Digital Commons Network^™

Streamlining The Detection Of Human Thyroid Receptor Ligand Interactions With Xl1-Blue Cell-Free Protein Synthesis And Beta-Galactosidase Fusion Protein Biosensors, J. Porter Hunt, Tyler J. Free, Jackelyn Galiardi, Kevin M. Watt, David W. Wood, Bradley Charles Bundy

Faculty Publications

Thyroid receptor signaling controls major physiological processes and disrupted signaling can cause severe disorders that negatively impact human life. Consequently, methods to detect thyroid receptor ligands are of great toxicologic and pharmacologic importance. Previously, we reported thyroid receptor ligand detection with cell-free protein synthesis of a chimeric fusion protein composed of the human thyroid receptor beta (hTRβ) receptor activator and a β-lactamase reporter. Here, we report a 60% reduction in sensing cost by reengineering the chimeric fusion protein biosensor to include a reporter system composed of either the full-length beta galactosidase (β-gal), the alpha fragment of β-gal (β-gal-α), or a …

Detection Of Cancer-Associated Gene Mutations In Urinary Cell-Free Dna Among Prostate Cancer Patients In South Africa, Dada Oluwaseyi Temilola, Martha Wium, Juliano Paccez, Azola Samkele Salukazana, Solomon O. Rotimi, Hasan H. Otu, Giuseppina M. Carbone, Lisa Kaestner, Stefano Cacciatore, Luiz Fernando Zerbini

Department of Electrical and Computer Engineering: Faculty Publications

Prostate cancer (PCa) is the most common cause of cancer death among African men. The presence of tumor-specific variations in cell-free DNA (cfDNA), such as mutations, microsatellite instability, and DNA methylation, has been explored as a source of biomarkers for cancer diagnosis. In this study, we investigated the diagnostic role of cfDNA among South African PCa patients. We performed whole exome sequencing (WES) of urinary cfDNA. We identified a novel panel of 31 significantly deregulated somatic mutated genes between PCa and benign prostatic hyperplasia (BPH). Additionally, we performed whole-genome sequencing (WGS) on matching PCa and normal prostate tissue in an …

Multi-Criteria Analysis Of The Possibility Of Retrofitting The System Of Rainwater Drainage From Subsidence Basins In A Liquidated Mine, Andrzej Chmiela, Małgorzata Wysocka, Adam Smoliński

Journal of Sustainable Mining

Mine closure is the natural final stage of mining activity. The process of financing mine liquidation is complex and expensive. The many years of conducted hard coal extraction affect the surface height differences. Analyses of the shifts in hydrogeological conditions and water hazard states in mining plants led to legal regulation adaptations, primarily in terms of hydrogeological documentation preparation, and made it necessary to conduct work concerning new options for water hazard assessment and prevention. Current subjects of particular interest include shifts in terrain morphology and the water regime, resulting in periodic flooding and permanent flooding of the most depressed …

Fall Detection Method Of Digital Sequence Based On Fusion Strategy, Riming Sun, Hu Guo, Li Zou, Jiaqi Mao, Shengfa Wang

Journal of System Simulation

Abstract: Falls have become the primary cause of disability due to injury for the elderly. Timely and accurate warning of fall events is an important link to rescue work. In order to improve the accuracy of fall detection, a fall detection method based on a fusion strategy is proposed, which considers both the integrity of high-dimensional digital sequences and the specificity of different dimensions. The input digital sequences obtained from the wrist portable sensor are processed by window segmentation according to the saliency of resultant acceleration, so as to ensure the timing of the data and improve the identifiability of …

Virtual Navigation Path Planning Based On Octree Potential Field For Endonasal Endoscope, Wenjing Li, Yanlin Luo, Yuhui Wang, Li Zhu

Journal of System Simulation

Abstract: Virtual navigation can intuitively display the internal structure of human tissue from multiple viewpoints. The navigation path planning algorithm is the key to achieving excellent navigation effects. The traditional centerline extraction algorithm can ensure a wide field of view during navigation, but the time efficiency is not high enough on the complex nasal-skull base volume model. To solve the problem, a rapid navigation path planning algorithm based on the octree potential field is proposed. The space outside the obstacles is modeled by an octree, and the octree potential field is constructed by calculating the potential of all the octree …

Research On Artificial Population Generation And Application Based On Genetic Algorithm, Hongli Zhang, Jingshuang Deng

Journal of System Simulation

Abstract: High-precision micro-population data are one of the key basic data for simulation systems such as disease spread, traffic travel, and emergency events. In reality, computer-generated artificial populations are often used for simulation. Due to computational efficiency and standardization of generation steps, the iterative proportional fitting method is currently used for artificial population synthesis. However, it has strict requirements on basic data and faces zero-unit and data representational deviation problems, and it fails to guarantee the fitting at the individual and family levels at the same time. In order to overcome this deficiency, an improved genetic algorithm using a simulated …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Thermotolerance And Hydrogen Production Potential Of Salt-Tolerant Microflora From Salt Fields, Tsuyoshi Imai, Gede Adi Wiguna Sudiartha, Jantima Teeka, Prapaipid Chairattanamanokorn, Alissara Reungsang, Yung-Tse Hung

Civil and Environmental Engineering Faculty Publications

Upper mesophilic temperature acclimation of halophilic, hydrogen-producing bacteria from salt fields was investigated in this study, along with the changes in microbial abundance during anaerobic digestion (AD) process. Genomic approaches such as PCR-denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS) were performed to profile the microbial communities. During AD, there was a significant abundance of Halanaerobacter lacunarum at 48°C followed by the increase in hydrogen yield, signifying potential contribution from the halophile in the hydrogen production. A decrease in the dominance of H. lacunarum and Halanaerobium fermentans at 42°C, likely due to an increase in other bacterial species, was …

Asset-Based Approaches To Multilingual Students’ Computer Science Identity Development, Sharin Rawhiya Jacob, Mark Warschauer

Journal of Computer Science Integration

While computer science identity development has been examined in several studies, there is much to learn about the development of multilingual students’ computer science (CS) identities. To develop strong CS identities, multilingual students must engage in culturally and linguistically sustaining curriculum, pedagogy, and interaction that draws from their rich and varied resources. This theoretical paper is grounded in a justice-centered, asset-based framework that views the traditions and practices in students’ cultures and communities as strong contributors to knowledge construction in STEM. We draw on multiple studies exploring multilingual student CS identity development to better understand how their personal, familial, community-based, …

Spin-Acoustic Control Of Silicon Vacancies In 4h Silicon Carbide, Jonathan R. Dietz, Boyang Jiang, Aaron M. Day, Sunil A. Bhave, Evelyn L. Hu

Purdue University Libraries Open Access Publishing Fund

Bulk acoustic resonators can be fabricated on the same substrate as other components and can operate at various frequencies with high quality factors. Mechanical dynamic metrology of these devices is challenging as the surface information available through laser Doppler vibrometry lacks information about the acoustic energy stored in the bulk of the resonator. Here we report the spin-acoustic control of naturally occurring negatively charged silicon monovacancies in a lateral overtone bulk acoustic resonator that is based on 4H silicon carbide. We show that acoustic driving can be used at room temperature to induce coherent population oscillations. Spin-acoustic resonance is shown …

High-Sensitivity Electronic Stark Spectrometer Featuring A Laser-Driven Light Source, J. S. Huff, K. M. Duncan, C. J. Van Galen, M. S. Barclay, W. B. Knowlton, B. Yurke, P. H. Davis, D. B. Turner, R. J. Stanley, R. D. Pensack

Materials Science and Engineering Faculty Publications and Presentations

We report developmental details of a high-sensitivity Stark absorption spectrometer featuring a laser-driven light source. The light source exhibits intensity fluctuations of ∼0.3% over timescales ranging from 1 min to 12 h, minimal drift (≤ 0.1%/h), and very little 1/f noise at frequencies greater than 200 Hz, which are comparable to or better than an arc-driven light source. Additional features of the spectrometer include balanced detection with multiplex sampling, which yielded lower noise in A, and constant wavelength or wavenumber (energy) spectral bandpass modes. We achieve noise amplitudes of ∼7 × 10⁻⁴ and ∼6 × 10^{−6 …}

Dual Activation Of Peroxymonosulfate Using Mnfe2O4/G‑C3N4 And Visible Light For The Efficient Degradation Of Steroid Hormones: Performance, Mechanisms, And Environmental Impacts, Kitipong Poomipuen, Chainarong Sakulthaew, Chanat Chokejaroenrat, Athaphon Angkaew, Kanidrawee Techauay, Thapanee Poompoung, Kanokwan Teingtham, Piyaporn Phansak, Piyangkun Lueangjaroenkit, Daniel D. Snow

Daugherty Water for Food Global Institute: Faculty Publications

Single activation of peroxymonosulfate (PMS) in a homogeneous system is sometimes insufficient for producing reactive oxygen species (ROS) for water treatment applications. In this work, manganese spinel ferrite and graphitic carbon nitride (MnFe₂O₄/g-C₃N₄; MnF) were successfully used as an activator for PMS under visible light irradiation to remove the four-mostdetected- hormone-contaminated water under different environmental conditions. The incorporation of g-C₃N₄ in the nanocomposites led to material enhancements, including increased crystallinity, reduced particle agglomeration, amplified magnetism, improved recyclability, and increased active surface area, thereby facilitating the PMS activation and electron …

Social Vulnerability Of The People Exposed To Wildfires In U.S. West Coast States, Arash Modaresi Rad, John T. Abatzoglou, Erica Fleishman, Miranda H. Mockrin, Volker C. Radeloff, Yavar Pourmohamad, Megan Cattau, J. Michael Johnson, Philip Higuera, Nicholas J. Nauslar, Mojtaba Sadegh

Civil Engineering Faculty Publications and Presentations

Understanding of the vulnerability of populations exposed to wildfires is limited. We used an index from the U.S. Centers for Disease Control and Prevention to assess the social vulnerability of populations exposed to wildfire from 2000–2021 in California, Oregon, and Washington, which accounted for 90% of exposures in the western United States. The number of people exposed to fire from 2000–2010 to 2011–2021 increased substantially, with the largest increase, nearly 250%, for people with high social vulnerability. In Oregon and Washington, a higher percentage of exposed people were highly vulnerable (>40%) than in California (~8%). Increased social vulnerability of …

The Discovery, Characterization, And Engineering Of Autolytic Enzymes As Antimicrobials, Jacob M. Furlon

Dartmouth College Ph.D Dissertations

In an age of rising levels of antibiotic resistance, we are quickly running out of tools to address some of the most virulent and widespread infectious bacteria. One group of enzymes that show significant potential for use as next-generation antibiotics are antimicrobial peptidoglycan hydrolases, often referred to as lysins. These enzymes are responsible for the breakdown of peptidoglycan within the bacterial cell wall, and, when exogenously applied, can result in dramatic destabilization of the cell wall leading to rapid lysis of the bacteria. While phage endolysins have been widely investigated as potential antimicrobials, the therapeutic potential of endogenous autolysins from …

A Probabilistic View Of Protein Stability, Conformational Specificity, And Design, Jacob A. Stern, Tyler J. Free, Kimberlee L. Stern, Spencer Gardiner, Nicholas A. Dalley, Bradley Charles Bundy, Joshua L. Price, David Wingate, Dnnis Della Corte

Faculty Publications

Various approaches have used neural networks as probabilistic models for the design of protein sequences. These "inverse folding" models employ different objective functions, which come with trade-offs that have not been assessed in detail before. This study introduces probabilistic definitions of protein stability and conformational specificity and demonstrates the relationship between these chemical properties and the p(stucture|seq) Boltzmann probability objective. This links the Boltzmann probability objective function to experimentally verifiable outcomes. We propose a novel sequence decoding algorithm, referred to as “BayesDesign”, that leverages Bayes’ Rule to maximize the p(stucture|seq) objective instead of the p(seq|structure) objective common in inverse folding …

Correlative Imaging Of Three-Dimensional Cell Culture On Opaque Bioscaffolds For Tissue Engineering Applications, Mone’T Sawyer, Josh Eixenberger, Olivia Nielson, Jacob Manzi, Cadré Francis, Raquel Montenegro-Brown, Harish Subbaraman, David Estrada

Materials Science and Engineering Faculty Publications and Presentations

Three-dimensional (3D) tissue engineering (TE) is a prospective treatment that can be used to restore or replace damaged musculoskeletal tissues, such as articular cartilage. However, current challenges in TE include identifying materials that are biocompatible and have properties that closely match the mechanical properties and cellular microenvironment of the target tissue. Visualization and analysis of potential 3D porous scaffolds as well as the associated cell growth and proliferation characteristics present additional problems. This is particularly challenging for opaque scaffolds using standard optical imaging techniques. Here, we use graphene foam (GF) as a 3D porous biocompatible substrate, which is scalable, reproducible, …

Design And Development Of Clinical Decision Support System For Breast Cancer Diagnosis Using Artificial Intelligence, Karthiga R

Theses and Dissertations

The prevalence of breast cancer in women worldwide is far higher than that of cancers of the lungs, brain, or liver. Increasing ageing populations and poor lifestyle habits among the general public, primarily in industrialized nations, are significant factors contributing to the rise in cancer-related mortality rates worldwide. Approximately one woman in every three will develop breast cancer. This research proposes several advanced computer methods for analyzing breast cancer images. This work analyses breast cancer in four imaging modalities: mammography, thermography, ultrasonography and histopathology.

Each modality has some limitations in diagnosing tumors in the breast region. Heavy dose in mammogram …

Exploring Water Quality On The Reclaimed Surface Mines Lands In Eastern Kentucky, Whitney Tara Maynard, Buddhi Gyawali, George Antonious

Kentucky Water Resources Annual Symposium

No abstract provided.

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.

Impacts Of Land Use And Groundwater Inputs On Biological Stream Health And Habitat Of Jennings Creek, Bowling Green, Kentucky, Allison Francis, Jason S. Polk

Kentucky Water Resources Annual Symposium

No abstract provided.

The Role Of Beavers In Mediating Short-Term Organic Matter Accretion In Kentucky Acep Wre Easements, Jessica B. Moon, Marissa Miles, Logan Firkins, Karen A. Baumann, Michael B. Flynn

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.

Temperature-Responsive Membrane With Nano-Sized Catalysts For The Treatment Of Contaminated Groundwater, Rollie Mills, Dibakar Bhattacharyya

Kentucky Water Resources Annual Symposium

No abstract provided.

Full Program Proceedings For 2023 Kentucky Water Resources Symposium, Kentucky Water Research Institute

Kentucky Water Resources Annual Symposium

No abstract provided.

Aptamer-Based Proteomics Measuring Preoperative Cerebrospinal Fluid Protein Alterations Associated With Postoperative Delirium, Simon T. Dillon, Sarinnapha M. Vasunilashorn, Hasan H. Otu, Long Ngo, Tamara Fong, Xuesong Gu, Michele Cavallari, Alexandra Touroutoglou, Mouhsin Shafi, Sharon K. Inouye, Zhongcong Xie, Edward R. Marcantonio, Towia A. Libermann

Department of Electrical and Computer Engineering: Faculty Publications

Delirium is a common postoperative complication among older patients with many adverse outcomes. Due to a lack of validated biomarkers, prediction and monitoring of delirium by biological testing is not currently feasible. Circulating proteins in cerebrospinal fluid (CSF) may reflect biological processes causing delirium. Our goal was to discover and investigate candidate protein biomarkers in preoperative CSF that were associated with the development of postoperative delirium in older surgical patients. We employed a nested case–control study design coupled with high multiplex affinity proteomics analysis to measure 1305 proteins in preoperative CSF. Twenty-four matched delirium cases and non-delirium controls were selected …

Recent Breakthroughs In Using Quantum Dots For Cancer Imaging And Drug Delivery Purposes, Aisha Hamidu, William G. Pitt, Ghaleb A. Husseini

Faculty Publications

Cancer is one of the leading causes of death worldwide. Because each person’s cancer may be unique, diagnosing and treating cancer is challenging. Advances in nanomedicine have made it possible to detect tumors and quickly investigate tumor cells at a cellular level in contrast to prior diagnostic techniques. Quantum dots (QDs) are functional nanoparticles reported to be useful for diagnosis. QDs are semiconducting tiny nanocrystals, 2–10 nm in diameter, with exceptional and useful optoelectronic properties that can be tailored to sensitively report on their environment. This review highlights these exceptional semiconducting QDs and their properties and synthesis methods when used …

Experiences Of African Women In Stem Careers: A Systematic Literature Review., Kaluwa Siwale, Gwamaka Mwalemba, Ulrike Rivett

African Conference on Information Systems and Technology

The discourse on women's underrepresentation in science, technology, engineering, and mathematics (STEM) mainly centres on the global north, leaving a gap in understanding the perspectives of African women in STEM. To address this, a systematic literature review was conducted to explore African women's experiences in STEM careers and education. After applying inclusion and criteria, 18 published articles were analysed. 8 key issues emerge: work environment, education system, work-life balance, gender-based stereotypes, racial bias, sexual harassment, inadequate support/mentorship, and self-imposed limits. These themes intertwine, with some aspects influencing others. Grasping the complexities and interactions of these factors provides insights into challenges …