Quantifying the Effects of Measures to Control Highly Pathogenic Avian Influenza H5N1 in Poultry in Southeast Asia

Despite the ongoing efforts to contain its spread, H5N1 is now considered endemic within poultry in various settings worldwide, threatening both the livelihoods of those involved in poultry production in affected countries and posing a continuous public health risk. The reasons for the varying levels of success in controlling H5N1 in Southeast Asia need to be better understood. In this thesis, various different methods of quantifying the effects of individual control measures, using the types of data available in various different contexts, are discussed and applied. In the first half of this thesis a spatio-temporal survival model is fitted to H5N1 outbreak surveillance data from Vietnam and Thailand using a Bayesian framework in order to account for unobserved infection times. Following vaccination in Vietnam it was found that transmissibility had been successfully reduced but, during a wave of outbreaks in 2007, that this coincided with a reduction in the rate of at which outbreaks were reported following the introduction of infection, limiting the overall impact this reduction in transmissibility had on the total epidemic size. In Thailand, active surveillance was found to be successful in contributing to the control of infection. Furthermore, backyard producers, whilst responsible for the majority of outbreaks, were, on average, less likely to transmit infection than those involved in more intensive production. In the second half of the thesis, the use of final size methods to assess the effectiveness of vaccination from trial data is explored. This involved an investigation into the effects of different assumptions regarding the action by which vaccination confers immunity and fitting estimates of transmissibility to data collected from outbreak investigations in the context of a field trial of vaccination in Indonesia, where, making strong assumptions about the underlying infection process, a reduction in both within and between flock transmissibility was detected for outbreaks occurring in areas where vaccination was being carried out

Method for deducing anisotropic spin-exchange rates

Using measured spin-transfer rates from alkali atoms to He-3, combined with spin-relaxation rates of the alkali atoms due to He-3 and He-4, it should be possible to differentiate between isotropic and anisotropic spin-exchange. This would give a fundamental limit on the He-3 polarization attainable in spin-exchange optical pumping. For K-He, we find the limit to be 0.90+-0.11

Circular Dichroism of RbHe and RbN2_2 Molecules

We present measurements of the circular dichroism of optically pumped Rb vapor near the D1 resonance line. Collisions with the buffer gases $^3$He and N$_2$ reduce the transparency of the vapor, even when fully polarized. We use two methods to measure this effect, show that the He results can be understood from RbHe potential curves, and show how this effect conspires with the spectral profile of the optical pumping light to increase the laser power demands for optical pumping of very optically thick samples

Effects of Nitrogen Quenching Gas on Spin-Exchange Optical Pumping of He-3

We consider the degree of conservation of nuclear spin polarization in the process of optical pumping under typical spin-exchange optical pumping conditions. Previous analyses have assumed that negligible nuclear spin precession occurs in the brief periods of time the alkali-metal atoms are in the excited state after absorbing photons and before undergoing quenching collisions with nitrogen molecules. We include excited-state hyperfine interactions, electronic spin relaxation in collisions with He and N_2, spontaneous emission, quenching collisions, and a simplified treatment of radiation trapping

Deterministic entanglement of two neutral atoms via Rydberg blockade

We demonstrate the first deterministic entanglement of two individually addressed neutral atoms using a Rydberg blockade mediated controlled-NOT gate. Parity oscillation measurements reveal an entanglement fidelity of $F=0.58\pm0.04$, which is above the entanglement threshold of $F=0.5$, without any correction for atom loss, and $F=0.71\pm0.05$ after correcting for background collisional losses. The fidelity results are shown to be in good agreement with a detailed error model.Comment: 4 figure

Stellar Mixing and the Primordial Lithium Abundance

We compare the properties of recent samples of the lithium abundances in halo stars to one another and to the predictions of theoretical models including rotational mixing, and we examine the data for trends with metal abundance. We find from a KS test that in the absence of any correction for chemical evolution, the Ryan, Norris, & Beers (1999} sample is fully consistent with mild rotational mixing induced depletion and, therefore, with an initial lithium abundance higher than the observed value. Tests for outliers depend sensitively on the threshold for defining their presence, but we find a 10$--$45% probability that the RNB sample is drawn from the rotationally mixed models with a 0.2 dex median depletion (with lower probabilities corresponding to higher depletion factors). When chemical evolution trends (Li/H versus Fe/H) are treated in the linear plane we find that the dispersion in the RNB sample is not explained by chemical evolution; the inferred bounds on lithium depletion from rotational mixing are similar to those derived from models without chemical evolution. We find that differences in the equivalent width measurements are primarily responsible for different observational conclusions concerning the lithium dispersion in halo stars. The standard Big Bang Nucleosynthesis predicted lithium abundance which corresponds to the deuterium abundance inferred from observations of high-redshift, low-metallicity QSO absorbers requires halo star lithium depletion in an amount consistent with that from our models of rotational mixing, but inconsistent with no depletion.Comment: 39 pages, 9 figures; submitted Ap