Digital Commons Network^™

The Organization Of Serotonergic Fibers In The Pacific Angelshark Brain: Neuroanatomical And Supercomputing Analyses, Skirmantas Janušonis, Ralf Metzler, Thomas Vojta

Physics Faculty Research & Creative Works

Serotonergic axons (fibers) are a universal feature of all vertebrate brains. They form meshworks, typically quantified with regional density measurements, and appear to support neuroplasticity. The self-organization of this system remains poorly understood, partly because of the strong stochasticity of individual fiber trajectories. In an extension to our previous analyses of the mouse brain, serotonergic fibers were investigated in the brain of the Pacific angel shark (Squatina californica), a representative of a unique (ray-like) lineage of the squalomorph sharks. First, the fundamental cytoarchitecture of the angel shark brain was examined, including the expression of ionized calcium-binding adapter molecule 1 (Iba1, …

Efficacy Of Stress Acclimation Techniques In Coastal Wetland Plants (Spartina Alterniflora And S. Patens): Implications For Restoration And Nursery Production, Taylor M. Sloey, Kylie D. Gieser, Kaitlyn Pounders, Sofía E. Báez, Jennifer L. Whytlaw

Biological Sciences Faculty Publications

The implementation of coastal nature-based features, created wetlands, and wetland restoration has increased globally over recent years. Many of these projects have been successful in meeting their goals, however, when projects fail, it is often attributed to mortality of transplanted vegetation. Transplant mortality may be due to inappropriate timing, poor site selection, or abiotic stressors associated with transplant shock. Science-backed guidelines have been well established in many coastal regions regarding site specifications and species selection, but nursery practices for reducing transplant shock remain inconsistent. In this study, we tested a combination of four salinity acclimation treatments and two inundation acclimation …

The Reliability Response To Patent Law’S Ai Challenges, Arti K. Rai

Faculty Scholarship

Pervasive AI use adds newfound importance to longstanding debates over patent timing and reliability. Patent claims on speculative ideas generated by AI, or even the infusion of speculative AI-generated ideas into the public domain, may defeat patent incentives for more careful research. Although challenges that AI use poses for patent validity requirements like human inventorship and nonobviousness have received more attention, reliability is equally important.

Indeed, as this Article argues, the issues are linked. If requirements for inventorship and nonobviousness were adjusted to emphasize reliability, a human role could be preserved, and AI use would not necessarily threaten patents. Currently, …

The Future Of Ai Regulation In Drug Development: A Comparative Analysis, Gabriela Lenarczyk, Timo Minssen, Nicholson Price, Arti Rai

Faculty Scholarship

As artificial intelligence (AI) transforms drug development, regulatory frameworks are evolving to oversee its implementation, particularly at the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA). This paper makes three contributions to understanding emerging regulatory approaches. First, we offer a comparative analysis of how these agencies have responded to AI-driven advances, incorporating new US executive orders and the European Union (EU)’s AI Act. Second, we propose a novel analytical framework to understand regulatory divergence: the FDA’s flexible, dialog-driven model contrasts with the EMA’s structured, risk-tiered approach, reflecting broader institutional and political-economic differences. While the former encourages …

Strategic Identification Of Prognostic Biomarkers For Knee Osteoarthritis Via Optimized Regression Techniques, Varun Sri Sai Vemuri

Selected Full-Text Master Theses 2021-

Knee Osteoarthritis (KOA) is a progressive musculoskeletal disease involving cartilage matrix degradation, subchondral bone remodeling, and systemic inflammation, significantly impairing joint function and mobility. Existing KOA prediction models are not designed to account for nonlinear multimodal biomarker interactions or to integrate biochemical and imaging data, thus limiting their clinical utility. The current method for early detection and prediction of KOA disease progression is primarily based on machine learning-based approaches using radiographic imaging data, static feature selection, and deterministic outputs. These machine learning approaches often fail to capture the pathophysiology of KOA disease progression, which involves a complex cascade of processes, …

Adverse Childhood Experiences, Depression And Subjective Cognitive Decline By Gender: A Moderated Mediation Analysis, Monique J. Brown, Darlingtina K. Esiaka, Jaya Viswanathan

Behavioral Science Faculty Publications

Studies assessing depression as a mediating factor between adverse childhood experiences (ACEs) and subjective cognitive decline (SCD) are lacking. Therefore, the aims of this study were to: (1) determine the mediating role of depression in the association between ACEs and SCD; and (2) assess the moderating role of gender. Data were obtained from the 2023 Behavioral Risk Factor Surveillance Study (BRFSS) survey (N = 38,600). Crude and adjusted path analyses were used to determine the mediating role of depression between ACEs and SCD. Adjusted analyses controlled for sociodemographic confounders. ACEs were positively associated with depression (B = 0.129, p …

Oil-Oil Correlation Across Sedimentary Basins In Kansas Using Molecular Geochemistry And Fourier Transform Infrared Spectroscopy, Oluwaseun V. Omoyemi

Master's Theses or Doctor of Nursing Practice

Hydrocarbons are produced from different subbasins and stratigraphic intervals in Kansas. However, the geochemical characteristics and sources of these hydrocarbons are still poorly understood. While reservoir rocks, seals, and traps that are essential for petroleum systems are well defined within the state, the possible source rocks are often considered thermally immature, raising questions about their ability to generate the volume of hydrocarbons currently being produced. This research project tries to evaluate the geochemical characteristics of hydrocarbons produced in the state of Kansas and determine if the hydrocarbons from the different subbasins and stratigraphic units are genetically related. Thirty-seven crude oil …

A Histological Survey Of A Large, Sub-Adult Tylosaurus Nepaeolicus With Implications On The Validity Of Tylosaurus Kansasensis, Carson Cope

Master's Theses or Doctor of Nursing Practice

Tylosaurus nepaeolicus is a basal, medium-sized tylosaurine mosasaur that lived during the late Coniacian and early Santonian in the Western Interior Seaway. Despite being a well-studied species, there is debate over whether Tylosaurus kansasensis represents the juvenile form of T. nepaeolicus, or if the two species are distinct. Osteohistology can determine organism age at time of death and can be used to help resolve this debate and provide a better understanding of the growth of T. nepaeolicus. Thin-sections were taken from a humerus, rib, and vertebra of a single individual (FHSM VP-2209). All thin-sections show primarily parallel-fibered cortical …

Leveraging Data Science For Resilience: Improving Trauma-Informed Care Practice For Adverse Childhood Experience With Ai & Data Science Application, Mohmmad Arif Shaik

Master's Theses

Adverse Childhood Experiences (ACEs) have long-lasting effects on physical health, mental well-being, education, and socioeconomic outcomes. Resilient Georgia (RG), a statewide initiative, seeks to address ACEs through trauma-informed care and data-driven strategies. However, challenges in data collection, analysis, and tracking set back the effectiveness of these efforts. This study explores the role of data science and interactive visualization tools in improving outcomes for individuals and communities affected by ACEs. A key focus of this research is the development of a data science management application designed to enhance data collection and improve real-time decision-making. The application features interactive dashboards that allow …

Evaluating The Chemical Reactivity Of Wildfire-Derived Dissolved Organic Molecules: Glutathione Binding Through Kendrick Mass Defect Analysis, Hannah M. Hamontree, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The emerging risks to organisms of pyrogenic-derived dissolved organic matter (PyDOM) from forest fires are of concern due to its toxic and mutagenic potential (e.g., pro-oxidative responses in fauna through the depletion of glutathione, a nitrogen- and sulfur-containing tripeptide found in cells). This study simulates this phenomenon in a laboratory setting by identifying bonding between reduced l-glutathione and organic molecules in leachates from environmentally weathered biomass samples (charred and uncharred) using Kendrick Mass Defect (KMD) analysis from formula lists obtained from negative-mode electrospray ionization-Fourier transform-ion cyclotron resonance-mass spectrometry ((-)ESI-FT-ICR-MS). These formula lists reveal a 10-fold increase in nitrogen- and sulfur-containing …

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 …

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 …

Low Salinities Impair Heat Tolerance And Alter Reproductive Traits With No Implications For Survival In A Marine Annelid From Coastal Habitats, Gabrielle Newton, Gloria Massamba-N'Siala

Biological Sciences Faculty Publications

Climate change is expected to intensify salinity and temperature fluctuations in estuarine and coastal habitats. However, the impact of salinity variation on ectotherms’ thermal tolerance remains underexplored, limiting our understanding of the interplay between these stressors. This study investigated salinity-dependent changes in life history traits (survival, growth rate, fecundity, and egg size) over a 33-day exposure to a salinity gradient (12, 17, 22, 27, 32, 35, 40, 45, 50) in the marine annelid Ophryotrocha labronica. Individuals that survived the salinity treatments were assessed for their upper and lower thermal tolerance limits. Female individuals, the target of the study, exhibited …

Cellular Responses Of Astrangia Poculata (Ellis And Solander, 1786) And Its Symbiont To Experimental Heat Stress, Tyler E. Harman, Daniel Barshis, Briana Hauff Salas, Kevin B. Strychar

Biological Sciences Faculty Publications

Climate change has had devastating effects on tropical coral reefs; however, much less is known regarding how heat stress affects temperate coral. This research focuses on Astrangia poculata (Ellis and Solander, 1786) collected from Narragansett Bay, RI, during the summer and winter seasons and understanding the effect of experimental thermal extremes (i.e., 26 °C) on seasonally different populations. Photosynthetic efficiency (Fv/Fm), symbiont density (via an inverse relationship with pixel intensity), and oxidative stress via reactive oxygen species (ROS) concentrations were measured on symbiotic and aposymbiotic A. poculata. Higher Fv/Fm rates were observed in summer- vs. winter-collected corals (p ≤ …

Alternative Splicing In A Coral During Heat Stress Acclimation And Recovery, Nitin Baliga, Kathryn Stanklewicz, Jacob Valenzuela, Serdar Turkarsian, Wei-Ju Wu, Kelly Gomez-Campo, Nicolas Locatelli, Trinity Conn, Veronica Radice, Katherine Parker, Rachel Alderdice, Line Bay, Christian Voolstra, Daniel Barshis, Iliana Baums

Biological Sciences Faculty Publications

Climate change has caused drastic declines in corals. As sessile organisms, corals acclimate to environmental shifts through genome-wide changes in gene expression, epigenetic modifications, and alterations in microbiome composition. However, alternative splicing (AS), a conserved mechanism of stress response in many organisms, has been under-explored in corals. Using short-term acute thermal stress assays, we investigated patterns of AS in the scleractinian coral Acropora cervicornis during response to low (33°C), medium (35°C), and high (37°C) heat stress and subsequent overnight recovery. Our findings demonstrate reproducible dynamic shifts in AS of at least 40 percent of all genes during response to heat …

Analyzing Microbial Communities In Porites Astreoides, Sanaa Caldwell, Katie Parker, Daniel Barshis

Biological Sciences Faculty Publications

Coral reefs are vital marine ecosystems that support many different species and ecosystem services through protecting coastlines from storms and erosion, providing raw materials for medication, and facilitating diversity amongst marine species. Anthropogenic climate change is causing ocean temperatures to exceed the range of coral thermal tolerance resulting in more coral bleaching events globally. However, some corals have the capacity to withstand high temperatures through different thermal tolerance strategies. A balanced microbial community plays a critical role in coral health and recent studies have indicated that a balanced microbiome is associated with temperature-stress tolerant corals. Yet, there is a severe …

Summer Temperature Maxima Already Challenge Thermal Capacities Of Coral In The Southern Persian/Arabian Gulf, Rachel Alderdice, Gabriela Perna, Hannah Manns, Anna Fiesinger, Luigi Colin, Kathryn Stankiewicz, Kelly Gomez-Campo, Samantha Goyen, Line Bayse, Nitin Baliga, Jake Valenzuela, Iliana B. Baums, Daniel J. Barshis, John A. Burt, Christian R. Voolstra

Biological Sciences Faculty Publications

The future of coral reefs remains uncertain as intensifying ocean warming continues to drive coral decline and demise worldwide. Corals occurring in extreme environments such as the Persian/Arabian Gulf (PAG), the world’s warmest sea, represent a promising resource to study the genetic architecture of thermal tolerance. However, their thermal capacities remain unresolved. We applied short-term heat stress assays using the Coral Bleaching Automated Stress System (CBASS) to determine signatures of thermal tolerance from three common species (Porites harrisoni, Platygyra daedalea, and Cyphastrea microphthalma) across three sites (two in the extreme southern PAG and a more benign …

Selective Nutrient Incorporation May Underestimate Heterotrophy Of A Mixotrophic Reef-Building Coral, Connor R. Love, Marleen Stuhr, Michael D. Fox, Veronica Z. Radice, Maoz Fine, Kelton W. Mcmahon, David L. Valentine

Biological Sciences Faculty Publications

Mixotrophic reef-building corals acquire nutrition via photosynthate translocation from endosymbiotic microalgae and by heterotrophic prey/particle capture. Heterotrophy promotes resistance to, and recovery from, environmental stress, but quantifying coral heterotrophy remains difficult due to complex resource exchanges within the coral holobiont. We interrogated the response of multiple biomarkers to coral heterotrophy using fatty acid profiling and stable isotope analysis of Stylophora pistillata grown along a controlled feeding gradient from pure autotrophy to pure heterotrophy. We found that fatty acids and nitrogen were effectively incorporated into both coral host and symbiont tissues, while carbon, which is the primary target for conventional heterotrophy …

Biotime 2.0: Expanding And Improving A Database Of Biodiversity Time Series, Maria Dornelas, Laura H. Antão, Amanda E. Bates, Viviana Brambilla, Jonathan M. Chase, Cher F. Y. Chow, Ada Fontrodona-Eslava, Anne E. Magurran, Inês S. Martins, Faye Moyes, Alban Sagouis, Samuel Adu-Acheampong, Daniel Acquah-Lamptey, Dušan Adam, Penelope A. Ajani, Aitor Albaina, Pablo Almaraz, Jeongseop An, Roger Sigismund Anderson, Madelaine Jean Robertson Anderson, Alexsander Z. Antunes, Ivan Arismendi, Linda Armbrecht, Pedro Aros-Mardones, Sreejith Kalpuzha Ashtamoorthy, Narayanan Ayyappan, Gal Badihi, Joseph J. Bailey, Andrew H. Baird, Mark Edward Baird, Sreekumar Vadakkethil Balakrishnan, José António L. Barão-Nóbrega, Adi Barash, Miguel Barbosa, Jos Barlow, Claus Bässler, Matthieu Beaumont, Natalie Beenaerts, Tiago Octavio Begot, Wallace Beiroz, Ricardo Beldade, David M. Bell, Alecia Bellgrove, Jonathan Belmaker, Lisandro Benedetti-Cecchi, Cassandra E. Benkwitt, Pamela Medina-Van Berkum, Brandon T. Bestelmeyer, Matthew C. Betts, Maxwell Kelvin Billah, Anne D. Bjorkman, Magdalena Błażewicz, Christopher P. Bloch, Shane A. Blowes, Antonio Bode, Juliano A. Bogoni, Thomas Bolger, Timothy C. Bonebrake, Erik Bonsdorff, Roberta Bottarin, Luke N. Brokensha, Rob W. Brooker, Andrew J. Brooks, Helge Bruelheide, Thiago Almeida Bueno, Claire Laguionie, Mariana Lopes Campagnoli, James Cant, Erica Pellegrini Caramaschi, Alexandre Caron, Tadhg Carroll, Tancredi Caruso, Juan Carvajal-Quintero, Giuseppe Castaldelli, Edward Castañeda-Moya, Pedro V. Castilho, Sonia Zanini Cechin, Shahar Chaikin, Uchangi Manjunatha Chandrashekara, Tory J. Chase, Chaolun Allen Chen, Jorge José Cherem, Sei-Woong Choi, Erica M. Christensen, Alexander V. Christianini, Jackson Wing Four Chu, Peter Coad, Carl Van Colen, Lise Comte, Elisabeth J. Cooper, J. Hans C. Cornelissen, Eddy Cosson, Unai Cotano, Luc Crevecoeur, Shannan Kyle Crow, Graeme S. Cumming, Vanessa S. Daga, Gabriella Damasceno, Gergana N. Daskalova, Claire H. Davies, Robert A. Davis, Frank P. Day, Sussy De-La-Zerda, Amy Elizabeth Deacon, Indradatta De Castro-Arrazola, Steven Degraer, Kharran Deonarinesingh, Juan C. Diaz-Ricaurte, Christopher R. Dickman, Tara Dirilgen, Ciaran John Dolan, J. Emmett Duffy, Timothy E. Dunn, Giselda Durigan, Ciara Dwyer, Steven Earl, Dor Edelist, Graham John Edgar, Sally Edmonson, Ashley K. Elgin, Kari Elsa Ellingsen, Sarah C. Elmendorf, Ruth S. Eriksen, S. K. Morgan Ernest, Ruben Escribano, Paula Cabral Eterovick, Brian S. Evans, Jason D. Everett, Vesela Evtimova, Dan A. Exton, Andrew J. Fairbairn, Filipe Moreli Fantacini, Fabiano Turini Farah, Fábio Zanella Farneda, Mario E. Favila, Philippe Fernandez-Fournier, Braulio Fernández-Zapata, Diogo F. Ferreira, Carola Ferronato, Christopher R. Du Feu, Alessandra Fidelis, David A. Fifield, Vilmar Picinatto Filho, Walter Mesquita Filho, Robert N. L. Fitt, Carlos A. H. Flechtmann, William R. Fraser, Donna L. Fraser, Lídia Freixas, John Fryxell, Garrett J. Fundakowski, Scott Stanley Gabara, Elise Gallois, Mariana Garcia Criado, Emili García-Berthou, Joaquim Garrabou, Andrew R. Gates, Roberto Cazzola Gatti, Anna Gavioli, Tal Gavriel, Benoit Gendreau-Berthiaume, Xingli Giam, Carina Gjerdrum, Michael Glemnitz, Jasmin Annica Godbold, Daniel Gómez-Gras, Rodrigo Barbosa Gonçalves, Andy Goold, Richard R. Gordon, Menachem Goren, Fernando Vilas Boas Goulart, William G. Gould, Meagan M. Graboski, Nicholas A. J. Graham, Maurício Eduardo Graipel, Laura J. Grange, Aaron C. Greenville, Gary D. Grossman, Valeria A. Guinder, Peter Haase, Gary N. Haskins, Kris Havstad, Luise Hermanutz, Michael Julian Hames Hickford, Pamela Hidalgo, Pedro Higuchi, Andrew S. Hoey, Gert Van Hoey, Annika Hofgaard, Kristen T. Holeck, Robert D. Hollister, Richard T. Holmes, Mia Odell Hoogenboom, Joaquín Hortal, Tammy Horton, Chih-Hao Hsieh, Christine L. Huffard, Ida-Maria Huikkonen, Allen H. Hurlbert, Julian Hynes, Pascal Irz, Natalia Macedo Ivanauskas, Akemi Iwayama, Darren K. James, Ute Jandt, Anna M. Jażdżewska, Merlijn Jocque, Sophie T. Johnston, Samuel E. I. Jones, Faith A. M. Jones, Julia A. Jones, Edite Jucevica, Ugis Kagainis, Maiko Kagami, Jungwon Kang, Xuejia Ke, Erin Colleen Keeley, Rebecca Kinnear, Kari Klanderud, Uwe Klinck, Roel Van Klink, Stefan Klotz, Carolien Kockaert, Halvor Knutsen, Matti Koivula, Alessandra Kortz, Peter Kriegel, Chao-Yang Kuo, David J. Kushner, Rosina Kyerematen, Raphaël Lagarde, Lesley T. Lancaster, Ori Frid Landau, Wouter Van Landuyt, Eric R. Larson, Mai Lazarus, Cheol Min Lee, Jonathan S. Lefcheck, Jonas J. Lembrechts, Renato A. Ferreira De Lima, Romullo Guimarães Lima, Nathália G. S. Lima, Cristina Linares, Sandra C. Lindstrom, Francisco Lloret, John David Lloyd, Cleonice Maria Cardoso Lobato, David M. Lodge, Peter Richard Long, Celeste López-Abbate, Adrià López-Baucells, Julio Louzada, Maite Louzao, Antonella Lugliè, Micheli Ribeiro Luiz, S. Ellen Macdonald, Joshua S. Madin, André Lincoln Barroso Magalhães, Rajindra Mahabir, David Maphisa, Thomas Edward Martin, Marcio Martins, Patrick T. Martone, Silvia Matesanz, Shin-Ichiro S. Matsuzaki, Thomas J. Matthews, Iain Mccombe Matthews, Connie J. Maxwell, Kent P. Mcfarland, Brian J. Mcgill, Diane Marie Mcknight, Michael J. Mcwilliam, Jason Meador, Henning Meesenburg, Kristin Meier, Viesturs Melecis, Peter L. Meserve, Christoph F. J. Meyer, Anders Michelsen, Natali Olivia Roman Miiller, Marco Milardi, Nataliya Milchakova, Robert J. Miller, Jonathan Millett, Tom Moens, Luciano F. A. Montag, Jon Moore, Jörg Müller, Akhil Murali, Shauna Ann Murray, Isla H. Myers-Smith, Randall W. Myster, Masahiro Nakamura, Sasi Nayar, Francis Neat, James A. Nelson, Michael Paul Nelson, Boris P. Nikolov, Rym Nouioua, Collins Ayine Nsor, Michael O' Connor, Edward Adzesiwor Obodai, Amy Marie Offland, Romà Ogaya, Hisako Ogura, Thomas A. Okey, Julian D. Olden, Luiz Gustavo Rodrigues Oliveira-Santos, Jeffrey C. Oliver, Esben Moland Olsen, Vladimir G. Onipchenko, Daniel Oro, Dais Ozolins, Krzysztof Pabis, Bachisio Mario Padedda, Facundo X. Palacio, Alain Paquette, Sinta Trilestari Pardede, David M. Patersib, Sarah Pausina, Raphaël Pélissier, Steven C. Pennings, Josep Penuelas, Felipe Walter Pereira, Nivaldo Peroni, Sergio Picó, Francesca Pilotto, Hudson Tercio Pinheiro, Oscar Pizarro, Roberto Pizzolotto, Francesco Pomati, Paulo Santos Pompeu, Dominique Ponton, Eric Post, Nicolas Poulet, Juha Pöyry, Steven J. Presley, Herbert H. T. Prins, Pieter Provoost, Kathleen L. Prudic, Vignesh Punjayil, Petr Pyšek, Pascal Querner, Juan Pablo Quimbayo, Indar W. Ramnarine, Daniel C. Reed, Peter Bernard Reich, Suzanne M. Remillard, Cerren Richards, Anthony James Richardson, Itai Van Rijin, Victor H. Rivera-Monroy, Christian Rixen, Kevin Peter Robinson, Ricardo Rocha, Ricardo R. Rodrigues, Cassy Rodrigues, Bjørn De Roos, Denise De C. De Rossa-Feres, Loreta Rosselli, Peter Charles Rothlisberg, Ana Rubio, Lars G. Rudstam, Catalina S. Ruz, Nancy B. Rybicki, Gunther Van Ryckegem, Andrew L. Rypel, Jon P. Sadler, Victor Satoru Saito, Sofia Sal, Renato Portela Salomão, Nathan J. Sanders, Flavio A. M. Santos, Tiago Gomes Dos Santos, Swapan Kumar Sarker, Sara E. Scanga, Marcus Schaub, Jochen Schmidt, Inger Kappel Schmidt, Robert L. Schooley, Alfred Schultz, Alberto Scotti, Amanda Serpell-Stevens, Filipe C. Serrano, Elizabeth H. Shadwick, Matthew Shaft, Thomas W. Sherry, Erika Mayumi Shimabukuro, Jacek Siciński, Caya Sievers, Fernando Rodrigues Da Silva, Ana Carolina Da Silva, Juliana M. Silveira, Tadeu Siqueira, Arunkumar Kavidapadinjattathil Sivadasan, Prasad Theruvil Parambil Sivan, Agnija Skuja, Amalia L. Slaughter, Jasper A. Slingsby, Joseph R. Smith, Bruno Eleres Soares, Martin Solan, Flaviana Maluf Souza, Gabriel B. G. Souza, Joshua L. Sprague, Ulrich Stachow, J. John Stadt, Christopher D. Stallings, Radoslav Hristov Stanchev, Emily H. Stanley, Brian M. Starzomski, Jose Mauro Sterza, Maarten Stevens, F. Gary Stiles, Stefan Stoll, Rick D. Stuart-Smith, Yzel Rondon Súarez, Laura Super, Sarah R. Supp, Tapio Sutela, Iain M. Suthers, Anna Suuronen, Kerrie M. Swadling, Daniel K. Szydlowski, Hisatomo Taki, Sara Jeanne Snell Taylor, Pablo A. Tedesco, Nils Teichert, Akira Terui, Gary P. Thiede, Anne Thimonier, Oliver Thomas, Peter Allan Thompson, Simon Thorn, Jeremy S. Tiemann, Luís Felipe Toledo, Anne Tolvanen, Maria Teresa Zugliani Toniato, Ignasi Torre, Marcos Adriano Tortato, Kumiko Totsu, Andrew Trant, Robert R. Twilley, Hirokazu Urabe, Pierre Valade, Nelson Valdivia, Martha Isabel Vallejo, Thomas J. Valone, Jan Vanaverbeke, Tiago Silveira Vasconcelos, Teppo Vehanen, Fábio Venturoli, Hans M. Verheye, Hendrik Jannes Wietse Vermeulen, Arne Verstraeten, Marcelo Vianna, Rui Vieira, João Paulo Santos Vieira-Alencar, Marc Vilella, Jean Ricardo Simões Vitule, Lien Van Vu, Robert B. Waide, Paige S. Warren, Joseph Paul Wayman, Sara L. Webb, Benjamin Weigel, Ellen A. R. Welti, Fritha West, Fulgor Westermann, Matthew A. Whalen, Ethan P. White, Claire E. Widdicombe, Richard Williams, Mark Williamson, Michael R. Willig, Sonja Wipf, Eric J. Woehler, Alje Woldering, Kerry D. Woods, Wu-Bing Xu, Ruthy Yahel, Zeren Yang, Kyle J. A. Zawada, Camila Zornosa-Torres, Assaf Zvuloni

Biological Sciences Faculty Publications

Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database.

Main Types of Variables Included: The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised …

Demystifying Misconceptions In Introductory Undergraduate Chemistry Education With 3d Printed Molecular Orbitals, Hiwot Endeshaw, Daniel J. O'Leary

Pomona Senior Theses

Spatial abilities are invaluable skills for the science, technology, engineering, and mathematics (STEM) subjects. However, women, people from low socioeconomic backgrounds, and ethnic minorities are more likely to have less developed spatial abilities, which is one of the many contributing factors for the lack of diversity in STEM subjects like chemistry. Teaching spatial skills to undergraduate chemistry students may address this issue and help increase the diversity of students who go on to continue their education in the subject. 3D printing technology in higher education has exploded in recent years, presenting a unique opportunity to teach “hard to grasp” concepts …

Optimizing And Scaling Up Tcfh–Nmi Pyrrole Acylation For Organic Syntheses, Grant H. Miller

Pomona Senior Theses

Traditional ketone synthesis often depends on toxic reagents and hazardous solvents, which limits its scalability and environmental compatibility. The TCFH–NMI method has shown strong potential for amide, ester, and thioester formation, but its use in ketone synthesis has only been recently described, and only on small scales. This thesis addresses that gap by optimizing a scalable synthesis of 2-(monomethyl succinyl)-3,5-dimethylpyrrole using monomethyl succinate and 2,4-dimethylpyrrole as model substrates. Key reaction parameters were systematically refined to improve yield, reproducibility, and sustainability. The final protocol avoids chromatography, operates at room temperature, and consistently delivers high yields. These features position it as a …

Swimming In Sh*T: Quantifying Lagoon Flushing Impacts On Fecal Indicator Bacteria In Surf Zones Of Three Beaches On The East End Of Long Island, Ny, Brody C. Eggert

Pomona Senior Theses

This thesis investigates how lagoon flushing influences fecal indicator bacteria (FIB) concentrations—specifically enterococcus bacteria—in the surf zones of East Hampton and Southampton, New York. Focusing on the coastal lagoons of Georgica Pond, Sagg Pond, and Mecox Bay, the study analyzes how episodic inlet openings and environmental conditions affect enterococcus levels at adjacent recreational beaches. Using over 700 observations from the Surfrider Foundation’s Blue Water Task Force (BWTF) database, I construct a series of statistical models ranging from ordinary least squares to mixed effects frameworks; this thesis shows my process in developing this model. My analysis reveals that open inlets between …

Rwanda's Natural Remedies: A Fresh Look At The Fight Against Malaria, Leandre Nsabimana Ndisanze

Pomona Senior Theses

Malaria remains one of the most devastating parasitic diseases globally, disproportionately affecting sub-Saharan Africa, where Rwanda continues to face high transmission rates and rising resistance to conventional interventions. Despite decades of control efforts, the emergence of drug-resistant Plasmodium falciparum and insecticide-resistant Anopheles mosquitoes threatens to reverse recent gains. This research responds to the urgent need for sustainable and culturally relevant alternatives by exploring the therapeutic potential of Rwandan traditional medicinal plants. These indigenous remedies, long used by local healers, offer an underexplored reservoir of bioactive compounds that may provide the basis for novel antimalarial drugs.

The central hypothesis of this …

Ecology-Driven Machine Learning For Predicting Risk Of Spread For Aquatic Invasive Species., Leif Eric Howard

Graduate Student Theses, Dissertations, & Professional Papers

Effective management of aquatic invasive species (AIS) requires predictive tools that leverage environmental and ecological data to forecast spread into uninvaded areas. However, species distribution models (SDMs) often struggle to capture key invasion processes such as dispersal, propagule pressure, and biotic interactions. This thesis integrates ecological, dispersal, and environmental predictors within a machine learning framework to enhance AIS risk prediction and model transferability across space.

In Chapter 2, 61 novel predictors were developed for 2,203 Minnesota lakes to model zebra mussel (Dreissena polymorpha) occurrence, incorporating variables related to propagule pressure (e.g., boat visitation), community composition (e.g., fish species …

Mathematical Modeling Of Cancer Tumor Evolution, Belgacem Al-Azem

CGU Theses & Dissertations

Several mathematical models of cancer tumor evolution are presented. The aim of this endeavor is to write a thesis that fosters numerical and analytical understanding of certain mathematical models in the area of oncology as well as to offer potential predictive tools of therapeutic and clinical applicability. In this work, we give a panoramic view of the cancer phenotype, for to understand cancer, we need to "see" its biophysics. Indeed, the discovery of oncogenes led to the thinking that cancer tumor is perhaps a genetic disease. But the role of angiogenesis and other microenvironment-related discoveries (such as the role of …

Geometric Dimensionality Reduction, Daniel Livschitz

CGU Theses & Dissertations

The emergence of AI models developed through computationally intensive training has resulted in a surge of research into dimensionality reduction techniques that spans across numerous mathematical disciplines. In this thesis we establish Geometric Dimensionality Reduction, a non-linear data compression technique that utilizes low dimensional manifolds embedded in dimensional spaces to form composite contraction-and-projection maps. Geometric Dimensionality Reduction is predominantly demonstrated through a novel algorithm entitled LGE (Livschitz-Gu-Eyunni) that utilizes Multicomplex rotation groups and polyspherical coordinates to define a single tuneable logarithmic map from ℝ 2푛 to ℝ 푛+1 with deterministic time complexity, geometric tunability, and semi-reversibility. Significant breakthroughs in the …

Gene Expression Changes In Human Cerebral Arteries Following Hemoglobin Exposure: Implications For Vascular Responses In Sah, Chathathayil M Shafeeque, Arif O Harmanci, Sithara Thomas, Ari C Dienel, Devin W Mcbride, Kumar T Peeyush, Spiros L Blackburn

Faculty, Staff and Student Publications

Subarachnoid hemorrhage (SAH), characterized by the presence of hemoglobin (Hb) in the subarachnoid space, significantly impacts cerebral vessels, leading to various pathological outcomes. The toxicity of cell-free Hb released from erythrocytes and its metabolites after SAH causes vasoconstriction and neuronal damage, and correlates with delayed ischemic neurological deficits (DIND). While animal models have provided substantial and invaluable data in the research of aneurysmal SAH, the specific effects of subarachnoid blood on cerebral arteries remain greatly understudied. Here, we describe the changes in the genetic profile of human cerebral arteries exposed to free Hb for 48 h. We performed an ex …

Some Types Of Hyperneutrosophic Set (7): Type-M, Nonstationary, Subset-Valued, And Complex Refined, Takaaki Fujita, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

This paper builds upon the foundational advancements introduced in [26,39–43]. TheNeutrosophic Set provides a versatile mathematical framework for addressing uncertainty through its three membership functions: truth, indeterminacy, and falsity [84]. Extensions such as the Hyperneutrosophic Set and the SuperHyperneutrosophic Set have been recently proposed to address increasingly complex and multidimensional problems. Detailed formal definitions of these concepts can be found in [33]. In this paper, we extend the Type-𝑚, Nonstationary, Subset-Valued, and Complex Refined Neutrosophic Sets using the Hyperneutrosophic Set and the SuperHyperneutrosophic Set frameworks.

Superhypergraph Neural Networks And Plithogenic Graph Neural Networks: Theoretical Foundations, Takaaki Fujita, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Hypergraphs extend traditional graphs by allowing edges to connect multiple nodes, while superhypergraphs further generalize this concept to represent even more complex relationships. Neural networks, inspired by biological systems, are widely used for tasks such as pattern recognition, data classification, and prediction. Graph Neural Networks (GNNs), a well-established framework, have recently been extended to Hypergraph Neural Networks (HGNNs), with their properties and applications being actively studied. The Plithogenic Graph framework enhances graph representations by integrating multi-valued attributes, as well as membership and contradiction functions, enabling the detailed modeling of complex relationships. In the context of handling uncertainty, concepts such as …

Some Types Of Hyperneutrosophic Set (6): Multineutrosophic Set And Refined Neutrosophic Set, Takaaki Fujita, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

This paper builds on the foundational advancements introduced in [22, 29–32]. The Neutrosophic Set pro-vides a flexible mathematical framework for managing uncertainty by utilizing three membership functions: truth, indeterminacy, and falsity. Recent extensions, such as the HyperNeutrosophic Set and the SuperHy-perNeutrosophic Set, have been developed to address increasingly complex and multidimensional challenges. Comprehensive formal definitions of these concepts are provided in [26]. In this paper, we further extend various specialized classes of Neutrosophic Sets. Specifically, we explore extensions of the MultiNeutrosophic Set and the Refined Neutrosophic Set using HyperNeutrosophic Sets and 𝑛-SuperHyperNeutrosophic Sets, providing detailed analysis and examples.