Senior Thesis

Senior recital for Trevor Vincent, playing the alto saxophone. Accompanied by Mike Benson (saxophone), Sierra Summers (piano), Alfredo Balcacer (guitar), Kelin Gibbons (guitar), Emily Pack (piano/keyboard), Thomas Pratt (bass), and Nick Miner (drums)

Religion, Spirituality and Resilience of HIV Positive Children in Zimbabwe

HIV has widely affected many people including children and young people and has posed a threat to their lives. Various studies have, therefore, focused on bringing about interventions directed at improving the lives of people living with HIV. Religion and spirituality emerge as other factors enhancing the coping capacity of children living with HIV. The study aimed to explore the impact of religion and spirituality on the resilience of HIV positive children in Zimbabwe. The study was qualitative in nature and it targeted clients of a not for profit organizations (NPO) that provides psycho-social support to HIV positive children in Bulawayo, Zimbabwe. The study was informed by the resilience theory which explains the importance of the coping capacity of children in adverse situations. A sample of 24 HIV positive children and three caregivers participated in the study. Data were collected through in-depth interviews, focus group discussions and key informant interviews. The findings reflected that religion and spirituality are crucial in offering psychosocial support to HIV positive children. The key findings indicated that religion and spirituality help with emotional healing, acceptance of HIV status, conflict resolution and strengthens bonds promoting their resilience. However, it was shown that they also have negative impacts including involuntary disclosure, stigma and discrimination, poor adherence to medication and caused depression and anxiety. It was therefore recommended that there is need to create platforms for child participation, promote inclusion of children in religious organizations and sensitize religious leaders on HIV and its effects on the lives of children infected

Unequal mass binary neutron star simulations with neutrino transport: Ejecta and neutrino emission

We present 12 new simulations of unequal mass neutron star mergers. The simulations are performed with the SpEC code, and utilize nuclear-theory-based equations of state and a two-moment gray neutrino transport scheme with an improved energy estimate based on evolving the number density. We model the neutron stars with the SFHo, LS220, and DD2 equations of state (EOS) and we study the neutrino and matter emission of all 12 models to search for robust trends between binary parameters and emission characteristics. We find that the total mass of the dynamical ejecta exceeds 0.01  M⊙ only for SFHo with weak dependence on the mass ratio across all models. We find that the ejecta have a broad electron fraction (Y_e) distribution (≈0.06–0.48), with mean 0.2. Y_e increases with neutrino irradiation over time, but decreases with increasing binary asymmetry. We also find that the models have ejecta with a broad asymptotic velocity distribution (≈0.05–0.7c). The average velocity lies in the range 0.2c−0.3c and decreases with binary asymmetry. Furthermore, we find that disk mass increases with binary asymmetry and stiffness of the EOS. The Y_e of the disk increases with softness of the EOS. The strongest neutrino emission occurs for the models with soft EOS. For (anti) electron neutrinos we find no significant dependence of the magnitude or angular distribution or neutrino luminosity with mass ratio. The heavier neutrino species have a luminosity dependence on mass ratio but an angular distribution which does not change with mass ratio

Discrete and statistical approaches to genetics

This thesis presents a number of major innovations in related but different areas of research. The contributions range along a continuum from mathematical phylogenetics, to development of statistical methodology for detecting recombination and finally to the application of statistical techniques to understand Feline Immunodeficiency Virus (FIV) an important pathogen. An underlying theme is the application of combinatorial and statistical ideas to problems in evolutionary biology and genetics.Chapter 2 and Chapter 3 give a number of results relevant to mathematical phylogenetics, in particular maximum parsimony. Chapter 2 presents a new formulation of maximum parsimony in terms of character subdivision, providing a direct link with the character compatibility problem, also known as the perfect phylogeny problem. Specialization of this result to two characters gives a simple formula based on the intersection graph for calculating the parsimony score for a, pair of characters. Chapter 3 further explores maximum parsimony. In particular, it is shown that a maximum parsimony tree for a sequence of characters minimizes a subtree-prune and regraft (SPR) distance to the sets of trees on which each character is convex. Similar connections are also drawn between the Robinson-Foulds distance and a new variant of Dollo parsimony.Chapter 4 presents an application of the work in Chapters 2 and 3 to develop a statistical test for detecting recombination. An extensive coalescent based simulation study shows that this new test is both robust and powerful in a variety of different circumstances compared to a number of current methods. In fact, a simple model of mutation rate correlation is shown to mislead a number of competing tests, causing recombination to be falsely inferred. Analysis of empirical data sets confirm that the new test is one of the best approaches to distinguish recurrent mutation from recombination.Finally, Chapter 5 uses the test developed in Chapter 4 to localize recombinant breakpoints in 14 genomic strains of FIV taken from a wild population of cougars. Based on the technique, three recombinant strains of FIV are identified. Previous studies have focused on the epidemiology and population structure of the virus and this study shows that recombination has also played an important role in the evolution of FIV

The influence of Schizotypy on Event Related Oscillations in Sensory Gating during early Infant Development

Maternal personality is known to influence childhood risk factors for mental health. More specifically, maternal psychopathologies, such as those on the schizophrenia-spectrum have been associated with P50 sensory gating abilities. Schizotypy is a personality dimension within the general population elevated among schizophrenia-spectrum patients and their first-degree relatives. Sensory gating is the pre-attentional habituation of responses distinguishing between important and irrelevant information. Neurooscillatory deficits have been observed in this ability in individuals diagnosed with schizophrenia. The current study investigated whether mothers with schizotypy (n=33) and their 6-month-old infants (n=38) display reduced evoked-oscillatory activity. The mothers completed the Oxford-Liverpool Inventory of Feelings and Experiences – Short Form as an index of schizotypy dimensionality, which was used to categorise the participants into infants of control mothers and mothers with schizotypy. The paired-tone paradigm: two identical auditory tones (Stimulus 1 and Stimulus 2) played 500ms apart, were used to probe evoked oscillatory activity. Data revealed that although the infants’ evoked-oscillations displayed differences between Stimulus 1 and Stimulus 2, there were no group differences between infants of mothers with schizotypy and of control mothers. Their mothers, however, displayed differences, with reduced power toward Stimulus 1 observed in the mothers with schizotypy between 13-30Hz. These findings are consistent that early sensory processes, such as sensory gating are impaired in schizophrenia-spectrum disorders

Large Trees, Supertrees, and Diversification of the Grass Family

Phylogenetic studies of grasses (Poaceae) are advanced in comparison with most other angiosperm families. However, few studies have attempted to build large phylogenetic trees of the family and use these for evaluating patterns of diversification or other macroevolutionary hypotheses. Two contrasting approaches can be used to generate large trees: supermatrix analyses and supertrees. In this paper, we evaluated the suitability of each of these methods for the study of patterns and processes of evolution in the grasses. We collected data from DDBJ/EMBL/GenBank to determine sequence availability and asked how far we are from a complete generic-level phylogenetic tree of the grasses. We generated almost complete tribal-level supertrees (39 tribes) with over 400 genera using MRP methods, described their major clades, assessed their accuracy, and used them for the study of diversification. We generated a proportional supertree, by modifying the original supertree, to remove sampling bias associated with the original supertree that may affect diversification statistics. We used methods that incorporate information on the topological distribution of taxon diversity from all internal nodes of the phylogenetic tree to show that the grasses have experienced significant variations in diversification rates (M statistic P-value