Charles E. Schmidt College of Science

Anthropogenic impacts, including urbanization and development of the Greater Everglades ecosystem, have severely reduced and fragmented populations of Bletia purpurea. Differences across populations in Florida, such as habitat preferences, blooming periods, and self-fertilization abilities have been documented. Genetic data is becoming essential for developing effective conservation strategies to prevent the disappearance of threatened orchids from the wild. Using a target capture method with the Orchidaceae963 baitset, we assessed the genetic diversity of eight wild populations and five cultivated sources of B. purpurea. Our findings reveal two areas of concern; S1 which forms a distinct genetic cluster, and E3, where inbreeding rates are notably high. Additionally, three of the five cultivated sources showed significant differentiation from the wild populations, highlighting the need for more diverse maternal lines in cultivation efforts. These results emphasize the critical role of genetic assessments in informing conservation strategies for threatened orchid populations.

Emerging research in mammals supports relationships between an animal’s health, including the stress response and cognition, and its gut microbiome. Most of what is known about this “microbiota-gut-brain-HPA axis” stems from captive mammalian research, while these relationships are largely untested in wild, non-mammalian populations. To test this in avian taxa, I conducted a series of studies with captive Zebra Finches (Taeniopygia guttata) and a wild population of Northern Cardinals (Cardinalis cardinalis). First, I quantified performance by Zebra Finches on cognitive tasks measuring learning and memory for comparison to alpha and beta diversity of the gut microbiome sampled via cloacal swab. Performance on cognitive tasks related to beta diversity but not alpha diversity, providing some of the first evidence of an avian microbiota-gut-brain axis. Next, testing for relationships between host fitness and the microbiome, I sought baseline relationships between free-living cardinals’ microbiomes and their sexual ornamentation, stress response, and body condition index. Bacterial diversity related to individual variation in body condition and several sexual ornaments, but not glucocorticoid concentrations. Finally, in an empirical test that an acute stress response can cause microbiome dysbiosis, I captured wild cardinals to sample their gut microbiome, stress response, body condition, and beak ornamentation, then recaptured and resampled individuals after ~11 days. Between captures, I administered one of two challenges to each cardinal: a temporary hold of an additional hour in a cage post-capture, repeated simulated territorial intrusions (STIs), or no challenge (as a control). Challenge type had no effect on change in alpha diversity between sample timepoints, but it had a significant impact on microbiome dissimilarity assessed by beta diversity between timepoints. Overall, the birds that showed the largest beta diversity and greatest decrease in alpha diversity between samples experienced the greatest increase in CORT scope; there were mixed results supporting a link between a reduction in beak ornamentation and microbiome dysbiosis. This is some of the first evidence of a proximate effect of a fitness challenge on the microbiome of an adult free-living songbird, with concurrent data on shifts in glucocorticoids, body condition, and ornamentation.

Analysis of fossilized Triceratops horridus remains within the Chicxulub Event Deposit of the uppermost Hell Creek Formation, and footprints of non-avian dinosaurs and flying reptiles from the excavated paleo surface underlying the Cretaceous-Tertiary (K/T) Boundary as marked by the Iridium anomaly, is used to interpret the very last moments of the terminal Cretaceous Period on the latest paleo surface available.
The research included characterization of the Triceratops’ bone histology and taphonomy, in addition to the preservation and diversity of the footprints. The data is used to interpret a “temporal snapshot” of the last days to weeks of the Late Cretaceous, offering insight to the site`s paleoenvironment immediately prior to the K/T impact event. Data from the Triceratops histological analysis indicates the animal died in the Spring, coinciding with the end of the Cretaceous. The tracks indicate a diverse non-avian dinosaur population composed of several families and breeding age individuals.

A common topological data analysis approach used in the experimental sciences involves creating machine learning pipelines that incorporate discriminating topological features derived from persistent homology (PH) of data samples, encoded in persistence diagrams (PDs) and associated topological feature vectors. Often the most computationally demanding step is computing PH through an algorithmic process known as boundary matrix reduction. In this work, we introduce several methods to generate topological feature vectors from unreduced boundary matrices. We compared the performance of classifiers trained on vectorizations of unreduced PDs to vectorizations of fully-reduced PDs across several benchmark ML datasets. We discovered that models trained on PDs built from unreduced diagrams can perform on par and even outperform those trained on full-reduced diagrams. This observation suggests that machine learning pipelines which incorporate topology-based features may benefit in terms of computational cost and performance by utilizing information contained in unreduced boundary matrices.

Glioblastoma multiforme (GBM) is an aggressive and highly resistant brain tumour, necessitating advanced treatment approaches to improve patient outcomes. This thesis provides a comprehensive review of recent advancements in GBM treatment, including innovations in treatment planning, radiation therapy, and their impacts on patient survival. The study also involves a detailed analysis of five GBM patients, examining critical dosimetric and radiobiological parameters, including Dose Volume Histogram, CT and MRI Images, T1, T2, T3 and T4 images. These parameters are analyzed using key radiobiological models, such as the linear-quadratic model, and factors like α/β, dose per fraction, and survival fractions. Through this data analysis, the study aims to evaluate the effectiveness of the treatment protocols and their impact on tumour control probability (TCP) and normal tissue complication probability (NTCP). The results will contribute to the understanding of GBM radiotherapy outcomes and provide insights for optimizing future treatment strategies.

This study applies the Response Escalation Paradigm (REP) to examine jealousy scores across five stages of increasing relationship threat (Huelsnitz et al., 2018). Participants rated their jealousy in scenarios involving a romantic partner with either a human or AI rival in virtual reality (VR), among other conditions. Consistent with hypothesis 1, jealousy rates increased across the stages in each condition. Consistent with hypothesis 2, people reported higher jealousy for the human rival in VR compared to the AI rival in VR at Stage 1. Inconsistent with hypothesis 3, participants did not experience faster escalation (the rate of increase in jealousy as the level of threat increases across the scenarios) for the human rival in VR relative to the AI rival in VR. Exploratory analyses did not reveal significant gender differences in jealousy responses. Overall, results indicate that individuals feel jealous about AI rivals as they do with human rivals.

Microplastics are a ubiquitous pollutant that has emphasized major concern for several benthic ecosystems and for the species that inhabit them especially as temperatures have begun to warm at an exponential rate. This study has investigated the abundance and trophic transfer intensity of microplastics through exposure experimentation to two different benthal organisms, the stone crab (Menippe mercenaria) and hard clam (Mercenaria mercenaria), under three different temperature gradients. Within a laboratory setting, hard clams were exposed to a concentration of different sizes and types of microplastics in three different temperatures to observe the accumulation rate of these particles from direct ingestion. The exposed clams were then fed to predatory stone crabs from the Indian River Lagoon, under the same three temperature treatments, to detect MP trophic transfer. To examine the disposition of ingested plastics, histology and fluorescent microscopy were used to quantify the locations and numbers of microplastics in the tissues.

This study investigates the spatial disparities in flood risk and social vulnerability across 66,543 census tracts in the Conterminous United States (CONUS), emphasizing urban–rural differences. Utilizing the American Community Survey (ACS) 2016–2020 data, we focused on 16 social factors representing socioeconomic status, household composition, racial and ethnic minority status, and housing and transportation access. Principal Component Analysis (PCA) reduced these variables into five principal components: Socioeconomic Disadvantage, Elderly and Disability, Housing Density and Vehicle Access, Youth and Mobile Housing, and Group Quarters and Unemployment. An additive model created a comprehensive Social Vulnerability Index (SVI). Statistical analysis, including the Mann–Whitney U test, indicated significant differences in flood risk and social vulnerability between urban and rural areas. Spatial cluster analysis using Local Indicators of Spatial Association (LISA) revealed significant high flood risk and social vulnerability clusters, particularly in urban regions along the Gulf Coast, Atlantic Seaboard, and Mississippi River. Global and local regression models, including Ordinary Least Squares (OLS) and Geographically Weighted Regression (GWR), highlighted social vulnerability’s spatial variability and localized impacts on flood risk. The results showed substantial regional disparities, with urban areas exhibiting higher flood risks and social vulnerability, especially in southeastern urban centers.

We propose an approach to the quantization of the interior of a Schwarzschild black hole, represented by a Kantowski-Sachs (KS) framework, by requiring its covariance under a notion of residual diffeomorphisms. We solve for the family of Hamiltonian constraint operators satisfying the associated covariance condition, in addition to parity covariance, preservation of the Bohr Hilbert space of Loop Quantum KS and a correct (naïve) classical limit. We further explore imposing minimality of the number of terms, and compare the solution with other Hamiltonian constraints proposed for Loop Quantum KS in the literature, with special attention to a most recent case. In addition, we discuss a lapse commonly chosen to decouple the evolution of the two degrees of freedom of the model, yielding exact solubility of the model, and we show that such choice can indeed be quantized as an operator densely defined on the Bohr Hilbert space, but must include an infinite number of shift operators. Also, we show the reasons why we call the classical limit “naïve”, and point this out as a reason for one limitation of some present prescriptions.

The goal of these studies was to quantify mechanical properties of elasmobranch (sharks and batoids) skin to understand the functional relationships between mechanics and morphology, and how these correspond to differences in swimming and ecology. I relate mechanical behaviors with morphological structures to elucidate the underlying contributions of the skin toward elasmobranch skin mechanics. I mechanically tested skin in uniaxial tension to failure to assess the tensile strain at maximum load (extensibility), ultimate tensile strength, Young’s Modulus of elasticity (stiffness), and toughness among diverse groups of elasmobranchs. Across three chapters, I compare mechanical behaviors of the skin among species of sharks and batoids (separately) among body regions, and between sexes and axes of stress (longitudinal and hoop). Among 20 shark species, I quantified mechanical properties among ecomorphotypes and ontogenetically (across three maturity stages) and found that mechanical behaviors increase ontogenetically and are governed by two different underlying trends (maturity and ecomorphology). I found that shark skin oriented in the hoop direction was stronger and stiffer compared to skin oriented longitudinally, as hoop-oriented skin maintains internal volume and hydrostatic pressure by resisting deformation. Shark skin oriented longitudinally was more extensible, allowing for increased stretchability anteroposterior as a shark’s body undulates along the longitudinal axis. Dermal denticles (placoid scales), tooth-like structures of enameloid and dentine, are rooted in the stratum compactum layer of the dermis, embedded in a collagen fiber network.