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Effects Of Nitro-Substitution On The Spectroscopic And Self-Assembly Properties Of Bodipy Dyes, Caroline Gwaro, Caroline Ndung’U, Petia Bobadova-Parvanova, Dylan Goliber, Quynh Do, Ashley R. Walker, Evan Murders, Daniel Lamaster, Frank R. Fronczek, Jayne Garno, Maria Da Graça H. Vicente Apr 2025

Effects Of Nitro-Substitution On The Spectroscopic And Self-Assembly Properties Of Bodipy Dyes, Caroline Gwaro, Caroline Ndung’U, Petia Bobadova-Parvanova, Dylan Goliber, Quynh Do, Ashley R. Walker, Evan Murders, Daniel Lamaster, Frank R. Fronczek, Jayne Garno, Maria Da Graça H. Vicente

Faculty Publications

A series of boron dipyrromethene (BODIPY) dyes were nitrated in high yields using nitronium tetrafluoroborate at positions 2, 3, and 2,6 of the BODIPY core. This method allows for the regioselective nitration of the pyrrolic positions under milder conditions than previously reported methods. The photophysical properties and electronic transitions of these BODIPYs were investigated by using UV-vis spectroscopy, fluorescence spectroscopy, and density-functional theory (DFT) calculations. The introduction of one nitro group dramatically increases the dipole moment of the molecule, induces marked blue shifts in the absorption and emission bands, decreases the molar absorptivity, and increases the Stokes shifts of the …


Feature Typology And L2 Proficiency Matter: L3 Acquisition Of Portuguese, Mila Tasseva-Kurktchieva, Danielle Fahey Apr 2025

Feature Typology And L2 Proficiency Matter: L3 Acquisition Of Portuguese, Mila Tasseva-Kurktchieva, Danielle Fahey

Faculty Publications

To determine the source of transfer in third language acquisition (L3A), we tested the effects of grammatical feature typology and L2 Spanish proficiency on the comprehension and production of grammatical [gender] and [number] in the early stages of L3A of Portuguese. We distinguish between the two features based on their participation in the lexical-conceptual structure of the lemma and its interaction with the morpho-syntactic derivation. L1 English speakers were tested on their knowledge of the features in both their L2 and their L3 through a grammaticality judgment task and an elicited production task. Results show that L3 learners transfer only …


Examining Physiological Responses To Misophonic Triggers, Christian O'Reilly, Xuan Yang, Sewon Oh, Doug Wedell, Svetlana Shinkareva Apr 2025

Examining Physiological Responses To Misophonic Triggers, Christian O'Reilly, Xuan Yang, Sewon Oh, Doug Wedell, Svetlana Shinkareva

Faculty Publications

We collected and analyzed an array of biosignals (face electromyogram, skin electrodermal activity, peripheral temperature, and electrocardiogram) in 60 participants with and without misophonia, a condition characterized by decreased tolerance to innocuous sounds. Our goal was to objectively characterize the physiological response to misophonia triggering sounds. We found that misophonic responses can be objectively identified in some cases through atypical physiological reactions to triggering stimuli, though not all participants exhibited this response. Our analyses suggest a large interindividual variability in response to misophonic triggers and highlights the need for methodological adjustments in future experiments to increase the detectability of misophonic …


A Reliable And Efficient Detection Pipeline For Rodent Ultrasonic Vocalizations, Sabah Shahnoor Anis, Devin Mark Kellis, Kris Ford Kaigler, Marlene A. Wilson, Christian O'Reilly Apr 2025

A Reliable And Efficient Detection Pipeline For Rodent Ultrasonic Vocalizations, Sabah Shahnoor Anis, Devin Mark Kellis, Kris Ford Kaigler, Marlene A. Wilson, Christian O'Reilly

Faculty Publications

Analyzing ultrasonic vocalizations (USVs) is crucial for understanding rodents' affective states and social behaviors, but the manual analysis is time-consuming and prone to errors. Automated USV detection systems have been developed to address these challenges. Yet, these systems often rely on machine learning and fail to generalize effectively to new datasets. To tackle these shortcomings, we introduce ContourUSV, an efficient automated system for detecting USVs from audio recordings. Our pipeline includes spectrogram generation, cleaning, pre-processing, contour detection, post-processing, and evaluation against manual annotations. To ensure robustness and reliability, we compared ContourUSV with three state-of-the-art systems using an existing open-access USV …


Deep Jansen-Rit Parameter Inference For Model-Driven Analysis Of Brain Activity, Deepa Tilwani, Christian O'Reilly Apr 2025

Deep Jansen-Rit Parameter Inference For Model-Driven Analysis Of Brain Activity, Deepa Tilwani, Christian O'Reilly

Faculty Publications

Accurately modeling effective connectivity (EC) is critical for understanding how the brain processes and integrates sensory information. Yet, it remains a formidable challenge due to complex neural dynamics and noisy measurements such as those obtained from the electroencephalogram (EEG). Model-driven EC infers local (within a brain region) and global (between brain regions) EC parameters by fitting a generative model of neural activity onto experimental data. This approach offers a promising route for various applications, including investigating neurodevel- opmental disorders. However, current approaches fail to scale to whole-brain analyses and are highly noise-sensitive. In this work, we employ three deep-learning architectures—a …


Re-Framing The Master Narratives Of Learning Dis/Abilities Through An Emotion And Intersectional Lens, David I. Hernández-Saca Apr 2025

Re-Framing The Master Narratives Of Learning Dis/Abilities Through An Emotion And Intersectional Lens, David I. Hernández-Saca

Faculty Publications

In this conceptual framework paper, I critically chronicle the historiography, policy, and scientific literatures of learning disabilities (ld) and provide a conceptual framework for reframing these as master narratives. I defined master narratives as the pre-existent sociocultural forms of interpretation. I interrogated the a) cultural-historical; b) the federal definition of ld within idea, c) the educational-professional academic and focused on, the d) social and emotional literature of ld. The master narratives from these literatures included: a) ld as a boy who struggles with reading, ld as a symbolic complex, and the legacy of the term "feebleminded", d) assumptions about learning, …


Actor–Partner Model Of Parenting And Co-Parenting Practices And Youth Resilience During The Covid-19 Pandemic, Olivia Aspiras, Jaimie O'Gara, Justine Radunzel Apr 2025

Actor–Partner Model Of Parenting And Co-Parenting Practices And Youth Resilience During The Covid-19 Pandemic, Olivia Aspiras, Jaimie O'Gara, Justine Radunzel

Faculty Publications

The present research examined parents' perspectives of co-parenting and supportive and hostile parenting as predictors of youth resilience during the COVID-19 pandemic. Participants were 47 mother/father dyads who had at least one K-12 child (Mage = 11.40, SD = 3.92). Mothers and fathers each completed an online survey that measured parenting, co-parenting, and youth resilience during the pandemic. Data were analyzed using the actor–partner interdependence model. Results revealed a positive relationship between mother supportiveness and perceived youth resilience; in contrast, increased father supportiveness was associated with lower perceived youth resilience. For both mothers and fathers, increases in their own hostility …


A Skill Assessment Framework For The Fisheries And Marine Ecosystem Model Intercomparison Project, Nina Rynne, Camilla Novaglio, Julia Blanchard, Daniele Bianchi, Villy Christensen, Marta Coll, Jerome Guiet, Jeroen Steenbeek, Andrea Bryndum-Buchholz, Tyler D. Eddy, Cheryl Harrison, Olivier Maury, Kelly Ortega-Cisneros, Colleen M. Petrik, Derek P. Tittensor, Ryan F. Heneghan Apr 2025

A Skill Assessment Framework For The Fisheries And Marine Ecosystem Model Intercomparison Project, Nina Rynne, Camilla Novaglio, Julia Blanchard, Daniele Bianchi, Villy Christensen, Marta Coll, Jerome Guiet, Jeroen Steenbeek, Andrea Bryndum-Buchholz, Tyler D. Eddy, Cheryl Harrison, Olivier Maury, Kelly Ortega-Cisneros, Colleen M. Petrik, Derek P. Tittensor, Ryan F. Heneghan

Faculty Publications

Understanding climate change impacts on global marine ecosystems and fisheries requires complex marine ecosystem models, forced by global climate projections, that can robustly detect and project changes. The Fisheries and Marine Ecosystems Model Intercomparison Project (FishMIP) uses an ensemble modeling approach to fill this crucial gap. Yet FishMIP does not have a standardised skill assessment framework to quantify the ability of member models to reproduce past observations and to guide model improvement. In this study, we apply a comprehensive model skill assessment framework to a subset of global FishMIP models that produce historical fisheries catches. We consider a suite of …


Monitoring Molecular Interactions With Cell Membranes Using Time-Dependent Second Harmonic Generation Microscopy, Prakash Hamal, Sushant P. Sahu, Peter P. Piers, Huy Nguyen, Shashank S. Kamble, Robin L. Mccarley, Manas R. Gartia, Louis H. Haber Apr 2025

Monitoring Molecular Interactions With Cell Membranes Using Time-Dependent Second Harmonic Generation Microscopy, Prakash Hamal, Sushant P. Sahu, Peter P. Piers, Huy Nguyen, Shashank S. Kamble, Robin L. Mccarley, Manas R. Gartia, Louis H. Haber

Faculty Publications

Time-resolved second harmonic generation (SHG) microscopy is used to investigate the physicochemical interactions between positively charged, hydrophobic, drug-like molecules and the plasma membrane of human cells (nonsmall cell lung cancer, H596). In the present study, molecular adsorption and transport of the cationic molecules, malachite green (MG) and malachite green isothiocyanate (MGITC), are studied in real time in living H596 cells and in dead, fixed H596 cells. MGITC is shown to have stronger adsorption and more rapid transport kinetics as compared to MG due to increased dipole-dipole interactions. Additionally, MGITC is found to have faster adsorption and transport kinetics in living …


Endothelial Dysfunction Promotes Age-Related Reorganization Of Collagen Fibers And Alters Aortic Biomechanics In Mice, Liya Du, Jeffrey Rodgers, Nazli Gharraee, Olivia Gary, Tarek Shazly, John F. Eberth, Susan M. Lessner Apr 2025

Endothelial Dysfunction Promotes Age-Related Reorganization Of Collagen Fibers And Alters Aortic Biomechanics In Mice, Liya Du, Jeffrey Rodgers, Nazli Gharraee, Olivia Gary, Tarek Shazly, John F. Eberth, Susan M. Lessner

Faculty Publications

Endothelial dysfunction, defined as a reduction in the bioavailability of nitric oxide (NO), is a risk factor for the occurrence and progression of various vascular diseases. This study investigates the effect of endothelial dysfunction on age-related changes in aortic extracellular matrix (ECM) microstructure and the relationship between microstructural adaptation and the mechanical response. Here, we used groups of NOS3 knockout (KO), NOS3 heterozygotes (Het), and wild-type (WT) B6 mice (controls) to study changes in hemodynamic parameters, collagen fiber organization, and both active and passive aortic mechanics using biaxial pressure myography over a time course from 1.5 to 12 mo. Our …


Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah Williams, Tancia Bradshaw, Alissa R. Armstrong Apr 2025

Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah Williams, Tancia Bradshaw, Alissa R. Armstrong

Faculty Publications

In addition to energy storage, adipose tissue communication to other organs plays a key role in regulating organismal physiology. While the link between adipose tissue dysfunction and pathophysiology, including diabetes, chronic inflammation, and infertility, is clear, the molecular mechanisms that underlie these associations have not been fully described. We use Drosophila melanogaster as a model to better understand how adipose tissue communicates to the ovary. In this study, we utilized D. melanogaster’s robust genetic toolkit to examine the role of five adipokines known to control larval growth during development, CCHamide-1, CCHamide-2, eiger, Growth-blocking peptide 3, and unpaired 2 in regulating …


Endothelial Dysfunction Promotes Age-Related Reorganization Of Collagen Fibers And Alters Aortic Biomechanics In Mice, Liya Du, Jeffrey Rodgers, Nazli Gharraee, Olivia Gary, Tarek Shazly, John F. Eberth, Susan M. Lessner Apr 2025

Endothelial Dysfunction Promotes Age-Related Reorganization Of Collagen Fibers And Alters Aortic Biomechanics In Mice, Liya Du, Jeffrey Rodgers, Nazli Gharraee, Olivia Gary, Tarek Shazly, John F. Eberth, Susan M. Lessner

Faculty Publications

Endothelial dysfunction, defined as a reduction in the bioavailability of nitric oxide (NO), is a risk factor for the occurrence and progression of various vascular diseases. This study investigates the effect of endothelial dysfunction on age-related changes in aortic extracellular matrix (ECM) microstructure and the relationship between microstructural adaptation and the mechanical response. Here, we used groups of NOS3 knockout (KO), NOS3 heterozygotes (Het), and wild-type (WT) B6 mice (controls) to study changes in hemodynamic parameters, collagen fiber organization, and both active and passive aortic mechanics using biaxial pressure myography over a time course from 1.5 to 12 mo. Our …


Kinetic Control And Trapping In The Supramolecular Polymerization Of M-Terphenyl Bis-Urea Macrocycles, Sophya V. Garashchuk, Gamage Isuri P. Wijesekera, Isabella G. Rushton, Vaibhavi A. Samant, Fahidat A. Gbadamosi, Dr. Md Faizul Islam, Sophya V. Garashchuk, Prof. Dr. Linda S. Shimizu Apr 2025

Kinetic Control And Trapping In The Supramolecular Polymerization Of M-Terphenyl Bis-Urea Macrocycles, Sophya V. Garashchuk, Gamage Isuri P. Wijesekera, Isabella G. Rushton, Vaibhavi A. Samant, Fahidat A. Gbadamosi, Dr. Md Faizul Islam, Sophya V. Garashchuk, Prof. Dr. Linda S. Shimizu

Faculty Publications

Herein, we examine pathway complexity in the supramolecular polymerization of a novel m-terphenyl bis-urea macrocycle. Designed to induce kinetically metastable states, the macrocycle‘s concentration-dependent aggregation was studied via 1H NMR and IR spectroscopy in THF and CHCl₃. Temperature-dependent UV-Vis spectroscopy in water/THF revealed a cooperative nucleation-growth mechanism, indicated by a shift in λmax to longer wavelengths upon cooling. Morphological studies using DLS, AFM, and SEM demonstrated fibrous aggregate formation. Thermal hysteresis observed in assembly-disassembly cycles indicated kinetically trapped species, with cooling governed by kinetic control and heating by thermodynamic processes. Deviations in ΔH values during cooling, compared to van′t …


Shear-Thinning Hydrogel For Delayed Delivery Of A Small Molecule Metalloproteinase Inhibitor Attenuates Myocardial Infarction Remodeling, Joshua E. Mealy, William M. Torres, Lisa A. Freeburg, Shayne C. Barlow, Alison A. Whalen, Chima V. Maduka, Tarek Shazly, Jason A. Burdick, Francis G. Spinale Apr 2025

Shear-Thinning Hydrogel For Delayed Delivery Of A Small Molecule Metalloproteinase Inhibitor Attenuates Myocardial Infarction Remodeling, Joshua E. Mealy, William M. Torres, Lisa A. Freeburg, Shayne C. Barlow, Alison A. Whalen, Chima V. Maduka, Tarek Shazly, Jason A. Burdick, Francis G. Spinale

Faculty Publications

No abstract provided.


Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah H. Williams, Tancia W. Bradshaw, Alissa R. Armstrong Apr 2025

Adipocyte-Derived Cchamide-1, Eiger, Growth-Blocking Peptide 3, And Unpaired 2 Regulate Drosophila Melanogaster Oogenesis, Chad Simmons, Isaiah H. Williams, Tancia W. Bradshaw, Alissa R. Armstrong

Faculty Publications

In addition to energy storage, adipose tissue communication to other organs plays a key role in regulating organismal physiology. While the link between adipose tissue dysfunction and pathophysiology, including diabetes, chronic inflammation, and infertility, is clear, the molecular mechanisms that underlie these associations have not been fully described. We use Drosophila melanogaster as a model to better understand how adipose tissue communicates to the ovary. In this study, we utilized D. melanogaster’s robust genetic toolkit to examine the role of five adipokines known to control larval growth during development, CCHamide-1, CCHamide-2, eiger, Growth-blocking peptide 3, and unpaired 2 in regulating …


Racial And Ethnic Inequalities In Actual Vs Nearest Delivery Hospitals, Nansi S. Boghossian, Lucy T. Greenberg, Jeffrey S. Buzas, Joshua Radack, Molly Passarella, Jeannette Rogowski, George R. Saade, Ciaran S. Phibbs, Scott A. Lorch Mar 2025

Racial And Ethnic Inequalities In Actual Vs Nearest Delivery Hospitals, Nansi S. Boghossian, Lucy T. Greenberg, Jeffrey S. Buzas, Joshua Radack, Molly Passarella, Jeannette Rogowski, George R. Saade, Ciaran S. Phibbs, Scott A. Lorch

Faculty Publications

IMPORTANCE Minoritized racial and ethnic groups, such as American Indian and Black individuals, often receive lower quality health care compared with White individuals. There is limited understanding of how these disparities extend to obstetric care, particularly when comparing the quality of care at the actual delivery hospital vs the nearest obstetric hospital based on the birthing individual’s residence. OBJECTIVE To examine inequality in care based on the actual delivery hospital and the closest delivery hospital to the birthing individual’s residential zip code centroid. DESIGN, SETTING, AND PARTICIPANTS This population-based retrospective cohort study used data from 5 states (2008 to 2020 …


Special Delivery Of Proteinaceous Matter To Deep-Sea Microbes, Yuan Shen, Ronald Benner, Taylor A.B. Broek, Brett D. Walker, Matthew D. Mccarthy Mar 2025

Special Delivery Of Proteinaceous Matter To Deep-Sea Microbes, Yuan Shen, Ronald Benner, Taylor A.B. Broek, Brett D. Walker, Matthew D. Mccarthy

Faculty Publications

Earth’s deep ocean holds a vast reservoir of dissolved organic carbon, traditionally considered old and resistant to microbial degradation. Radiocarbon analyses indicate the hidden occurrence of younger dissolved organic carbon components, assumed to be accessible to deep-sea microorganisms but not yet demonstrated. Using compound-class radiocarbon analysis, molecular characterization, and bioassay experiments, we provide direct evidence for rapid microbial utilization of young, labile, high–molecular weight proteinaceous material in bathypelagic waters. The abundance of labile proteinaceous material diminishes from epipelagic to mesopelagic waters but notably increases in bathypelagic waters, where it exhibits a short turnover time (days) and resembles surface plankton in …


No Evidence Of Fisheries-Induced Evolution Observed From Bluegill Populations In Small Kansas Impoundments, Morganne C. Borsh, Ben C. Neely, Peter B. Berendzen Mar 2025

No Evidence Of Fisheries-Induced Evolution Observed From Bluegill Populations In Small Kansas Impoundments, Morganne C. Borsh, Ben C. Neely, Peter B. Berendzen

Faculty Publications

Objective: Bluegill Lepomis macrochirus support recreational fisheries throughout much of their geographic distribution. One characteristic of the species is for males to exhibit alternative reproductive tactics to maximize production of progeny. These divergent strategies coupled with size-selective harvest by anglers create the potential for fisheries-induced evolution (FIE). As such, we sought to characterize genetic diversity of five fished and five unfished Bluegill populations to test for the occurrence of FIE. Methods: Fin clips from 100 Bluegill across 10 populations in southeast Kansas were collected to examine genetic diversity and test for the occurrence of FIE associated with long-term selective harvest. …


Forb Diversity Globally Is Harmed By Nutrient Enrichment But Can Be Rescued By Large Mammalian Herbivory, Rebecca A. Nelson, Lauren L. Sullivan, Erika I. Hersch-Green, Eric W. Seabloom, Elizabeth T. Borer, Pedro M. Tognetti, Peter B. Adler, Lori Biederman, Miguel N. Bugalho, Maria C. Caldeira, Juan P. Cancela, Kenneth J. Elgersma Mar 2025

Forb Diversity Globally Is Harmed By Nutrient Enrichment But Can Be Rescued By Large Mammalian Herbivory, Rebecca A. Nelson, Lauren L. Sullivan, Erika I. Hersch-Green, Eric W. Seabloom, Elizabeth T. Borer, Pedro M. Tognetti, Peter B. Adler, Lori Biederman, Miguel N. Bugalho, Maria C. Caldeira, Juan P. Cancela, Kenneth J. Elgersma

Faculty Publications

Forbs (“wildflowers”) are important contributors to grassland biodiversity but are vulnerable to environmental changes. In a factorial experiment at 94 sites on 6 continents, we test the global generality of several broad predictions: (1) Forb cover and richness decline under nutrient enrichment, particularly nitrogen enrichment. (2) Forb cover and richness increase under herbivory by large mammals. (3) Forb richness and cover are less affected by nutrient enrichment and herbivory in more arid climates, because water limitation reduces the impacts of competition with grasses. (4) Forb families will respond differently to nutrient enrichment and mammalian herbivory due to differences in nutrient …


Msbzip55 Regulates Salinity Tolerance By Modulating Melatonin Biosynthesis In Alfalfa, Tingting Wang, Jiaqi Yang, Jiamin Cao, Qi Zhang, Huayue Liu, Peng Li, Yizhi Huang, Wenwu Qian, Xiaojing Bi, Hui Wang, Yunwei Zhang Mar 2025

Msbzip55 Regulates Salinity Tolerance By Modulating Melatonin Biosynthesis In Alfalfa, Tingting Wang, Jiaqi Yang, Jiamin Cao, Qi Zhang, Huayue Liu, Peng Li, Yizhi Huang, Wenwu Qian, Xiaojing Bi, Hui Wang, Yunwei Zhang

Faculty Publications

No abstract provided.


Synthesis Of A Series Of Rare-Earth-Based Multi-Anion Chalcogenide Iodides Re3Si2SeXS8-XI (Re = La, Ce, Pr, And Nd) Using The Flux-Assisted Boron-Chalcogen Mixture Method, Gopabandhu Panigrahi, Habiba Binte Kashem, Gregory Morrison, Hans Conrad Zur Loye Mar 2025

Synthesis Of A Series Of Rare-Earth-Based Multi-Anion Chalcogenide Iodides Re3Si2SeXS8-XI (Re = La, Ce, Pr, And Nd) Using The Flux-Assisted Boron-Chalcogen Mixture Method, Gopabandhu Panigrahi, Habiba Binte Kashem, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Single crystals and polycrystalline powders of rare earth mixed chalcogenide iodides La3Si2Se1.21S6.79I, Ce3Si2Se1.39S6.61I, Pr3Si2Se1.22S6.78I, and Nd3Si2Se1.18S6.82I were prepared using the reactive flux-assisted boron-chalcogen mixture (BCM) method at 850 °C. All compounds crystallized in the monoclinic crystal system, space group C2/c (space group number 15). The series adopts the La3Si2O8Cl structure type, containing isolated SiQ4 tetrahedra connected by REQ8 (RE = La, Ce, Pr and Nd) polyhedra; this arrangement creates tunnels that are filled by I atoms. The partial substitution of S by Se was carried out to modulate the optical properties. Phase pure samples and uniform solid solutions were obtained …


Commodity Thermoplastic Elastomer-Enabled Templated Synthesis Of Large-Pore Ordered Mesoporous Materials, Anthony Griffin, Parker Frame, Yizhi Xiang, Zhe Qiang Mar 2025

Commodity Thermoplastic Elastomer-Enabled Templated Synthesis Of Large-Pore Ordered Mesoporous Materials, Anthony Griffin, Parker Frame, Yizhi Xiang, Zhe Qiang

Faculty Publications

Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated. …


Ec2vec: A Machine Learning Method To Embed Enzyme Commission (Ec) Numbers Into Vector Representations, Mengmeng Liu, Xialong Ni, J. Ramanujam, Michal Brylinski Mar 2025

Ec2vec: A Machine Learning Method To Embed Enzyme Commission (Ec) Numbers Into Vector Representations, Mengmeng Liu, Xialong Ni, J. Ramanujam, Michal Brylinski

Faculty Publications

Enzyme commission (EC) numbers play a vital role in classifying enzymes and understanding their functions in enzyme-related research. Although accurate and informative encoding of EC numbers is essential for enhancing the effectiveness of machine learning applications, simple EC encoding approaches suffer from limitations such as false numerical order and high sparsity. To address these issues, we developed EC2Vec, a multimodal autoencoder that preserves the categorical nature of EC numbers and leverages their hierarchical relationships, resulting in more meaningful and informative representations. EC2Vec encodes each digit of the EC number as a categorical token and then processes these embeddings through a …


Tropical Cyclone Response In Annual Tree Growth At Three Different Coastal Sites Along The Gulf Of Mexico, Usa, Clay S. Tucker, Alyssa C. Crowell, Kayla D. Stan, Thomas W. Patterson Mar 2025

Tropical Cyclone Response In Annual Tree Growth At Three Different Coastal Sites Along The Gulf Of Mexico, Usa, Clay S. Tucker, Alyssa C. Crowell, Kayla D. Stan, Thomas W. Patterson

Faculty Publications

Coastal forests are highly vulnerable to disturbances from tropical cyclones (TCs), yet the long-term impacts of storm surges on tree growth remain understudied. This study examines the relationship between TC-induced storm surges and annual tree-ring growth in Pinus elliottii at three coastal sites along the northern Gulf of Mexico. Using dendrochronological methods, we analyzed total ring width, earlywood, and latewood growth patterns to assess suppressions in response to past TC activity. Our results indicate that storm surge events consistently cause growth suppression, with recovery periods averaging two to three years. However, suppression patterns vary by site, with trees in more …


Comparison Of Deep Learning And Traditional Machine Learning Models For Predicting Mild Cognitive Impairment Using Plasma Proteomic Biomarkers, Kesheng Wang Phd, Ma, Bs, Donald A. Adjeroh, Wei Fang, Suzy M. Walter, Danqing Xiao, Ubolrat Piamjariyakul, Chun Xu Mar 2025

Comparison Of Deep Learning And Traditional Machine Learning Models For Predicting Mild Cognitive Impairment Using Plasma Proteomic Biomarkers, Kesheng Wang Phd, Ma, Bs, Donald A. Adjeroh, Wei Fang, Suzy M. Walter, Danqing Xiao, Ubolrat Piamjariyakul, Chun Xu

Faculty Publications

Mild cognitive impairment (MCI) is a clinical condition characterized by a decline in cognitive ability and progression of cognitive impairment. It is often considered a transitional stage between normal aging and Alzheimer’s disease (AD). This study aimed to compare deep learning (DL) and traditional machine learning (ML) methods in predicting MCI using plasma proteomic biomarkers. A total of 239 adults were selected from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort along with a pool of 146 plasma proteomic biomarkers. We evaluated seven traditional ML models (support vector machines (SVMs), logistic regression (LR), naïve Bayes (NB), random forest (RF), k-nearest neighbor …


Enhancing Mucus Flow And Clearance By Grafting Zwitterionic Hydrogel Films To Luminal Surfaces, Ryan Horne, Caleb Escudero, Morgan Ellerman, C. Allan Guymon, Marlan Hansen Mar 2025

Enhancing Mucus Flow And Clearance By Grafting Zwitterionic Hydrogel Films To Luminal Surfaces, Ryan Horne, Caleb Escudero, Morgan Ellerman, C. Allan Guymon, Marlan Hansen

Faculty Publications

Objective

To determine the effects of zwitterionic hydrogel films on mucus contact angles, flow, and stasis with respect to medical polymer surfaces, both flat and tubular.

Methods

A zwitterionic hydrogel thin film was photografted onto medical rubber surfaces and compared against non-zwitterionic hydrogel thin films and untreated surfaces to determine its impact on mucus contact angles, mucus flow on sheets and tubes, and mucus plugging.

Results

Zwitterionic and conventional hydrogel films significantly reduce the mucus contact angles and the tilt required to initiate mucus flow on sheets and in tubular systems. Preliminary experiments show that these films may also shorten …


Trans-Arg: Predicting Antibiotic Resistance Genes With A Transformer-Based Model And Pretrained Protein Language Model, Mohd Manzar Abbas, Amit Ranjan, Aixin Hou, Supratik Mukhopadhyay Mar 2025

Trans-Arg: Predicting Antibiotic Resistance Genes With A Transformer-Based Model And Pretrained Protein Language Model, Mohd Manzar Abbas, Amit Ranjan, Aixin Hou, Supratik Mukhopadhyay

Faculty Publications

Antibiotic resistance presents an emerging challenge to global health by reducing the efficacy of antibiotics administered to treat bacterial infections. Traditional approaches for detecting antibiotic resistance genes (ARGs) involve alignment-based sequence similarity techniques, which are time-consuming and resource-intensive. This signifies the necessity for developing advanced computational methods to detect ARGs early. To address this challenge, we introduce Trans-ARG, a novel multi-head attention transformer-based model designed to predict potential ARGs. Our approach leverages the pretrained ESMFold model to extract embeddings from protein sequences, capturing intricate structural and functional information. Protein sequences labelled as ARG or non-ARG were used as the dataset. …


Kg-Dta: A Knowledge Graph-Based Meta-Path Learning Framework To Predict Drug-Target Binding Affinity, Amit Ranjan, Adam Bess, Md Saiful Islam Sajol, Magesh Rajasekaran, Chris Alvin, Supratik Mukhopadhyay Mar 2025

Kg-Dta: A Knowledge Graph-Based Meta-Path Learning Framework To Predict Drug-Target Binding Affinity, Amit Ranjan, Adam Bess, Md Saiful Islam Sajol, Magesh Rajasekaran, Chris Alvin, Supratik Mukhopadhyay

Faculty Publications

Drug target affinity (DTA) prediction is essential at different phases of drug discovery and virtual drug screening. However, traditional wet lab experiments are time and resource-intensive owing to the complex interactions within the vast biological and chemical spaces. Computational methods have proven their potential to predict DTA, but none have considered the association of drugs and proteins to capture the complex interactions in the biological network between drugs and proteins. To address this, we propose a novel framework leveraging knowledge graph-based meta-path learning (KG-DTA) to enhance DTA prediction. First, we construct a weighted heterogeneous network of drugs and proteins that …


Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis Mar 2025

Nucleoredoxin Regulates Wnt Signaling During Pituitary Stem Cell Differentiation, Michelle L. Brinkmeier, Leonard Y M Cheung, Sean P. O'Connell, Diana K. Gutierrez, Eve C. Rhoads, Sally A. Camper, Shannon W. Davis

Faculty Publications

Nucleoredoxin (Nxn) encodes a multi-functional enzyme with oxidoreductase activity that regulates many different signaling pathways and cellular processes in a redox-dependent manner. Rare NXN mutations are reported in individuals with recessive Robinow syndrome, which involves mesomelic skeletal dysplasia, short stature, craniofacial dysmorphisms, and incompletely penetrant heart and palate defects. Here we report that Nxn is expressed in the ventral diencephalon and developing pituitary gland, and that Nxn deficient mice have pituitary dysmorphology and craniofacial abnormalities that include defects in the skull base and cleft palate. Nxn mutant mice exhibit reduced WNT signaling and reduced differentiation of pituitary stem …


Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss Mar 2025

Disruption Of G3bp1 Granules Promotes Mammalian Cns And Pns Axon Regeneration, Pabitra K. Sahoo, Manasi Agrawal, Nicholas Hanovice, Patricia J. Ward, Meghal Desai, Terika P. Smith, Hao Min Sima, Jennifer N. Dulin, Lauren S. Vaughn, Mark H. Tuszynski, Kristy Welshhans, Larry I. Benowitz, Arthur W. English, John D. Houle, Jeffery L. Twiss

Faculty Publications

Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in Caenorhabditis elegans, increases the growth of spontaneously regenerating axons. Inhibition of G3BP1 by expression of its acidic or “B-domain” accelerates axon regeneration after nerve injury, bringing a potential therapeutic strategy for peripheral nerve repair. Here, we asked whether G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system (CNS) where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as in …