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Full-Text Articles in Physical Sciences and Mathematics

Match Accuracy Of Burned Teeth: A Pilot Study Of Allied Dental Professionals, Brenda T. Bradshaw, Marsha A. Voelker, Samantha C. Vest, Sinjini Sikdar Jan 2025

Match Accuracy Of Burned Teeth: A Pilot Study Of Allied Dental Professionals, Brenda T. Bradshaw, Marsha A. Voelker, Samantha C. Vest, Sinjini Sikdar

Dental Hygiene Faculty Publications

Purpose: The purpose of this pilot study was to assess allied dental professionals' match accuracy of burned teeth; a skill required by disaster victim identification (DVI) team members.

Methods: This cross-sectional study used a convenience sample of registered dental hygienists (RDH) (n=15) and dental assistants (DA) (n=15) to assess their match accuracy of burned teeth with simulated antemortem (AM) and postmortem (PM) images. Fifteen human teeth were heated at 400°C for 15 minutes. Prior to and following heat alteration, each tooth was photographed and radiographed. Images were presented to participants in randomized order, and they were instructed to correctly match …


Clinician Perspectives On Virtual Reality Use In Physical Therapy Practice In The United States, Danielle T. Felsberg, Jared T. Mcguirt, Scott E. Ross, Louisa D. Raisbeck, Charlend K. Howard, Christopher K. Rhea Jan 2025

Clinician Perspectives On Virtual Reality Use In Physical Therapy Practice In The United States, Danielle T. Felsberg, Jared T. Mcguirt, Scott E. Ross, Louisa D. Raisbeck, Charlend K. Howard, Christopher K. Rhea

Rehabilitation Sciences Faculty Publications

The primary goal of physical rehabilitation is to assess movement impairments and restore function to improve overall quality of life. Virtual reality (VR) may provide the optimal environment to promote these goals due to its motivating and modifiable nature which can be difficult to accomplish through traditional real-world therapeutic methods. Current research of VR for rehabilitation has demonstrated that VR interventions can produce clinically meaningful change in motor outcomes. Despite this, adoption and usage of VR by physical therapy professionals is unclear due to the limited research in this area. Thus, the purpose of this study was to identify the …


Skinrisk Ai, Spencer Simms Jan 2025

Skinrisk Ai, Spencer Simms

Williams Honors College, Honors Research Projects

SkinRisk AI is an exploration of the opportunities for implementing machine learning (ML) and artificial intelligence (AI) in the medical technology field, specifically in the early detection of skin cancer. This project presents the design, development, and evaluation of a mobile application that allows users to capture images of skin lesions and receive a machine learning assisted risk assessment. The system combines a convolutional neural network (CNN) for image analysis with an intuitive mobile app built using Flutter, FastAPI, and Supabase to deliver real time screening.

Motivated by the rising skin cancer rates and importance of early detection, SkinRisk AI …


Comparative Efficacy Of Hallucinogens In Treating Mood Disorders Through A Meta-Analysis Of Symptom Reduction, Dosage, And Duration, John Marco D.F. Muniz Jan 2025

Comparative Efficacy Of Hallucinogens In Treating Mood Disorders Through A Meta-Analysis Of Symptom Reduction, Dosage, And Duration, John Marco D.F. Muniz

Honors Undergraduate Theses

Background: Hallucinogens including psilocybin, lysergic acid diethylamide (LSD), ketamine, N,N-dimethyltryptamine (DMT) (as ayahuasca), have re-emerged as potential rapid-acting treatments for mood disorders. We conducted a meta-analysis of placebo-controlled trials evaluating their efficacy in depression and anxiety disorders. Methods: A systematic review identified 12 trials (Total ≈ 670) meeting inclusion criteria (randomized, placebo-controlled). Data on Cohen’s d and Hedges’ g effect sizes for depression- and anxiety-related outcomes were extracted. We computed pooled effect sizes (weighted by sample size and inverse variance), performed subgroup analyses by drug, diagnosis, follow-up duration, and outcome measure type, and assessed heterogeneity (I2, Q …


“Regression To The Mean”: The Confluence Of Eugenics And Statistics In The 19th And 20th Centuries, Emrys G. King Jan 2025

“Regression To The Mean”: The Confluence Of Eugenics And Statistics In The 19th And 20th Centuries, Emrys G. King

Pomona Senior Theses

The work of this thesis is twofold — first, qualitatively characterizing the confluence between the British eugenics and statistics movements in the late 19th and early 20th centuries, and second, quantitatively analyzing the effect of this foundation on pedagogical materials in the growing field of statistics between 1880 and 1970. Towards the first goal, the history of the method of least squares, state statistics, and positive and negative eugenics are outlined, followed by a close reading of the foundational texts authored by Francis Galton and Karl Pearson that introduced linear regression. Towards the latter goal, English-language statistics textbooks published between …


Biomechanics Of The Atherosclerotic Lipidome: (Un)Expected Statin Interactions And Membrane Remodelling, Ethan M. Fong Jan 2025

Biomechanics Of The Atherosclerotic Lipidome: (Un)Expected Statin Interactions And Membrane Remodelling, Ethan M. Fong

Pomona Senior Theses

Statins interact with lipid membranes in ways that shape their pharmacokinetics, off-target effects, and pleiotropic actions, yet these interactions' mechanical and biophysical consequences remain poorly understood. This thesis employs a combination of surface plasmon resonance (SPR), quartz crystal microbalance with dissipation monitoring (QCM-D), and rheological modelling to characterize how representative statins intercalate within biomimetic supported lipid bilayers (SLBs) of healthy and diseased composition. SPR reveals that lipophilic statins exhibit higher apparent affinities and slower dissociation kinetics, especially in cholesterol- and anionic lipid-rich membranes. QCM-D analyses demonstrate that statins alter membrane mass, dissipation, and interfacial stiffness in a statin- and membrane-dependent …


Application Of Machine Learning And Large Language Models In Healthcare For Data Prediction And Summarization, Chiazam Chisom Izuchukwu Jan 2025

Application Of Machine Learning And Large Language Models In Healthcare For Data Prediction And Summarization, Chiazam Chisom Izuchukwu

College of Graduate Studies: Theses & Dissertations

This study aims to examine the use of machine learning (ML) and large language models (LLMs) in healthcare to enhance disease prediction, clinical decision-making, and information management. Five supervised ML models—Logistic Regression (LR), Support Vector Machine (SVM), Random Forest (RF), Decision Trees (DT), and Naïve Bayes (NB)—on three different computing platforms—Google Colab, Databricks, and Snowflake—were employed for disease classification. Data preprocessing included treating missing values, encoding categorical variables utilizing one-hot-encoding, feature scaling when needed, and tackling class imbalance with Synthetic Minority Over-sampling Technique (SMOTE) before an 80-20 train-test separation. Models were created with Scikit-learn (Google Collab), Spark MLlib (Databricks), and …


Establishing A Conventional Linac-Based Electron Flash Beam, Justin Defrancisco Jan 2025

Establishing A Conventional Linac-Based Electron Flash Beam, Justin Defrancisco

Theses and Dissertations

Problems: A rediscovered radiotherapy technique, FLASH, involves increasing the dose rate to >40 Gy/s. For a given dose, FLASH is shown to decrease the normal tissue complication probability without affecting the tumor control probability. More preclinical studies are necessary to confirm and enable these desirable properties on humans. Current preclinical investigations have diverse constraints, requiring FLASH apparatuses with flexible parameters and accurate control. However, there are limited FLASH platforms available, the existing ones are costly. Our institution is not in possession of any such infrastructure. Even if available, dosimetry and beam control in FLASH are extremely lacking. There is …


A Fast Framework For Generating Radioactive Mixture Spectra And Its Application To Remote High-Performance Mixture Identification, Chiman Kwan, Bulent Ayhan, Adam Stavola, Kazi Aminul Islam, Hongfang Zhang, Jiang Li Jan 2025

A Fast Framework For Generating Radioactive Mixture Spectra And Its Application To Remote High-Performance Mixture Identification, Chiman Kwan, Bulent Ayhan, Adam Stavola, Kazi Aminul Islam, Hongfang Zhang, Jiang Li

Electrical & Computer Engineering Faculty Publications

Remote detection of radioactive materials in mixtures using handheld or portal detectors remains a challenge because of factors such as low concentration, environmental interference, sensor noise, and other complications. This work introduces a fast framework for generating realistic mixture spectra. Moreover, we present mixture isotope identification using data generated by the fast framework. Researchers have examined a range of conventional and recent algorithms within the fields of machine learning and deep learning. An application to uranium enrichment-level prediction has been included. Extensive simulation experiments validated the efficacy of the proposed framework.


High-Fidelity Soh Prediction In Lithium-Ion Batteries Using Hybrid Ml Networks, Shafiyee Islam, Gon Namkoong Jan 2025

High-Fidelity Soh Prediction In Lithium-Ion Batteries Using Hybrid Ml Networks, Shafiyee Islam, Gon Namkoong

Electrical & Computer Engineering Faculty Publications

Accurate and efficient prediction of lithium-ion battery state of health (SOH) is critical for ensuring reliability in electric vehicles, grid storage, and aerospace systems. Traditional SOH estimation methods often struggle with nonlinear degradation behaviors and lack sensitivity to subtle electrochemical signals, limiting their real-world deployment. To address these challenges, this study examines hybrid deep learning models that integrate differential capacity (dQ/dV) analysis to enhance predictive accuracy. Four hybrid architectures - hybrid CNN-LSTM multihead, CNN extractor for LSTM, DNN-LSTM, and DNN Bi-LSTM - were developed and evaluated using the NASA randomized battery usage dataset, offering a realistic benchmark under diverse operational …


Interaction Of Cardiac Leiomodin With The Native Cardiac Thin Filament, Madison Little, Cristina M. Risi, Tania M. Larrinaga, Mason D. Summers, Tyler Nguyen, Garry E. Smith Jr., Jennifer Atherton, Carol C. Gregorio, Alla S. Kostyukova, Vitold E. Galkin Jan 2025

Interaction Of Cardiac Leiomodin With The Native Cardiac Thin Filament, Madison Little, Cristina M. Risi, Tania M. Larrinaga, Mason D. Summers, Tyler Nguyen, Garry E. Smith Jr., Jennifer Atherton, Carol C. Gregorio, Alla S. Kostyukova, Vitold E. Galkin

Department of Biomedical and Translational Sciences Faculty Publications

Every heartbeat depends on cyclical contraction-relaxation produced by the interactions between myosin-containing thick and actin-based thin filaments (TFs) arranged into a crystalline-like lattice in the cardiac sarcomere. Therefore, the maintenance of thin filament length is crucial for myocardium function. The thin filament is comprised of an actin backbone, the regulatory troponin complex and tropomyosin that controls interactions between thick and thin filaments. Thin filament length is controlled by the tropomodulin family of proteins; tropomodulin caps pointed ends of thin filaments, and leiomodin (Lmod) promotes elongation of thin filaments by a “leaky-cap” mechanism. The broader distribution of Lmod on the thin …


Predicting Mental Health Disparities Using Machine Learning For African Americans In Southeastern Virginia, Ismail El Moudden, Michael C. Bittner, Matvey V. Karpov, Isaac O. Osunmakinde, Akosua Acheamponmaa, Breshell J. Nevels, Mamadou T. Mbaye, Tonya L. Fields, Karthiga Jordan, Messaoud Bahoura Jan 2025

Predicting Mental Health Disparities Using Machine Learning For African Americans In Southeastern Virginia, Ismail El Moudden, Michael C. Bittner, Matvey V. Karpov, Isaac O. Osunmakinde, Akosua Acheamponmaa, Breshell J. Nevels, Mamadou T. Mbaye, Tonya L. Fields, Karthiga Jordan, Messaoud Bahoura

Department of Obstetrics & Gynecology Faculty Publications

This study examined mental health disparities among African Americans using AI and machine learning for outcome prediction. Analyzing data from African American adults (18–85) in Southeastern Virginia (2016–2020), we found Mood Affective Disorders were most prevalent (41.66%), followed by Schizophrenia Spectrum and Other Psychotic Disorders. Females predominantly experienced mood disorders, with patient ages typically ranging from late thirties to mid-forties. Medicare coverage was notably high among schizophrenia patients, while emergency admissions and comorbidities significantly impacted total healthcare charges. Machine learning models, including gradient boosting, random forest, neural networks, logistic regression, and Naive Bayes, were validated through 100 repeated 5-fold cross-validations. …


Symbol-Temporal Consistency Self-Supervised Learning For Robust Time Series Classification, Kevin Garcia, Cassandra Garza, Brooklyn Berry, Yifeng Gao Jan 2025

Symbol-Temporal Consistency Self-Supervised Learning For Robust Time Series Classification, Kevin Garcia, Cassandra Garza, Brooklyn Berry, Yifeng Gao

Computer Science Faculty Publications

The surge in the significance of time series in digital health domains necessitates advanced methodologies for extracting meaningful patterns and representations. Self-supervised contrastive learning has emerged as a promising approach for learning directly from raw data. However, time series data in digital health is known to be highly noisy, inherently involves concept drifting, and poses a challenge for training a generalizable deep learning model. In this paper, we specifically focus on data distribution shift caused by different human behaviors and propose a self-supervised learning framework that is aware of the bag-of-symbol representation. The bag-of-symbol representation is known for its insensitivity …


An Analytical Model Of Motion Artifacts In A Measured Arterial Pulse Signal—Part I: Accelerometers And Ppg Sensors, Md Mahfuzur Rahman, Subodh Toraskar, Mamun Hasan, Zhili Hao Jan 2025

An Analytical Model Of Motion Artifacts In A Measured Arterial Pulse Signal—Part I: Accelerometers And Ppg Sensors, Md Mahfuzur Rahman, Subodh Toraskar, Mamun Hasan, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

This paper, the first of two parts, presents an analytical model of motion artifacts (MAs) in measured pulse signals by accelerometers and photoplethysmography (PPG) sensors. As the transmission path from the true pulse signal in an artery to the sensor output (measured pulse signal), the tissue-contact-sensor (TCS) stack is modeled as a 1DOF (degree-of-freedom) system. MAs cause baseline drift of the mass and simultaneously time-varying system parameters (TVSPs) of the TCS stack. With arterial wall displacement and pulsatile pressure serving separately as the true pulse signal, an analytical model is developed to mathematically relate baseline drift and TVSP to a …


An Analytical Model Of Motion Artifacts In A Measured Arterial Pulse Signal—Part Ii: Tactile Sensors, Md Mahfuzur Rahman, Subodh Toraskar, Mamun Hasan, Zhili Hao Jan 2025

An Analytical Model Of Motion Artifacts In A Measured Arterial Pulse Signal—Part Ii: Tactile Sensors, Md Mahfuzur Rahman, Subodh Toraskar, Mamun Hasan, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

This paper, the second of two parts, presents an analytical model of motion artifacts (MA) in measured pulse signals by a tactile sensor, which contains a deformable microstructure sitting on a substrate. While the tissue-contact-sensor (TCS) stack and the sensor are both treated as a 1DOF (degree-of-freedom) system, tissue–sensor contact joins their mass together to form a 1DOF system with springs and dampers on both sides. MA on the sensor substrate causes baseline drift and time-varying system parameters (TVSP) of the TCS stack simultaneously. An analytical model is developed to mathematically relate baseline drift and TVSP to a measured pulse …


Motion Artifacts Removal From Measured Arterial Pulse Signals At Rest: A Generalized Sdof-Model-Based Time-Frequency Method, Zhili Hao Jan 2025

Motion Artifacts Removal From Measured Arterial Pulse Signals At Rest: A Generalized Sdof-Model-Based Time-Frequency Method, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

Motion artifacts (MA) are a key factor affecting the accuracy of a measured arterial pulse signal at rest. This paper presents a generalized time–frequency method for MA removal that is built upon a single-degree-of-freedom (SDOF) model of MA, where MA is manifested as time-varying system parameters (TVSPs) of the SDOF system for the tissue–contact-sensor (TCS) stack between an artery and a sensor. This model distinguishes the effects of MA and respiration on the instant parameters of harmonics in a measured pulse signal. Accordingly, a generalized SDOF-model-based time–frequency (SDOF-TF) method is developed to obtain the instant parameters of each harmonic in …


Insights Into Factors Influencing Radical Coupling Chemistry Of Monolignols During Lignification And Induced Changes In Plant Secondary Metabolism, Rachel Poornima Sutherland Jan 2025

Insights Into Factors Influencing Radical Coupling Chemistry Of Monolignols During Lignification And Induced Changes In Plant Secondary Metabolism, Rachel Poornima Sutherland

Theses and Dissertations--Chemistry

Lignin is a complex aromatic biopolymer and an important constituent in plant cell walls. The process of lignin biosynthesis, known as lignification, is poorly understood and challenging to study but has important implications in a variety of fields including sustainable energy, bioengineering, and materials science and is therefore of interest to pursue. In the final stage of lignification, H-, G-, and S-monolignols are oxidized by laccase and peroxidase enzymes to generate radical species that couple to form dimers and further oligomeric species to ultimately produce the lignin polymer. Biomimetic lignin model systems utilize in vitro oxidative coupling reactions as an …


Redox Control In A Fused Electron Transfer Flavoprotein From A Thermophilic Archaeon And Expanded Significance Of A Hydrogen Bond From A Conserved Histidine Residue That Contributes To Flavin Redox Tuning And Activation For Covalent Modification, Debarati Das Jan 2025

Redox Control In A Fused Electron Transfer Flavoprotein From A Thermophilic Archaeon And Expanded Significance Of A Hydrogen Bond From A Conserved Histidine Residue That Contributes To Flavin Redox Tuning And Activation For Covalent Modification, Debarati Das

Theses and Dissertations--Chemistry

In absence of O2 as terminal electron acceptors in anaerobic bacteria and archaea, carbohydrate metabolism is 15 times less efficient compared to aerobic energy metabolism resulting in energy deficit conditions. Despite their meager resources these anaerobes were able to generate H2 and a chemiosmotic potential able to drive energy demanding reactions such as CO2 or N2 fixation. These observations raised concerns as production of high energy reductants (H2) from mediocre fuels (NADH) defied the laws of thermodynamics.

In 2008, a known mechanism “electron bifurcation” but with flavins as redox mediators instead of quinones was …


Monte Carlo Modeling Of Spin Polarized Photoemission From Gaas At Low Temperatures And Positive Electron Affinity Surfaces, John Rison Callahan Jan 2025

Monte Carlo Modeling Of Spin Polarized Photoemission From Gaas At Low Temperatures And Positive Electron Affinity Surfaces, John Rison Callahan

Graduate Research Theses & Dissertations

Research and development of new photocathode materials are essential to the continuing success and productivity of accelerator technology. High-quality photocathodes characterized by high quantum efficiencies, long lifetimes, low mean transverse energies, and robustness to vacuum environments and operation loads are becoming increasingly essential to the successful operation of the next generation of high brightness accelerator applications. For nuclear and high-energy physics experiments and other applications that rely on spin-polarized electron beams, photocathodes must also demonstrate high electron spin polarizations. The development of state of-the-art spin-polarized photocathodes will require both development of methods to improve the quality of already existing cathode …


Circadian Variation In Mgmt Promoter Methylation And Expression Predicts Sensitivity To Temozolomide In Glioblastoma, Maria F. Gonzalez-Aponte, Yitong Huang, William A. Leidig, Tatiana Simon, Omar H. Butt, Marc D. Ruben, Albert H. Kim, Joshua B. Rubin, Erik D. Herzog, Olivia J. Walch Jan 2025

Circadian Variation In Mgmt Promoter Methylation And Expression Predicts Sensitivity To Temozolomide In Glioblastoma, Maria F. Gonzalez-Aponte, Yitong Huang, William A. Leidig, Tatiana Simon, Omar H. Butt, Marc D. Ruben, Albert H. Kim, Joshua B. Rubin, Erik D. Herzog, Olivia J. Walch

Mathematics Sciences: Faculty Publications

Purpose Recent studies show that glioblastoma (GBM) is more sensitive to temozolomide (TMZ) in the morning. In cells, inhibiting O6-Methylguanine-DNA-Methyltransferase (MGMT) abolished time-dependent TMZ efficacy, suggesting that circadian regulation of this DNA repair enzyme underlies daily TMZ sensitivity. Here, we tested the hypotheses that MGMT promoter methylation and protein abundance vary with time-of-day in GBM, resulting in daily rhythms in TMZ efficacy.

Methods We assessed daily rhythms in MGMT promoter methylation in GBM in vitro and retrospectively analyzed MGMT methylation status in human GBM biopsies collected at different times of day. Next, we measured MGMT and BMAL1 protein …


Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger Jan 2025

Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger

Chemistry & Biochemistry Faculty Publications

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The …


Application Of Telc Model To Better Elucidate Neural Stimulation By Touch, James Weifu Lee Jan 2025

Application Of Telc Model To Better Elucidate Neural Stimulation By Touch, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Aim: This study is to better understand how the transient ion transport activity of touch receptors could change the graded potential to stimulate an action potential firing.

Methods: The latest transmembrane-electrostatically localized protons/cations charges (TELC) theory is employed for numerical analysis to calculate the neural touch signal transduction responding time required to fire an action potential spike.

Results: A neural action potential spike was constructed successfully using newly developed time-dependent TELC-based neural transmembrane potential integral equations (Equations 5, 6, and 7). The results explicated that the TELC curve has an inverse relationship with neural transmembrane potential since its curve appears …


Challenges Associated With Pfas Detection Method In Africa, Abdullahi Tunde Aborode, Ridwan Olamilekan Adesola, Ibrahim Idris, Waheed Sakariyau Adio, Segun Olapade, Gladys Oluwafisayo, Israel Ayobami Onifade, Sodiq Fakorede, Taiwo Bakare-Abidola, Jelil Olaoye, Adedeji Daniel Ogunyemi, Oluwaseun Adeolu Ogundijo, Olamilekan Gabriel Banwo, Adetolase Azizat Bakre, Peter Oladoye, Grace Adegoye, Noimat Abeni Jinadu Jan 2025

Challenges Associated With Pfas Detection Method In Africa, Abdullahi Tunde Aborode, Ridwan Olamilekan Adesola, Ibrahim Idris, Waheed Sakariyau Adio, Segun Olapade, Gladys Oluwafisayo, Israel Ayobami Onifade, Sodiq Fakorede, Taiwo Bakare-Abidola, Jelil Olaoye, Adedeji Daniel Ogunyemi, Oluwaseun Adeolu Ogundijo, Olamilekan Gabriel Banwo, Adetolase Azizat Bakre, Peter Oladoye, Grace Adegoye, Noimat Abeni Jinadu

Chemistry & Biochemistry Faculty Publications

Per- and polyfluoroalkyl substances (PFAS) are a group of man-made chemicals that are widely present in many industries. Monitoring and analyzing PFAS in Africa is challenging due to the limited availability of mass spectrometry (MS), which is an essential technique for detecting PFAS. This review assesses the scope and impact of the shortage of mass spectrometry instruments in Africa, emphasizing the resulting limitations in monitoring environmental and public health threats. The review analyzes the existing PFAS monitoring, the accessibility of MS instruments, and the technical capabilities within the continent. This study suggests that fewer African countries have sufficient MS instruments, …


Determination Of Structural Factors Contributing To Protection Of Zinc Fingers In Estrogen Receptor Α Through Molecular Dynamic Simulations, Patricia B. Lutz, Wesley R. Coombs, Craig A. Bayse Jan 2025

Determination Of Structural Factors Contributing To Protection Of Zinc Fingers In Estrogen Receptor Α Through Molecular Dynamic Simulations, Patricia B. Lutz, Wesley R. Coombs, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

The ERα transcription factor that induces tumor growth is a potential target for breast cancer treatment. Each monomer of the ERα DNA-binding domain (ERαDBD) homodimer has two conserved (Cys)4-type zinc fingers, ZF1 (N-terminal) and ZF2 (C-terminal). Electrophilic agents release Zn2+ by oxidizing the coordinating Cys of the more labile ZF2 to inhibit dimerization and DNA binding. Microsecond-length molecular dynamics (MD) simulations show that greater flexibility of ZF2 in the ERαDBD monomer leaves its Cys more solvent accessible and less shielded from electrophilic attack by sulfur-centered hydrogen bonds than ZF1 which is buried in the protein. In the …


The Importance Of Atomic Charges For Predicting Site-Selective Ir-, Ru-, And Rh-Catalyzed C-H Borylations, Shannon M. Stephens, Kyle M. Lambert Jan 2025

The Importance Of Atomic Charges For Predicting Site-Selective Ir-, Ru-, And Rh-Catalyzed C-H Borylations, Shannon M. Stephens, Kyle M. Lambert

Chemistry & Biochemistry Faculty Publications

A supervised machine learning model has been developed that allows for the prediction of site selectivity in late-stage C-H borylations. Model development was accomplished using literature data for the site-selective (≥95%) C-H borylation of 189 unique arene, heteroarene, and aliphatic substrates that feature a total of 971 possible sp² or sp³ C-H borylation sites. The reported experimental data was supplemented with additional chemoinformatic descriptors, computed atomic charges at the C-H borylation sites, and data from parameterization of catalytically active tris-boryl complexes resulting from the combination of seven different Ir-, Ru-, and Rh-based precatalysts with eight different ligands. Of the over …


Deciphering The Chemistry Of Condensed Aromatic "Black" Carbon And Nitrogen In Amazonian Anthrosols, João Vitor Dos Santos, Aleksandar I. Goranov, Laís G. Fregolente, Marcia C. Bisinoti, Zhenhuan Sun, Klaus Schmidt-Rohr, Patrick G. Hatcher Jan 2025

Deciphering The Chemistry Of Condensed Aromatic "Black" Carbon And Nitrogen In Amazonian Anthrosols, João Vitor Dos Santos, Aleksandar I. Goranov, Laís G. Fregolente, Marcia C. Bisinoti, Zhenhuan Sun, Klaus Schmidt-Rohr, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Amazonian anthrosols are renowned for their high fertility and dark color, properties primarily attributed to the abundance of condensed aromatic carbon (ConAC) in the soil organic matter. ConAC, commonly referred to as black carbon, play a key role in the stability and nutrient retention of these soils. However, the processes governing the formation of ConAC and its transformation into oxygenated derivatives remain poorly understood. In this study, we used multiple analytical platforms to investigate the chemistry of ConAC-rich humic acids (HA) extracted from Terra Mulata de Indio, a type of Amazonian anthrosol. The results reveal that ConAC are predominantly …


The Importance Of Solution Studies For The Structural Characterization Of The Enterovirus 5' Cloverleaf, Morgan G. Daniels, Meagan E. Werner, Xiaobing Zuo, Steven M. Pascal Jan 2025

The Importance Of Solution Studies For The Structural Characterization Of The Enterovirus 5' Cloverleaf, Morgan G. Daniels, Meagan E. Werner, Xiaobing Zuo, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5' cloverleaf (5'CL). Here, we present a biophysical analysis of the 5'CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5'CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed …


Corporate ‘Capture Strategies’ Impacting Human And Ecosystem Health, Alex T. Ford, Marlene Ågerstrand, Michael G. Bertram, Miriam L. Diamond, Rainer Lohmann, Andreas Schäffer, Martin Scheringer, Gabriel Sigmund, Anna Soehl, Maria Clara V.M. Starling, Noriyuki Suzuki, Marta Venier, Penny Vlahos Jan 2025

Corporate ‘Capture Strategies’ Impacting Human And Ecosystem Health, Alex T. Ford, Marlene Ågerstrand, Michael G. Bertram, Miriam L. Diamond, Rainer Lohmann, Andreas Schäffer, Martin Scheringer, Gabriel Sigmund, Anna Soehl, Maria Clara V.M. Starling, Noriyuki Suzuki, Marta Venier, Penny Vlahos

Graduate School of Oceanography Faculty Publications

The concept of regulatory capture has been extensively studied in academic literature, primarily within the social sciences. This phenomenon has been increasingly discussed in the environmental sciences as the impacts of regulatory capture on human and ecosystem health have become increasingly apparent. Regulatory capture is just one tactic employed by vested interests in the strategy of delaying, weakening, or abolishing policies designed to protect the public interest. Here, we define capture strategies as ‘the act of influencing individuals, organizations, or governments to prioritize corporate interests over those of human and ecosystem health’. Similar to the evolution of terms like whitewashing …


Is It Getting Better? An Evaluation Of Two Successive Generations Of Chatgpt In Answering Specialized Vascular Surgery Questions, Dongjin Suh, Quang Le, Leana Dogbe, Kedar Lavingia, Michael Amendola Jan 2025

Is It Getting Better? An Evaluation Of Two Successive Generations Of Chatgpt In Answering Specialized Vascular Surgery Questions, Dongjin Suh, Quang Le, Leana Dogbe, Kedar Lavingia, Michael Amendola

Department Surgery Faculty Publications

Purpose: Large language models (LLMs) can generate clinically relevant text; however, their performance in highly specialized medical domains remains uncertain. This study evaluated ChatGPT-3.5 and ChatGPT-4 (OpenAI) using vascular surgery board–style questions from the Vascular Education and Self-Assessment Program, version 4 (VESAP4) and compared the two public model versions (June and November 2023).


Materials and Methods: All non-image VESAP4 questions (n=384) were presented independently three times to each model version (ChatGPT-3.5 June/November; ChatGPT-4, June/November). Outcomes included accuracy (proportion correct), consistency (same option letter across all three attempts and “consistently correct”), explanation length (word count), and modes of failure classified for …


Calcium Carbonate Microparticles As Acid Responsive Targeted Drug Delivery Carriers For Oral Diseases And Its Anti-Bacterial Activity, Hem Raj Joshi Jan 2025

Calcium Carbonate Microparticles As Acid Responsive Targeted Drug Delivery Carriers For Oral Diseases And Its Anti-Bacterial Activity, Hem Raj Joshi

Dissertations and Theses

Dental diseases are mostly caused by bacterial infections in the teeth, forming biofilms that release acids and decay the enamel of the teeth. More than half of the world's population were affected by oral diseases, including periodontitis (gum disease), dental caries (cavities), and oral cancer. Chlorhexidine (CHX) is the mostly used antimicrobial drug for dental diseases, but its overexposure to the healthy teeth causes many side effects, such as tooth staining, taste alteration, and many more. Taking advantage of the acidic environment of infected teeth, we designed a pH responsive targeted drug delivery system using calcium carbonate microparticles (CCMPs) as …