24 women completed an online survey which included a demographic questionnaire, the Five Factor Model Rating Form (FFMRF), and the Performance Perfectionism Scale for Sport (PPSS) inventories. Descriptive results for the FFMRF were Openness (18.17±3.12), Conscientiousness (25.58±3.33), Extraversion (19.96±3.46), Agreeableness (19.88±4.58), and Neuroticism (15.67±4.94), and for the PPS-S were Self-oriented performance perfectionism (20.96±3.53), Socially prescribed performance perfectionism (13.96±4.26), and Other-oriented performance perfectionism (10.54±4.23). Pearson’s correlation coefficients and Shapiro-Wilk tests revealed that …

Perspectives On Water Policies And Alternative Land Uses Among Alfalfa Farmers In The Great Salt Lake Basin, Bryn Watkins, Stacia Ryder

Publications

Climate change threatens many resources necessary for life. In arid and semiarid regions like Utah, water represents one of the key climate-related conflicts (1,2). In Utah, a changing climate paired with human overconsumption has contributed to the drying of the Great Salt Lake. Rising temperatures will lead to greater evapotranspiration and decreasing headwater streamflow and groundwater storage, resulting in increasing dryness in the Great Salt Lake Basin regardless of human water consumption (3). This in turn threatens the ecosystems, economies, and cultures of the Great Salt Lake Basin, accelerating the local impacts of climate change (4).

Hillslope Flow Paths In Snowmelt And Rainfall Seasons In Permafrost-Underlain Areas, Northeastern Tibetan Plateau: Investigation Based On Hydrochemical Tracers And End-Member Mixing Analysis, Xiong Xiao, Fan Zhang, Fengjing Liu, Xiaoyan Li, Xiaonan Shi, Chen Zeng, Tao Che

Michigan Tech Publications

Study area: The Binggou and adjacent Yakou catchments in the northeastern Tibetan Plateau. Study focus: Hillslope flow paths were studied using hydrochemical data of various water types in the spring snowmelt and summer rainfall periods based on hydrochemical tracers and end-member mixing analysis. New hydrological insights for the study region: End-member mixing analysis confirmed the dominance of surface and near-surface runoff during the spring snowmelt. Specifically, the spring Binggou stream water had 61 % surface runoff, 22 % shallow groundwater, and 17 % near-surface runoff. The spring Yakou stream water had 64 % snowmelt, 25.5 % near-surface runoff, and 10.5 …

Fisheries Research Report No. 353: Ecological Risk Assessment For The North Coast Demersal Scalefish Resource, Kimberley A. Smith, Brett Crisafulli, Gabby E. Mitsopoulos, Fabian I. Trinnie, Taylor Grosse, T Thompson, Stephen J. Newman

Fisheries Research Reports

On the 26 March 2025, the Department of Primary Industries and Regional Development (DPIRD) convened an ecological risk assessment (ERA) of the fisheries that access the North Coast Demersal Scalefish Resource (Resource). This Resource comprises a large number of tropical demersal scalefish species that occur in waters of the North Coast Bioregion, including tropical snappers, emperors and cods.

This document contains the results of the ERA along with the background information used to support the risk scoring process. This includes an overview of the Western Australian commercial fisheries that access the Resource, namely the Pilbara Fish Trawl Interim Managed Fishery, …

Assessment Of Social Media Use And Strategies For Combating Misinformation Among Extension Educators In Arkansas, Enoch Teye Kwao Ametepey

Graduate Theses and Dissertations

This study assessed the use of social media by Extension educators in Arkansas and examines strategies for identifying and combating misinformation within agricultural extension services. Guided by the Uses and Gratifications Theory, the Unified Theory of Acceptance and Use of Technology (UTAUT), and the Third-Person Effect Theory for objectives one, two, and three, this research employed quantitative and qualitative approaches, specifically, two quantitative cross-sectional surveys and a qualitative focus group study developed into a three article dissertation. The first article assessed the extent to which Extension educators utilize social media for professional activities, revealing that social media is predominantly used …

Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins

Biology Faculty Works

Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …

Influence Of Exercise Opportunities On Bone Health In Laying Hens, Jaden Costner, Alexis Clark, Ahmed Ali

Publications

Laying hens are often housed in environments that restrict movement, which may contribute to bone fragility and decreased welfare. These confined environments, such as conventional cage systems, limit exercise and result in poor skeletal development. This study investigates the impact of exercise opportunities on bone health in laying hens by comparing the tibiotarsi and humeri bone characteristics in enriched and unenriched housing environments. A total of 200 hens were housed in pens (20 birds/pen) from 0 to 40 weeks of age. Five pens, which served as the experimental group, were equipped with multi-tier perches and ledges, providing exercise opportunities. In …

Fisheries Research Report No. 361: 2024 Assessment Of The Status Of The Elasmobranch Resource Of Western Australia, Matias Braccini, Alex Hesp

Fisheries Research Reports

This document provides the 2024 risk-based weight of evidence stock assessment for the elasmobranch (sharks and rays) resource of Western Australia (WA). Gummy (Mustelus antarcticus), dusky (Carcharhinus obscurus), whiskery (Furgaleus macki), and sandbar (C. plumbeus) sharks are the most commonly captured species (~80% of the elasmobranch catch) and have been selected as indicator species for the status of the temperate elasmobranch ‘suite’. However, over 100 elasmobranch species have been caught in commercial and/or recreational fisheries in WA and, with the increasing number of elasmobranch species being listed in national and international protection lists, species-specific scientific advice on stock status at …

Immune Modulation Affects Olfactory Glomerular Recovery In Zebrafish, Bonnie E. Ebendick

Dissertations

Adult zebrafish regenerate neurons throughout their lifetime and exhibit rapid recovery from neuronal damage with support from their immune system, making them an excellent model for studying neuroinflammation and brain repair mechanisms. When olfactory sensory neurons are lesioned, their cell death stimulates the immune system by activating microglia and other immune cells in the olfactory bulb, initiating tissue repair and neuronal replacement. This dissertation investigates how the immune system influences recovery from neuronal damage, testing the hypothesis that immune perturbation in zebrafish alters neural recovery.

To investigate the link between immune function and neuronal regeneration, zebrafish received a unilateral lesion …

Mosquitoes: The 5 C’S Of Developing Disease- Commensals Changing To Consequential Pathogens, Alan L. Gillen, Caleb Mast, Robert Braden Somerville

Faculty Publications and Presentations

Hotter, longer summers and changing weather patterns in the United States are bringing more than just sweat and discomfort. In May 2025, a summer heat wave of 107⁰F hit Austin, Texas, and in humid Houston and San Antonio, Texas, temperatures felt over 100⁰ for several days. Normally, these temperatures don’t come until July and August. With temperatures reaching these marks early and heavy rains coming, mosquito activity and ranges expand. Many state and federal health officials report a rise in mosquito-borne illnesses across the US and globe in the last five years.

Farming With Data: Tracing Critical Tensions Using Data Science For Food Justice, Marc Sager, Maximilan Sherard, Anthony Petrosino

Publications

In this manuscript, we explore the intersection of artificial intelligence (AI) and equitable learning in higher education, focusing on data science as a subset of AI and social justice as the core theme of equity. Our investigation sheds light on the nuanced tensions inherent in employing data science for social justice. Rooted in situated perspectives of learning and consequential learning, our study employs an instrumental case-study methodology and analysis techniques from interaction and conversation analysis. Collaborating with three undergraduate students and an urban farm, the students used data science practices to highlight inequities surrounding food justice and access to food. …

Warming Of The Southern Ocean During The Paleocene-Eocene Thermal Maximum: Inferences From Foraminifera At Site U1580, Samina Anee

All Graduate Reports and Creative Projects, Fall 2023 to Present

The Paleocene-Eocene Thermal Maximum (PETM, ~56 million years ago) represents an ancient episode of rapid global warming, offering critical insights into climate dynamics and the Earth's response to increased greenhouse gases. This project aims to quantify the magnitude of warming across the PETM at newly recovered IODP Site U1580 (Agulhas Plateau, Southern Ocean) through the analysis of Mg/Ca and δ¹⁸O ratios of planktic foraminifera. Understanding the extent of warming at Site U1580 is crucial for comprehending past climate variability and improving future climate predictions. Site U1580 is particularly well-suited to foraminiferal geochemistry because of high carbonate content throughout …

Groundwater-Dependent Ecosystems In Southeastern Utah: An Integrated Analysis Of Hydrology, Ecology, And Landscape Change, Colten Lay

All Graduate Reports and Creative Projects, Fall 2023 to Present

In Southeastern Utah, springs play a critical role in sustaining groundwater-dependent ecosystems (GDEs) in a semi-arid environment. However, they remain understudied and face growing threats from climate change, land use modifications, and hydrologic alterations. This study addresses knowledge gaps in spring occurrence, hydrologic function, and ecological condition by integrating field surveys, remote sensing, and geospatial analysis across multiple spatial scales. It provides a comprehensive assessment of spring hydrology, water quality, and ecological conditions using field surveys, remote sensing, and GIS analysis to establish a foundational baseline of GDE resources in the region. I applied a multi-scale monitoring approach across the …

Validation Of Head Above And Head Submerged Hydrostatic Weighing Equations And Air Displacement Plethysmography, Axel M. Miller

All Graduate Reports and Creative Projects, Fall 2023 to Present

Traditional hydrostatic weighing (HW) involves full body submersion at residual volume (RV), which may be uncomfortable. Thus, the purpose of this study was to investigate a more comfortable way to perform this method. HW with the head above water (HW_HAW) was compared to the traditional method of HW with head below water (HW_HBW) and to another method that also measures density by displacement, air displacement plethysmography (ADP). Equivalence was tested by comparing the body fat percentage (BF%), body volume (Vb), and body density (Db) of 27 subjects (15 M, 12 F) between the three methods. Results …

A Toi Rna Editing In Three Members Of The Microbotryum Violaceum Fungal Complext And Characterization Of Adar Genes Of Microbotryum Superbum., Shikhi Baruri

Electronic Theses and Dissertations

A-to-I RNA editing is a process that occurs post-transcriptionally. Through this process, adenosine (A) is replaced by inosine (I) in RNAs by adenosine deaminase enzymes that act on the single-stranded RNA. These enzymes, also known as ADARs, act on RNA. The translation and splicing mechanisms subsequently interpret inosine as guanosine (G), which effectively alters genetic information. This kind of RNA alteration can cause both nonsynonymous and synonymous changes in codon, which may have an impact on protein function. A group of over 89 basidiomycete fungal species known as the Microbotryum violaceum complex infects a similarly large group of plant host …

Metabolic Regulation Of Cardiac Fibroblast Phenotype And Function., Collin Kleis Wells

Electronic Theses and Dissertations

Cardiac fibroblasts are central effectors of cardiac repair after myocardial infarction (MI). In response to signaling cues, they differentiate to a range of phenotypes with robust capacities to synthesize and secrete extracellular matrix (ECM) and signaling molecules. Although activated fibroblast phenotypes are associated with pronounced changes in metabolism, it remains unclear how the metabolic network upholds the effector functions of fibroblasts in the post-infarcted heart. Here, we identified that critical enzymes in the phosphoenolpyruvate (PEP) cycle, i.e. pyruvate kinase muscle-2 (PKM2) and phosphoenolpyruvate carboxykinase-2 (PCK2), are elevated in the heart after MI and examined their role in regulating post-MI remodeling …