Life Sciences Commons^™

Western Science And Eastern Zen To Seek The Origin Of Truth: Philosophical Background Of Scale Modeling, Kozo Saito

Progress in Scale Modeling, an International Journal

This article was written to introduce philosophical background of scale modeling, where Zen philosophy was applied to overcome the limitation of logical thinking and hypotheses-driven deductive science. Three specific reasons are as follows. The first is related to the law approach in scale modeling; it uses the kufu principle, originated in Zen Buddhism, together with the other three scientific methods: experimental, theoretical, and computational. The second reason is because scale modeling seeks relativistic understanding by attempting to realize similarity; the concept is closer to Eastern philosophy rather than absolute understanding cultivated by deductive science. The third is in the educational …

Molecular Understanding And Design Of Deep Eutectic Solvents And Proteins Using Computer Simulations And Machine Learning, Usman Lame Abbas

Theses and Dissertations--Chemical and Materials Engineering

Hydrophobic deep eutectic solvents (DESs) have emerged as excellent extractants. A major challenge is the lack of an efficient tool to discover DES candidates. Currently, the search relies heavily on the researchers’ intuition or a trial-and-error process, which leads to a low success rate or bypassing of promising candidates. DES performance depends on the heterogeneous hydrogen bond environment formed by multiple hydrogen bond donors and acceptors. Understanding this heterogeneous hydrogen bond environment can help develop principles for designing high performance DESs for extraction and other separation applications. This work investigates the structure and dynamics of hydrogen bonds in hydrophobic DESs …

Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta

Theses and Dissertations--Computer Science

End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and …

Tricritical Point As A Crossover Between Type-Is And Type-Iis Bifurcations, Prabakaran Rajamanickam, Joel Daou

Progress in Scale Modeling, an International Journal

A tricritical point as a crossover between (stationary finite-wavelength) type-I_s and (stationary longwave) type-II_s bifurcations is identified in the study of diffusive-thermal (Turing) instability of flames propagating in a Hele-Shaw channel in a direction transverse to a shear flow. Three regimes exhibiting different scaling laws are identified in the neighbourhood of the tricritical point. For these three regimes, sixth-order partial differential equations are obtained governing the weakly nonlinear evolution of unstable solutions near the onset of instability. These sixth-order PDES may be regarded as the substitute for the classical fourth-order Kuramoto­­­­­­–­­Sivashinsky equation which is not applicable near the …

Methane Dynamics Of Kentucky Bottomland Hardwood Forested Systems, Marissa Miles, Jessica B. Moon, Skylar Ross, Jarred Asselta, Niklas Klauss, Rosie Carey, Kabi Raj Khatiwada, Bassil El Masri, Gary Stinchcomb, Benjamin R. K. Runkle

Kentucky Water Resources Annual Symposium

No abstract provided.

Floating Vegetation As A Driver Of Ch4 Emissions In Small Ponds Across Louisville, Ky, Mark Tierney, C. Jalink, J. H. Loughrin, S. W. Antle, Andrew S. Mehring

Kentucky Water Resources Annual Symposium

No abstract provided.

Measuring The Contribution Of Bald Cypress “Knees” To Greenhouse Gas Emissions During Climate Extremes, Skylar Ross, Jessica B. Moon, Niklas Klauss, Marissa Miles, Kabi Raj Khatiwada4, Bassil El Masri, Gary Stinchcomb, Benjamin R. K. Runkle

Kentucky Water Resources Annual Symposium

No abstract provided.

Characterizing Louisville Wetlands From Above And Below To Better Predict Wetland Carbon Sink-Source Status, Andrea E. Gaughan, Andrew S. Mehring, Mark Tierney, David Brown, Kassidy Haynes, Madison Cicha

Kentucky Water Resources Annual Symposium

No abstract provided.

Scale Model Experiments Of Toxic Gas Production From The Combustion Of Polymers When Applied With Different Droplet Sizes Of Water Mist, Nicharee Thinnakornsutubutr, Masayuki Mizuno, Kazunori Kuwana

Progress in Scale Modeling, an International Journal

This research experimentally investigated the combustion of polymeric materials with water mist application in an enclosure, with an emphasis on the production of toxic gases. Two different diameters, ~100 and ~260 μm, were tested. The experimental conditions were determined based on Froude similarity laws for low drop Reynolds number conditions. Droplets and polymers’ physical and chemical properties influence the burning/extinguishing behavior and toxic-gas evolution. In general, larger droplets can extinguish a fire in a shorter time, and toxic gas concentrations in a test chamber decreased more rapidly. However, the large droplets tended to cause the flame expansion phenomenon for thermoplastics …

Clutch Analysis And Design For The Wildcat Pulling Team Quarter Scale Tractor Drivetrain, Lauren Doyle

Lewis Honors College Thesis Collection

The University of Kentucky (UK) Wildcat Pulling Team competes in the annual ASABE International Quarter Scale Tractor Student Design Competition. In 2022 the team placed 3rd overall in the competition, missing 1st place by 23 points. The loss in points was due to the clutch subassembly having issues related to maneuverability, manufacturability, and serviceability. The goal of this project was to redesign the 2022 tractor’s drivetrain for the new 2023 competition tractor. Background research was conducted on three types of clutches: manual, electric, and centrifugal. The electric clutch and centrifugal clutch with manual override were tested to determine their viability …

Applying Hermetic Storage And Multiple Abiotic-Stressed Germinations To Actuate Desirable Effects In Wheat Phytochemistry, Food, And Biological Functionalities, Bababode Kehinde

Theses and Dissertations--Biosystems and Agricultural Engineering

Wheat is one of the most widely consumed staple foods in the world, supplying both nutritional and caloric requirements for billions of people. The rising global population and increased food demand behooves all stakeholders across the wheat supply chain to significantly increase their output and efficiency. Beyond the target for increased farm yields, dietary, nutritional, and health requirements along with their continuous supply must be satisfied with improved storage and processing schemes. Post-harvest changes in wheat can result in a significant reduction in its quality. Such losses could be qualitative and/or quantitative, impacting its physical, physiological, organoleptic, and nutritional attributes. …

Improving Indoor Arenas For The Equine Industry, Staci Mcgill

Theses and Dissertations--Biosystems and Agricultural Engineering

Equine indoor arenas are a unique infrastructure investment found at equine farms and facilities. They are semi-indoor structures for exercising horses, exhibiting skills during competitive events, and other equine related activities. These spaces do not always include mechanical ventilation or stirring fans and occupancy by horses and humans can be sporadic and inconsistent, which creates a challenging space for understanding and predicting airflow. Typically, indoor arenas have a sand-based footing over which the horse travels. The impact of the hooves can cause dust to become a concern within the facilities. Environmental concerns within these facilities (temperature, respirable dust, moisture, and …

Session 3a: Karst And Groundwater, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Examining the Utility of Tryptophan-Like Fluorescence As a Proxy for Fecal Contamination in Karst Basins, Inner Bluegrass Region, Kentucky
• A Predictive Flood Model for Urban Karst Environments
• Improving Best Management Practices for the Siting, Maintenance, and Design of Urban Karst Groundwater Injection Wells

Session 3b: Sediments, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Sediment Degradation Experiments for a Low Gradient Stream Suggest the Watershed’s Connectivity Regime Exhibits Control on Stream Biogeochemistry
• Does Sediment Organic Matter Content Mediate the Effects of Chironomid Larvae on Benthic Nitrous Oxide Flux
• Drivers of Variability in Annual Sediment Accretion Rates Within Wetland Easements of Western Kentucky

Poster Session, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Evaluating the Effects of Beaver Dam Removal on the Hydrology, Water Quality, and Bioindicators of a Restored Wetland
• Predictive Sediment Flux Modeling of a Karst Spring Using High Resolution Sensors and Stable Carbon and Nitrogen Isotopes
• Development and Validation of qPCR Assays for Use in eDNA Detection of Four Species of Semiaquatic Salamanders .
• Analyzing Recent Spatio-Temporal Rainfall Erosivity Patterns and Trends Across Kentucky
• Development of eDNA Protocols for Detection of Four Darter (Percidae: Etheostomatinae) Species in Central Kentucky Streams
• Assessing Change in the Seasonality of Stable Isotopes δ18O and δ2H for Meteoric and Terrestrial Waters of Central Kentucky
• Coupling …

Session 2: Water And The Community, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Development of Human Health Criteria for Surface Waters of the Commonwealth of Kentucky
• Kentucky Workforce Survey Results
• Modeling, Managing, and Mitigating Stormwater Flooding using a Real-time Monitoring Network and Environmental Equity Approach

Session 1a: Watershed Management, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Motivations and Barriers to the Implementation of Riparian Buffer Zones on Central Kentucky Horse Farms
• Engaging Urban Watershed Stewards in Stormwater Management
• Efficacy Examination of Urban Reforestation Efforts on Streams in Lexington, KY: Macroinvertebrates and Water Quality Assessments
• Over a Decade of Monitoring Water Quality at McConnell Springs – What Have We Learned?
• Glenns Creek Watershed Characterization Efforts

Session 1b: Contaminant Exposure And Treatment, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

• Cyanobacteria, Cyanotoxin Synthetase Genes, and Cyanotoxin Occurrence Among Selected Large River Sites in the Lower Ohio River Basin, 2020–21
• Emerging Contaminant Exposure Following WWTP Processes to Surface Waters
• Reactive Membrane Synthesis for Capture and Degradation of Toxic Water Contaminants
• Implications to Tap and Stream Water Chemistry Due to Variations in Sampling Location and Watershed Land Use
• Examining Toxicity of 2D Nanomaterial Phosphorene, Free-Standing and Embedded onto Membranes, and Its Application for Removal of Per-and Polyfluoroalkyl Substances (PFAS)

Proceedings Of 2022 Kentucky Water Resources Annual Symposium, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

This symposium was planned and conducted as a part of the state water resources research institute annual program that is supported by Grant/Cooperative Agreement Number G21AP10631-00 from the United States Geological Survey (USGS). The contents of this proceedings document and the views and conclusions presented at the symposium are solely the responsibility of the individual authors and presenters and do not represent the official views of the USGS or of the symposium organizers and sponsors. This publication is produced with the understanding that the United States Government is authorized to reproduce and distribute reprints for government purposes. Mention of trade …

A Simplified Model For The Intermediate Structure Of Strong Fire Whirls, Forman A. Williams

Progress in Scale Modeling, an International Journal

A model is described for the overall structure of intense fire whirls, based on a spatially evolving vortex, with circulation enhancement driven by the axial acceleration of low-density gas in the core through the axial pressure gradient. The axial acceleration increases the entrainment rate into the core which, through mass conservation, increases the circulation if the angle between the tangential and radial velocity components remains fixed. The two-zone model employs general balance equations for regions inside and outside a cylinder of fixed radius, each inviscid, the inside region being presumed to have a constant density small compared with the (constant) …

Reduced-Scale Experiments And Numerical Simulations Of Informal Settlement Dwelling Fires, Vigneshwaran Narayanan, Antonio Cicicone, Ayden D. Botha, Richard Shaun Walls

Progress in Scale Modeling, an International Journal

Informal settlement dwellings (ISDs) house approximately one billion people in the developing world and this number is expected to double by the year 2030. Contemporary research on ISD fires has focused on understanding the fire dynamics within individual dwellings (micro-scale) and fire spread in settlements consisting of multiple dwellings (macro-scale). This paper aims to do two primary things: investigate if scaling methods that were derived for compartments with thermally thick boundaries can be applied to ISDs (compartments with thermally thin boundaries), and if they can adequately represent the most important phenomena associated with full-scale ISD fires; and demonstrate Fire Dynamics …

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …

Prostacyclin Promotes Degenerative Pathology In A Model Of Alzheimer’S Disease, Tasha R. Womack, Craig T. Vollert, Odochi Ohia-Nwoko, Monika Schmitt, Saghi Montazari, Tina L. Beckett, David Mayerich, M. Paul Murphy, Jason L. Eriksen

Molecular and Cellular Biochemistry Faculty Publications

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is the most common form of dementia in aged populations. A substantial amount of data demonstrates that chronic neuroinflammation can accelerate neurodegenerative pathologies. In AD, chronic neuroinflammation results in the upregulation of cyclooxygenase and increased production of prostaglandin H2, a precursor for many vasoactive prostanoids. While it is well-established that many prostaglandins can modulate the progression of neurodegenerative disorders, the role of prostacyclin (PGI2) in the brain is poorly understood. We have conducted studies to assess the effect of elevated prostacyclin biosynthesis in a mouse model of AD. Upregulated prostacyclin expression …

Therapeutic Treatment With The Anti-Inflammatory Drug Candidate Mw151 May Partially Reduce Memory Impairment And Normalizes Hippocampal Metabolic Markers In A Mouse Model Of Comorbid Amyloid And Vascular Pathology, David J. Braun, David K. Powell, Christopher J. Mclouth, Saktimayee M. Roy, D. Martin Watterson, Linda J. Van Eldik

Neuroscience Faculty Publications

Alzheimer's disease (AD) is the leading cause of dementia in the elderly, but therapeutic options are lacking. Despite long being able to effectively treat the ill-effects of pathology present in various rodent models of AD, translation of these strategies to the clinic has so far been disappointing. One potential contributor to this situation is the fact that the vast majority of AD patients have other dementia-contributing comorbid pathologies, the most common of which are vascular in nature. This situation is modeled relatively infrequently in basic AD research, and almost never in preclinical studies. As part of our efforts to develop …

Characterizing The Internal Porous Structure Of Equine Proximal Sesamoid Bones Subjected To Race Training Using Fast Fourier Transforms, Joseph Erik Davis

Theses and Dissertations--Biomedical Engineering

The equine racing industry is one of the main proponents in Kentucky’s economic infrastructure. In this industry there has come a need to investigate the nature of the proximal sesamoid bone (PSB). Breakdowns involving the PSBs are the leading cause in racehorse deaths in the industry, with still little known about what causes this bone to fracture. This study seeks to shed insight by investigating the internal structure of the PSB. Using microCT scanning, the internal porous structure was captured. From there, noticeable differences in the pores were noticed and quantified using fast Fourier transform (FFT) analysis.

The dominant peak …

Exploration Of Lignin-Based Superabsorbent Polymers (Hydrogels) For Soil Water Management And As A Carrier For Delivering Rhizobium Spp., Toby Adjuik

Theses and Dissertations--Biosystems and Agricultural Engineering

Superabsorbent polymers (hydrogels) as soil amendments may improve soil hydraulic properties and act as carrier materials beneficial to soil microorganisms. Researchers have mostly explored synthetic hydrogels which may not be environmentally sustainable. This dissertation focused on the development and application of lignin-based hydrogels as sustainable soil amendments. This dissertation also explores the development of pedotransfer transfer functions (PTFs) for predicting saturated hydraulic conductivity using statistical and machine learning methods with a publicly available large data set. A lignin-based hydrogel was synthesized, and its impact on soil water retention was determined in silt loam and loamy fine sand soils. Hydrogel treatment …

The Response Of Beef Cattle To Disturbances From Unmanned Aerial Vehicles (Uavs), Gabriel Abdulai

Theses and Dissertations--Biosystems and Agricultural Engineering

Unmanned aerial vehicles (UAVs) are increasingly becoming common in animal agriculture. However, research regarding the impact of UAV disturbance on animal wellbeing is lacking or limited. The goal of this study was to investigate the effect of UAV flights on beef cattle by measuring cattle heart and movement rate when introduced to single or multiple UAV flights. A total of 16 -18 crossbred beef heifers were introduced to different flights patterns at between 5 and 9 m above ground level (AGL) at approximately 1 to 2 m/s horizontal velocity for 4 weeks with flights repeated 3 days per week. Results …

Nondestructive Detection Of Codling Moth Infestation In Apples Using Pixel-Based Nir Hyperspectral Imaging With Machine Learning And Feature Selection, Nader Ekramirad, Alfadhl Y. Khaled, Lauren E. Doyle, Julia R. Loeb, Kevin D. Donohue, Raul T. Villanueva, Akinbode A. Adedeji

Electrical and Computer Engineering Faculty Publications

Codling moth (CM) (Cydia pomonella L.), a devastating pest, creates a serious issue for apple production and marketing in apple-producing countries. Therefore, effective nondestructive early detection of external and internal defects in CM-infested apples could remarkably prevent postharvest losses and improve the quality of the final product. In this study, near-infrared (NIR) hyperspectral reflectance imaging in the wavelength range of 900–1700 nm was applied to detect CM infestation at the pixel level for three organic apple cultivars, namely Gala, Fuji and Granny Smith. An effective region of interest (ROI) acquisition procedure along with different machine learning and data processing …

Pairwise Correlation Analysis Of The Alzheimer’S Disease Neuroimaging Initiative (Adni) Dataset Reveals Significant Feature Correlation, Erik D. Huckvale, Matthew W. Hodgman, Brianna B. Greenwood, Devorah O. Stucki, Katrisa M. Ward, Mark T. W. Ebbert, John S. K. Kauwe, The Alzheimer’S Disease Neuroimaging Initiative, The Alzheimer’S Disease Metabolomics Consortium, Justin B. Miller

Sanders-Brown Center on Aging Faculty Publications

The Alzheimer’s Disease Neuroimaging Initiative (ADNI) contains extensive patient measurements (e.g., magnetic resonance imaging [MRI], biometrics, RNA expression, etc.) from Alzheimer’s disease (AD) cases and controls that have recently been used by machine learning algorithms to evaluate AD onset and progression. While using a variety of biomarkers is essential to AD research, highly correlated input features can significantly decrease machine learning model generalizability and performance. Additionally, redundant features unnecessarily increase computational time and resources necessary to train predictive models. Therefore, we used 49,288 biomarkers and 793,600 extracted MRI features to assess feature correlation within the ADNI dataset to determine the …

Characterization Of Indoor Arenas Through An Anonymous Survey, Staci Mcgill, Morgan D. Hayes, Kimberly I. Tumlin, Robert Coleman

Biosystems and Agricultural Engineering Faculty Publications

Equine farms are building both stables for the horses to live in and additional facilities to train and work horses (Kidd et al., 1997). For many of these farms, an outdoor arena that has an all-weather footing is the first working facility built. During inclement weather the ability to train in the outdoor arenas is inhibited, which in turn means the trainers, riders, and farms lose income as money is only made when horses are working, training, and competing. Indoor arenas allow for horses to continue to be worked no matter the weather conditions. The equine industry contributes a total …