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Enhancing Biomedical Imaging With Ai: Compression, Prediction, And Multi-Modal Integration For Clinical Advancement, Mohammad Sadegh Nasr

Computer Science and Engineering Dissertations - Archive

This dissertation delves into the enhancement of biomedical image analysis through the deployment of artificial intelligence methodologies, focusing on the transition from theoretical innovation to practical clinical utility. Spanning four cornerstone projects, the work encapsulates the development of predictive models for spatial transcriptomics, efficient image compression for cancer pathology slides, and critical evaluations of histopathology slide search engines. The first project employs Random Forest Regression and spatial point processes to forecast cell distribution patterns, thereby offering a novel perspective on gene expression in embryogenesis at a single-molecule resolution. The second venture introduces a Variational Autoencoder (VAE) that sets a new …

Lip(S) Service: A Socioethical Overview Of Social Media Platforms’ Censorship Policies Regarding Consensual Sexual Content, Sage Futrell

Cybersecurity Undergraduate Research Showcase

The regulation of sexual exploitation on social media is a pressing issue that has been addressed by government legislation. However, laws such as FOSTA-SESTA has inadvertently restricted consensual expressions of sexuality as well. In four social media case studies, this paper investigates the ways in which marginalized groups have been impacted by changing censorship guidelines on social media, and how content moderation methods can be inclusive of these groups. I emphasize the qualitative perspectives of sex workers and queer creators in these case studies, in addition to my own experiences as a content moderation and social media management intern for …

Cooperative Observing At A Modest-Sized Observatory, Michael D. Joner, Denzil E. Watts Iv, Seneca H. Bahr, Oliver Hancock, Michael W. Holland, Hafsa Jamil, Eden Saxton, Malaya Williams-Jones

BYU West Mountain Observatory Project

The West Mountain Observatory is an astronomical research facility operated by Brigham Young University, located on an isolated mountain approximately 22 kilometers southwest of the main Provo UT campus. The observatory was upgraded 15 years ago and has since been utilized primarily as an undergraduate research facility. The observatory is well suited to do work on projects utilizing time series photometric observations and has been particularly successful at conducting multiple projects for undergraduate student researchers that require observations of different durations and cadences using various filter combinations. This requires additional planning and cooperation between the different programs that are often …

Phosphorus Dynamics In Calcareous Soils Amended With Organic Matter, Logan Banner

All Graduate Reports and Creative Projects, Fall 2023 to Present

Phosphorus (P) is considered immobile in calcareous soils. Organic matter is known to enhance P mobility in these soils. Few studies have considered what role iron oxides might play in P sorption in calcareous soils, especially in the presence of soluble organic matter. This study investigated P sorption dynamics in sand-based, simulated soil systems in the absence or presence of 5 mM carbon (C) as humic acid (HA). Treatments included combinations of dicalcium phosphate dihydrate (DCPD), calcite, and ferrihydrite. Solutions containing 10 mg P L^-1 in a background of 0.01 M CaCl₂were equilibrated with each solid treatment …

Molecularly Defined And Spatially Resolved Cell Atlas Of The Whole Mouse Brain, Meng Zhang, Xingjie Pan, Won Jung, Aaron R Halpern, Stephen W Eichhorn, Zhiyun Lei, Limor Cohen, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Xiaowei Zhuang

Faculty, Staff and Student Publications

In mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3, including several brain regions (for example, refs. 1-11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the …

Movement Patterns Of A Federally Endangered Minnow In A Fragmented Desert River, Martinique J. Chavez

All Graduate Theses and Dissertations, Fall 2023 to Present

Fishes are unified in their need to move within the systems they occupy, and their movement patterns can be fundamental to their ecology and survival. Many large rivers in North America are fragmented by dams that modify natural flow regimes, compromise connectivity, and imperil freshwater fishes dependent on unrestricted movement in order to complete their life history. Coincident with widespread river fragmentation, are the declines of numerous endemic desert fishes in the American southwest. The Rio Grande Silvery Minnow (Hybognathus amarus, RGSM), has experienced a 95% reduction in its historical range and is now restricted to a highly …

Reducing Inputs And Adding Value To Turfgrass Systems Through Clover Inclusion And Plant Growth-Promoting Rhizobacteria Applications, Paige E. Boyle

All Graduate Theses and Dissertations, Fall 2023 to Present

Recently, the US has seen an expansion in the amount of turfgrass land cover (lawns, parks, roadsides, sports fields, and golf courses), as well as an interest in reducing fertilizer, water, and pesticide use in these grass systems. To help maintain quality and function while reducing resource inputs, two promising approaches have emerged: planting clover into lawns and applying plant growth-promoting rhizobacteria.

White clover and grass mixtures have been studied for their ability to cut down on fertilizer usage and provide a uniform, dark green lawn, but other clover types have not been as widely studied and may provide similar …

Ecology And Management Of Dyer's Woad (Isatis Tinctoria) In Northern Utah, Erin Marie Hettinger

All Graduate Theses and Dissertations, Fall 2023 to Present

Dyer’s woad (Isatis tinctoria L.) is a non-native forb that continues to threaten natural areas throughout Northern Utah and much of the Intermountain West. Once introduced, dyer’s woad can become extremely invasive, decreasing forage quality, and displacing native species. While dyer’s woad is found throughout much of Northern Utah, its range in other states remains limited. If promptly managed, control success in these areas will be much higher and populations may be kept at bay before ecological damage becomes severe.

This project tested the ability of dyer’s woad seedlings to compete with common rangeland grasslands at varied densities as …

Effects Of A Protection Zone In A Reaction-Diffusion Model With Strong Allee Effect., Isaac Johnson

Electronic Theses and Dissertations

A protection zone model represents a patchy environment with positive growth over the protection zone and strong Allee effect growth outside the protection zone. Generally, these models are considered through the corresponding eigenvalue problem, but that has certain limitations. In this thesis, a general protection zone model is considered. This model makes no assumption on the direction of the traveling wave solution over the Strong Allee effect patch. We use phase portrait analysis of this protection zone model to draw conclusions about the existence of equilibrium solutions. We establish the existence of three types of equilibrium solutions and the necessary …

Resilient, Sustainable, And Secure Systems Support For Ultra-Low-Power Computational Things, Nicole Tobias

All Dissertations

Wireless battery-free and energy-harvesting devices are expanding the reach and vision of the Internet of Things, where trillions of embedded computational things interconnect ubiquitously around us and inform many different aspects of our everyday lives. Designing these systems without batteries and interconnecting wires lowers maintenance, environmental, and economic costs while also extending device lifetime and deployment opportunities. Over the last decade, research on these ultra-low-power embedded sensors and systems has dramatically increased — enabling new and exciting prospects in many different scientific fields, from smart building and health monitoring applications to animal and activity tracking.

These systems are not without …

Metrics For Comparison Of Complex Networks, Clarissa Reyes

Open Access Theses & Dissertations

Heuristic network statistics are used as a preliminary approach to identify change across networks. In networks where there is known node correspondence (KNC), conventional network comparison methods include taking a norm of the difference matrix, or calculating dissimilarity measures like DeltaCon and cut distance. Since different KNC measures provide varying insight to the network comparison problem, we propose employing Rank Score Characteristic Functions (RSCFs) and the rank-score process as a method for reaching a consensus when ranking quantified change across multiple pairs of networks â?? which is particularly useful for ranking change across subpopulations or subgraphs. Additionally, we propose a …

The Biological, Physical And Chemical Response Of The Little Creek Watershed To The 2020 Czu Lighting Complex Fire, Natalie Fontana

Master's Theses

This post-fire study was conducted to characterize and observe fire induced changes in physical habitat parameters, water-quality conditions and macroinvertebrate assemblages in the Little Creek watershed, a tributary to Scotts Creek located in Cal Poly’s Swanton Pacific Ranch in Davenport, California. Pre-fire data was collected by a Cal Poly student, John Hardy, for his 2017 thesis. Post-burn bioassessment surveys for this study were repeated at four of the same study sites used by Hardy to provide comparisons to the California Stream Condition Index via a modified version of the State of California’s Surface Water Ambient Monitoring Program protocol. Macroinvertebrates were …

A Multidisciplinary Approach To Resolving The End-Guadalupian Extinction, Christopher R. Fielding, Scott E. Bryan, James L. Crowley, Tracy D. Frank, Michael T. Hren, Chris Mays, Stephen Mcloughlin, Jun Shen, Peter J. Wagner, Arne Winguth, Cornelia Winguth

Geosciences Faculty Publications and Presentations

The transition from the middle to late Permian (Guadalupian–Lopingian) is claimed to record one or more extinction events that rival the ‘Big Five’ in terms of depletion of biological diversity and reorganization of ecosystem structure. Yet many questions remain as to whether the events recorded in separate regions were synchronous, causally related, or were of a magnitude rivaling other major crises in Earth's history. In this paper, we survey some major unresolved issues related to the Guadalupian–Lopingian transition and offer a multidisciplinary approach to advance understanding of this under-appreciated biotic crisis by utilizing records in Southern Hemisphere high-palaeolatitude settings. We …

Cvii: Enhancing Interpretability In Intelligent Sensor Systems Via Computer Vision Interpretability Index, Hossein Mohammadi, Krishnaprasad Thirunarayan, Lingwei Chen

Computer Science and Engineering Faculty Publications

In the realm of intelligent sensor systems, the dependence on Artificial Intelligence (AI) applications has heightened the importance of interpretability. This is particularly critical for opaque models such as Deep Neural Networks (DNN), as understanding their decisions is essential, not only for ethical and regulatory compliance, but also for fostering trust in AI-driven outcomes. This paper introduces the novel concept of a Computer Vision Interpretability Index (CVII). The CVII framework is designed to emulate human cognitive processes, specifically in tasks related to vision. It addresses the intricate challenge of quantifying interpretability, a task that is inherently subjective and varies across …

Changes In Physico-Chemical Properties Of A Sandy Loam Soil Depending On The Particle Size Of Hazelnut Shell-Derived Biochar, Damla Bender Özenç, Ceyhan Tarakçioğlu, Funda Irmak Yilmaz, Selahattin AygüN

The Philippine Agricultural Scientist

This study evaluated the effects of hazelnut shell-derived biochar particle sizes on the soil’s physical and chemical properties, and on various nutrient contents present in the sandy loamy soils. For this purpose, an incubation experiment in the plastic high tunnel has been performed under sixteen treatments (control-only soil), and at four incubation times (30, 60, 90, and 120 d), by using three different biochar sizes (≤ 1, 1 - 2, and 2 - 4 mm). The addition of 1 - 2 and 2 - 4 mm biochar during the incubation time decreased the bulk density in the soil by 26%. …

Stream Restoration Effectiveness In Mullins Creek In Fayetteville, Arkansas, Amadeo Scott

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

Lotic waterways are vital for habitat, food, water, and flood protection, but urbanization poses a major threat to their integrity. Runoff from urban surfaces leads to pollution, flashiness, loss of biodiversity, and other symptoms, also known as Urban Stream Syndrome (USS). To combat USS, streams can be restored, but most restorations are not monitored so their long-term effectiveness is unknown. This study quantitatively evaluated a decade-old stream restoration in Fayetteville, Arkansas, to assess its effectiveness in combating USS and achieving set restoration goals, and to gain insights for future restoration projects. Restoration goals included decreasing erosion and sedimentation, increasing pool …

Leveraging Generative Agents: Autonomous Ai With Simulated Personas For Interactive Simulacra And Collaborative Research, James Hutson, Jay Ratican

Faculty Scholarship

The advent of large language models (LLMs) and AI learning have fundamentally reshaped the research landscape, paving the way for novel problem-solving approaches. This paper introduces a unique framework that leverages the capabilities of autonomous AI agents with simulated personas to drive collaborative research in groundbreaking ways. Inspired by a recent study of autonomous agents mirroring human behavior, this concept encourages the use of a cadre of AI agents, each possessing specialized expertise for collective endeavors. By replicating human diversity in teamwork, this approach targets complex and hitherto unsolvable issues. The key to this strategy is persona and emotional simulation, …

Kape: Knn-Based Performance Testing For Deep Code Search, Yuejun Guo, Qiang Hu, Xiaofei Xie, Cordy Maxime, Mike Papadakis, Yves Le Traon

Research Collection School Of Computing and Information Systems

Code search is a common yet important activity of software developers. An efficient code search model can largely facilitate the development process and improve the programming quality. Given the superb performance of learning the contextual representations, deep learning models, especially pre-trained language models, have been widely explored for the code search task. However, studies mainly focus on proposing new architectures for ever-better performance on designed test sets but ignore the performance on unseen test data where only natural language queries are available. The same problem in other domains, e.g., CV and NLP, is usually solved by test input selection that …

Characterization Of The Long-Distance Dispersal Kernel Of White-Tailed Deer And Evaluating Its Impact On Chronic Wasting Disease Spread In Wisconsin, Mennatallah Gouda

All Graduate Theses and Dissertations, Fall 2023 to Present

Chronic Wasting Disease (CWD) is a fatal, untreatable neurodegenerative disease that infects deer and related species. It is highly contagious and caused by abnormal malfunction and assembly of normal cellular proteins into aggregation-prone proteins. The Centers for Disease Control and prevention report that the prevalence of CWD in free-ranging deer in the US is still relatively low. However, in several states the infection rates exceed 1 deer in 10. Deer may uptake CWD from direct interaction with infected individuals or from the environment. Infected individuals shed CWD into the environment through feces, urine, saliva or carcasses, and long-distance dispersal of …

Make The U In Uda Matter: Invariant Consistency Learning For Unsupervised Domain Adaptation, Zhongqi Yue, Qianru Sun, Hanwang Zhang

Research Collection School Of Computing and Information Systems

Domain Adaptation (DA) is always challenged by the spurious correlation between domain-invariant features (e.g., class identity) and domain-specific features (e.g., environment) that do not generalize to the target domain. Unfortunately, even enriched with additional unsupervised target domains, existing Unsupervised DA (UDA) methods still suffer from it. This is because the source domain supervision only considers the target domain samples as auxiliary data (e.g., by pseudo-labeling), yet the inherent distribution in the target domain—where the valuable de-correlation clues hide—is disregarded. We propose to make the U in UDA matter by giving equal status to the two domains. Specifically, we learn an …

The Hydrodynamic Performance Of Duck Feet For Submerged Swimming Resembles Oars Rather Than Delta-Wings, Gal Ribak, Roi Gurka

Physics and Engineering Science

Waterfowl use webbed feet to swim underwater. It has been suggested that the triangular shape of the webbed foot functions as a lift-generating delta wing rather than a drag-generating oar. To test this idea, we studied the hydrodynamic characteristics of a diving duck’s (Aythya nyroca) foot. The foot’s time varying angles-of-attack (AoAs) during paddling were extracted from movies of ducks diving vertically in a water tank. Lift and drag coefficients of 3D-printed duck-foot models were measured as a function of AoA in a wind-tunnel; and the near-wake flow dynamics behind the foot model was characterized using particle image velocimetry (PIV) …

Assessing The Morphological And Physiological Traits Of Smooth Brome Pastures Under Long Term Grazing And Nutrient Enrichment In Eastern Nebraska, Hassan Shehab

School of Natural Resources: Dissertations, Theses, and Student Research

Climate change together with the increase in demands for food, feed, fuel, and fiber are becoming a threat to sustainability and resilience of agriculture and pasture lands. Bromus inermis (smooth bromegrass) dominates pastures for cattle grazing in Eastern Nebraska, US, where it is planted in monocultures, and is considered high quality forage because of its palatability and high nutritional value for cattle, especially under intensive management practices. Sustainable management of these pastures is key to long-term resilience. This study aims to assess the performance of smooth bromegrass pastures to the combined effects of long-term management practices (since 2005) of fertilization …

Population Demography Of A Glacial-Relict Stream Fish Mediated Via Anthropogenic Alteration, Joseph M. Spooner

School of Natural Resources: Dissertations, Theses, and Student Research

Northern Pearl Dace Margariscus nachtriebi are a small-bodied glacial-relict fish species of greatest conservation need (SGCN) found throughout Canada and the northern United Sates. Their distribution within the Nebraska Sandhills Ecoregion is isolated from the northern core distribution of the species following the last glaciation period approximately 18,000 years ago. Headwater streams within the Nebraska Sandhills Ecoregion are predominately groundwater fed and provide the cool water temperatures needed to support Northern Pearl Dace and other glacial-relict SGCN. Headwater streams within the Nebraska Sandhills Ecoregion have been geomorphically altered through anthropogenic processes such as channelization whereby habitat homogenization has occurred. Evidence …

Human Dimensions Of Woody Encroachment Management In Nebraska, Emily Rowen

School of Natural Resources: Dissertations, Theses, and Student Research

Woody plant encroachment (WPE) is a social-ecological problem that will challenge conservation professionals and agricultural producers to adapt their management strategies. This research first examined WPE from the perspective of individual conservation professionals through an online survey. Conservation professionals’ attitudes about adaptation to vegetation transitions, such as WPE, were of interest because these attitudes are one measure of how prepared this group is to respond to WPE. Hypothesized predictors of adaptation attitude were tested through linear regression modeling. These predictors included ecological change, observation of WPE, or risk perception. It was found that risk perception was the strongest predictor of …

The Influence Of Invasive Species On Fishers’ Satisfactions, Caroline M. Laplante

School of Natural Resources: Dissertations, Theses, and Student Research

Invasives species are prevalent and widespread in North America. Outdoor recreational activities, such as fishing, introduce a point in which humans may interact with invasive species and have to adapt their own behaviors. Bigheaded carp in the Missouri River below Gavin’s Point Dam are a group of invasive fish species that were thought to be negatively relating to recreational fishers’ satisfactions. Using a content analysis and an importance-grid, we conclude that invasive species do not strongly relate to recreational paddlefish fishers’ satisfactions. Paddlefish fishers represent a small sub-set of recreational fishers in Nebraska and South Dakota. The content analysis revealed …

Understanding Avidities Of Recreational Activities For People Possessing Fishing Licenses And Residing In Urban Environments, Kyle F. Hansen

School of Natural Resources: Dissertations, Theses, and Student Research

Recreational fishing is one of the world's most popular pastimes, wherein participation is associated with sociodemographic factors. Even so, fishing license sales are declining in the USA in conjunction with a reduction in rural populations as people move to urban areas. Thus, urban areas are constantly growing in population size, population diversity, and geographic size suggesting a need to understand fishing participation in these growing areas. Natural resource managers often use participation to understand recreationists, yet avidity could provide a new way to understand recreationists. The goal of our study is to understand what sociodemographic factors influence the fishing avidity …

Game-Theoretic Approaches To Optimal Resource Allocation And Defense Strategies In Herbaceous Plants, Molly R. Creagar

Department of Mathematics: Dissertations, Theses, and Student Research

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, allocation to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We incorporate a neighborhood defense effect by applying spatial evolutionary game theory to optimal resource allocation in plants where cooperators are plants investing in defense and defectors are plants that do not. We use a stochastic dynamic programming model, along …

Seasonality In Terminus Ablation Rates For The Glaciers In Kalaallit Nunaat (Greenland), Aman K. C.

Boise State University Theses and Dissertations

Since the 1990s, the Greenland Ice Sheet (GrIS) has undergone accelerated mass loss, with a substantial portion due to the dynamic effects of terminus retreat. Conventional assessments of dynamic mass loss, however often overlook the critical aspect of terminus change, focusing primarily on inland ice flow. In this thesis, I construct and analyze mass loss due to both temporal variations in ice flow and detachment of ice from the glacier terminus, called terminus ablation, for 55 marine-terminating glaciers in Greenland over a ten-year period from 2013 to 2023. I calculated terminus ablation rates using openly accessible data for terminus positions, …

Motion Simulation And Risk Assessment Of Dropped Objects In Offshore Operations, Hanqi Yu

LSU New Orleans Theses and Dissertations

Subsea pipelines are a cost-effective and reliable way to transport hydrocarbons in offshore oil and gas development. However, dropped objects can pose hazards and cause damage to pipelines. This dissertation briefly introduces the hazards and hidden dangers caused by dropped containers, discusses motion simulation methods for different object shapes, and reviews risk assessment procedures for handling dropped objects in offshore operations. Ongoing research at the University of New Orleans' towing tank on dropped container models is also discussed. Using ANSYS Fluent, we simulate trajectories of container models and calculate relevant hydrodynamic coefficients for different dropped angles. We then apply risk …

Isotopic Ecology Of Bison And Bootherium At Big Bone Lick, Kentucky, Frances Stephenson

Electronic Theses and Dissertations

Big Bone Lick (BBL) is a late Pleistocene and Holocene fossil locality in the Ohio River valley of Kentucky. This study utilized stable isotopes (δ¹³C, δ¹⁸O, and ⁸⁷Sr/⁸⁶Sr) in tooth enamel to reconstruct mobility and diet in Bison, as well as diet in Bootherium bombifrons. Isotopic results from seven Bison and two B. bombifrons are reported. Results suggest Pleistocene Bison and Bootherium occupied different dietary niches. Although both had C3-dominated diets, Bison occupied more open environments than B. bombifrons. Two bison from the late Holocene deposit had diets that consisted …