Electronic Thesis or Dissertation

The largest barrier to treatment of HIV-1 infection is the establishment of a viral reservoir constituted mostly by quiescent latently infected CD4+ T cells. This reservoir is formed through two processes: i) the infection of resting CD4+ T cells; both naïve and memory, ii) the infection of activated CD4+ T cells which then become quiescent infected cells. One goal of this project was to understand the gene expression changes occurring in naïve CD4+ T cells following activation and subsequent HIV-1 infection and how this may contribute to the establishment of a latent infection in these cells. Utilizing RNA-Seq and a series of validation assays we have identified several genes which are regulated in opposite directions during activation versus infection which we termed DEOC genes. The DEOC genes include a group of physically- and functionally-associated proteins which are key regulators of T cell activation, the cell cycle, cellular proliferation, and cellular quiescence, suggesting that modulation of these DEOC genes may help transition the infected-activated cell from an activated state to a quiescent/resting state to induce a latent infection.

Salt marshes are highly dynamic ecosystems that rely on multiple environmental and physical drivers that determine species distribution and soil property distribution. However, climate change and human interference are threatening the delicate ecosystem. One of the easiest ways to monitor marsh dynamics is through remote sensing. Traditional methods may not handle the large, non-parametric datasets well and often do not spatially determine areas of uncertainty. This dissertation research developed a framework to map marsh species and predict ground soil properties using multiple remote sensing data sources by integrating modern Object-based Image Analysis (OBIA), machine learning, data fusion, and band indices techniques. It also sought to determine areas of uncertainty in the final outputs and differences between different spectral resolutions. Five machine learning classifiers were examined including Support Vector Machine (SVM) and Random Forest (RF) to map marsh species. Overall results illustrated that RF and SVM typically performed best, especially when using hyperspectral data combined with DEM information. Seven regressors were assessed to map three different soil properties. Again, RF and SVM performed the best no matter the dataset used, or soil property mapped. Soil salinity had r as high as 0.93, soil moisture had r as high as 0.91, and soil organic an r as high as 0.74 when using hyperspectral data.

Lysine-rich KED was previously identified from wounded tobacco (Nicotiana tabacum) leaves before the alignment of protein sequences between NtKED (Nicotiana tabacum KED) and SlKED (Solanum lycopersicum KED) were discovered to display 55.1% identity. Using previously generated SlKED knockout plants by CRISPR/Cas9, we performed biological assays, to investigate the role of KED in wound response to biotic and abiotic stress. Previous studies implied that the KED gene functions as a role in the wound-induced mechanism, as well as suggested that it may also function in the plant defense system against biotic stress and insect herbivory. The results from bioassays using tobacco hornworm (Manduca sexta) have proven inconclusive thus far. Expression of KED is induced not only by mechanical wounding but also by touching such as brushing the leaves, indicating that this gene is sensitive to subtle environmental signal and may be involved in defense response against abiotic stress. To further investigate the KED gene’s role in the plant defense system, biological assays using both specialist and generalist herbivores, transcription analysis using various phytohormone mutant plants, and Evans blue cellular damage assays were performed. Our findings imply that the KED gene does not seem to have a long-term effect on insect herbivory but may have a shortterm anti-feeding effect against insect herbivores. Results from the Evans blue membrane damage assay indicate the KED gene may provide some benefit to mechanically damaged plants in a short-term period post-wounding of leaf tissues. Using the SlKED knockout as genetic tool, we conclude that this gene does not confer resistance to insect herbivores over a long-term but seems to provide a beneficial defense response in the short-term. Our membrane damage assay results also imply that this gene may be involved in membrane stabilization and repair of cellular damage after mechanical wounding.

Making Wonder Women: Recursive Tendencies in Feminist Utopias argues that reduplications of patriarchal hegemonies exist in William Marston’s Wonder Women. Using several close readings of Marston’s original comics as well as three modern (2011, 2017, 2020) reimaginings by Greg Rucka, Grant Morrison, and Daniel Warren Johnson, this thesis highlights how the design of Paradise Island, the Amazons, and Wonder Woman serve to reproduce Rockwellian demands of femininity through the guise of sexual radicalism and the religious rhetoric of liberation through servitude. This culminates in the position that Marston’s feminist ideals calcified into pop-culture a confusing and muddled icon of white colonial feminism.

As the cryptographic community turns its focus toward post-quantum cryptography, the demand for classical cryptographic schemes such as Elliptic Curve Cryptography (ECC) remains high. ECC is mature, well studied, and used in a wide range of applications such as securing visits to web pages through a web browser, Bitcoin, and the Internet of Things (IoT). In this work we present an optimized implementation of the Edwards Curve Digital Signature Algorithm (EdDSA) operations Key Generation and Sign using the Ed25519 parameter on the ARM Cortex-M4, and we discuss the optimization of field and group arithmetic to produce high throughput cryptographic primitives. In addition, we discuss several techniques for optimizing scalar multiplication, and present timing and memory consumption for each, as well as comparisons to other works. Our fastest implementation performs an Ed25519 Key Generation operation in 250,785 cycles and signing in 435,426 cycles utilizing 6.1 kB of additional Read Only Memory (ROM) space.

Bioinformatics tools applied to large-scale genomic datasets have helped develop our understanding of primate phylogenetics. However, it is becoming increasingly evident that biological data are accumulating faster than the current capacity of the bioanthropological community to analyze, integrate, and mine the data. Subsequently, this affects how anthropologists create and distribute knowledge. There is a growing need for more training in bioinformatics within anthropological spaces and the development of user-friendly bioinformatic tools for analysis, mining, and modeling of both local and global datasets. This thesis showcases the use of (applied) bioinformatics tools to construct seven new whole mitochondrial genomes to study primate variation. Furthermore, this thesis entails an investigation of the guenon radiation to develop and document bioinformatics and statistical tools to perform a phylogenetic analysis of the genus Cercopithecus. Finally, the utility of the pipelines for other researchers in the Detwiler Lab Group and the potential for further phylogenetic studies are discussed.

Tiffany Aching and the Witches of the Discworld Series use knowledge that is based on working with and connecting to the natural world instead of against it, primarily through their use of magic without using magic and their use of “headology,” to create the desired effect without detriment to the ecology of the Discworld. This puts them in contrast with the male, Unseen-University wizards, whose magic works against the ecology of the Discworld as it changes and corrupts the world around it. Further, the relationship that Tiffany Aching has within her home, the land she was born in, and her ecology becomes a nexus between the natural world and human communities. This connection between herself and her land is comparable to the one that Ged learns through his journey in Ursula K. Le Guin’s A Wizard of Earthsea. This connection between the authors is not simply a categorical one but one that connects them, their work, and an ideological push against individualism that relies on interconnectedness between species.

This study examined the effect of repetitions per set as a function of changing load (percentage of one-repetition maximum) on the accuracy of intraset repetitions in reserve (RIR) predictions in the back squat and bench press. Twelve resistance trained men completed three multi-set back squat and bench press training sessions that differed in the number of target repetitions (session 1: 10 repetitions; session 2: 8 repetitions; session 3: 6 repetitions). The last set of each session was performed until muscular failure in which subjects verbally indicated when they perceived 4 RIR and 1 RIR. For each RIR prediction, RIRDIFF [perceived RIR - actual RIR] was calculated.
Differences in RIRDIFF were analyzed using both raw RIRDIFF (including positive and negative values) and absolute RIRDIFF (absolute values) via MANOVA and factorial ANOVA. The model controlled for the covariates session-type, percentage of 1RM, and total repetitions per set. Overall, RIR accuracy at the predicted 1 RIR was significantly greater (i.e., lower absolute RIRDIFF) than at the predicted 4 RIR in both the bench press (4 RIR: 1.00 ± 0.18 vs. 1 RIR: 0.69 ± 0.12; p = 0.028) and the squat (4 RIR: 1.43 ± 0.31 vs. 1 RIR: 0.79 ± 0.26; p = 0.007). No covariates significantly affected RIR accuracy (p = 0.085 – 0.518) at the predicted 1 RIR. However, at the predicted 4 RIR, the covariate repetitions per set affected raw RIRDIFF in both the squat (p = 0.007) and bench press (p < 0.001), indicating that subjects tended to overpredict RIR in lower repetition sets and underpredict RIR in higher repetition sets.

The Monaco treatment planning system offers three different dose calculation algorithms for use in calculating 3D treatment plans. These include Monte Carlo (MC), Collapsed Cone (CC) and the pencil beam algorithms. The aim of this study is an in-depth analysis of Monte Carlo and Collapsed Cone dose calculation methods to find the optimal parameters for clinical use for both algorithms.
An end-to-end phantom with inhomogeneities was scanned and the DICOM images were imported into Monaco for contouring and planning. Treatment plans were then created in Monaco for both MC and CC using different permutations of variables for approximately 400 plans. These variables include CT Slice thickness, grid size, statistical uncertainty, and beam energy. Following planning the end-to-end phantom was then irradiated on an Elekta Linac and plans for each beam energy were created. Clinical beam data was then compared to the computed plans for each dose calculation method.

Tropical storms and mid-latitude cyclones are major drivers of coastal change and damage in coastal communities. Beaches act as a first line of defense against storms, as well as provide recreation, contribute to the economy, and serve as ecological habitat for coastal flora and fauna. Throughout the year, meteorological event-driven increases in wave energy result in higher amounts of sediment transport that cause rapid coastal zone morphology alterations and threaten these beach functions. This study uses streamer traps to evaluate cohesionless sediment dynamics in the surf zone and storm-induced morphology change in Boca Raton, Florida. The quantitative and sedimentological characteristics of sediment collected in the bottom streamer trap bins was larger grains with a higher capture weight near the seabed compared to sediment captured in the middle and upper streamer trap bins during both the cold front and the tropical storm. A greater quantity of sediment was captured in transport due to the tropical storm compared to the cold front. Morphology change observed as a result of the cold front included berm erosion, swash zone and foreshore accretion, and erosion beyond the -1.0m contour elevation. Analysis of the morphology observed post-tropical storm included berm accretion, and swash zone and foreshore erosion that continued seaward to the end of the profile. Dean number calculations using pre-cold front sediments and wave parameters predicted erosion, and the post-cold front BMAP measurements confirmed this prediction. Dean number calculations using pre-tropical storm sediments and wave parameters predicted accretion and the post-tropical storm BMAP measurements invalidated this prediction at all capture locations, although above the 1.0m contour the berm did exhibit accretion. Results of this study aim to quantify granulometric differences in event-driven sediment transport in Boca Raton, FL for improved prediction capabilities. Given the current trajectory of climate change, sea-level rise, and increased storm intensity, better understanding the morphological impact of different classes of storms is necessary to ensure and improve coastal resiliency and management.