A Search for Muon Neutrinos in Coincidence with Gamma-Ray Bursts in the Southern Hemisphere Sky Using the IceCube Neutrino Observatory

The origin of observed ultra-high energy cosmic rays (UHECRs, energies in excess of $10^{18.5}$ eV) remains unknown, as extragalactic magnetic fields deflect these charged particles from their true origin. Interactions of these UHECRs at their source would invariably produce high energy neutrinos. As these neutrinos are chargeless and nearly massless, their propagation through the universe is unimpeded and their detection can be correlated with the origin of UHECRs. Gamma-ray bursts (GRBs) are one of the few possible origins for UHECRs, observed as short, immensely bright outbursts of gamma-rays at cosmological distances. The energy density of GRBs in the universe is capable of explaining the measured UHECR flux, making them promising UHECR sources. Interactions between UHECRs and the prompt gamma-ray emission of a GRB would produce neutrinos that would be detected in coincidence with the GRB’s gamma-ray emission. The IceCube Neutrino Observatory can be used to search for these neutrinos in coincidence with GRBs, detecting neutrinos through the Cherenkov radiation emitted by secondary charged particles produced in neutrino interactions in the South Pole glacial ice. Restricting these searches to be in coincidence with GRB gamma-ray emis- sion, analyses can be performed with very little atmospheric background. Previous searches have focused on detecting muon tracks from muon neutrino interactions fromthe Northern Hemisphere, where the Earth shields IceCube’s primary background of atmospheric muons, or spherical cascade events from neutrinos of all flavors from the entire sky, with no compelling neutrino signal found. Neutrino searches from GRBs with IceCube have been extended to a search for muon tracks in the Southern Hemisphere in coincidence with 664 GRBs over five years of IceCube data in this dissertation. Though this region of the sky contains IceCube’s primary background of atmospheric muons, it is also where IceCube is most sensitive to neutrinos at the very highest energies as Earth absorption in the Northern Hemisphere becomes relevant. As previous neutrino searches have strongly constrained neutrino production in GRBs, a new per-GRB analysis is introduced for the first time to discover neutrinos in coincidence with possibly rare neutrino-bright GRBs. A stacked analysis is also performed to discover a weak neutrino signal distributed over many GRBs. Results of this search are found to be consistent with atmospheric muon backgrounds. Combining this result with previously published searches for muon neutrino tracks in the Northern Hemisphere, cascade event searches over the entire sky, and an extension of the Northern Hemisphere track search in three additional years of IceCube data that is consistent with atmospheric backgrounds, the most stringent limits yet can be placed on prompt neutrino production in GRBs, which increasingly disfavor GRBs as primary sources of UHECRs in current GRB models.

Comparative transcriptome profiling of human foreskin fibroblasts infected with the Sylvio and Y strains of Trypanosoma cruzi

Trypanosoma cruzi, the causative agent of Chagas Disease, is phylogenetically distributed into nearly identical genetic strains which show divergent clinical presentations including differences in rates of cardiomyopathy in humans, different vector species and transmission cycles, and differential congenital transmission in a mouse model. The population structure of these strains divides into two groups, which are geographically and clinically distinct. The aim of this study was to compare the transcriptome of two strains of T. cruzi, Sylvio vs. Y to identify differences in expression that could account for clinical and biochemical differences. We collected and sequenced RNA from T. cruzi-infected and control Human Foreskin Fibroblasts at three timepoints. Differential expression analysis identified gene expression profiles at different timepoints in Sylvio infections, and between Sylvio and Y infections in both parasite and host. The Sylvio strain parasite and the host response to Sylvio infection largely mirrored the host-pathogen interaction seen in our previous Y strain work. IL-8 was more highly expressed in Sylvio-infected HFFs than in Y-infected HFFs.