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"This work was supported by the Center for Energy Policy Research of the M.I.T. Energy Laboratory."

Time series analysis of Synthetic Aperture Radar Interferometry (InSAR) data has become an important scientific tool for monitoring and measuring the displacement of Earth’s surface due to a wide range of phenomena, including earthquakes, volcanoes,landslides, changes in ground water levels, and wetlands. Time series analysis is a product of interferometric phase measurements, which become ambiguous when the observed motion is larger than half of the radar wavelength. Thus, phase observations must first be unwrapped in order to obtain physically meaningful results. Persistent Scatterer Interferometry (PSI), Stanford Method for Persistent Scatterers (StaMPS), Short Baselines Interferometry (SBAS) and Small Temporal Baseline Subset (STBAS)algorithms solve for this ambiguity using a series of spatio-temporal unwrapping algorithms and filters. In this dissertation, I improve upon current phase unwrapping algorithms, and apply the PSI method to study subsidence in Mexico City. PSI was used to obtain unwrapped deformation rates in Mexico City (Chapter 3),where ground water withdrawal in excess of natural recharge causes subsurface, clay-rich sediments to compact. This study is based on 23 satellite SAR scenes acquired between January 2004 and July 2006. Time series analysis of the data reveals a maximum line-of-sight subsidence rate of 300mm/yr at a high enough resolution that individual subsidence rates for large buildings can be determined. Differential motion and related structural damage along an elevated metro rail was evident from the results. Comparison of PSI subsidence rates with data from permanent GPS stations indicate root mean square(RMS) agreement of 6.9 mm/yr, about the level expected based on joint data uncertainty.The Mexico City results suggest negligible recharge, implying continuing degradation and loss of the aquifer in the third largest metropolitan area in the world. Chapters 4 and 5 illustrate the link between time series analysis and three-dimensional (3-D) phase unwrapping. Chapter 4 focuses on the unwrapping path.Unwrapping algorithms can be divided into two groups, path-dependent and path-independent algorithms. Path-dependent algorithms use local unwrapping functions applied pixel-by-pixel to the dataset. In contrast, path-independent algorithms use global optimization methods such as least squares, and return a unique solution. However, when aliasing and noise are present, path-independent algorithms can underestimate the signal in some areas due to global fitting criteria. Path-dependent algorithms do not underestimate the signal, but, as the name implies, the unwrapping path can affect the result. Comparison between existing path algorithms and a newly developed algorithm based on Fisher information theory was conducted. Results indicate that Fisher information theory does indeed produce lower misfit results for most tested cases. Chapter 5 presents a new time series analysis method based on 3-D unwrapping of SAR data using extended Kalman filters. Existing methods for time series generation using InSAR data employ special filters to combine two-dimensional (2-D) spatial unwrapping with one-dimensional (1-D) temporal unwrapping results. The new method,however, combines observations in azimuth, range and time for repeat pass interferometry. Due to the pixel-by-pixel characteristic of the filter, the unwrapping path is selected based on a quality map. This unwrapping algorithm is the first application of extended Kalman filters to the 3-D unwrapping problem. Time series analyses of InSAR data are used in a variety of applications with different characteristics. Consequently, it is difficult to develop a single algorithm that can provide optimal results in all cases, given that different algorithms possess a unique set of strengths and weaknesses. Nonetheless, filter-based unwrapping algorithms such as the one presented in this dissertation have the capability of joining multiple observations into a uniform solution, which is becoming an important feature with continuously growing datasets.

<p>Programmed death is often associated with a bacterial stress response. This behavior appears paradoxical, as it offers no benefit to the individual. This paradox can be explained if the death is `altruistic': the sacrifice of some cells can benefit the survivors through release of `public goods'. However, the conditions where bacterial programmed death becomes advantageous have not been unambiguously demonstrated experimentally. Here, I determined such conditions by engineering tunable, stress-induced altruistic death in the bacterium Escherichia coli. Using a mathematical model, we predicted the existence of an optimal programmed death rate that maximizes population growth under stress. I further predicted that altruistic death could generate the `Eagle effect', a counter-intuitive phenomenon where bacteria appear to grow better when treated with higher antibiotic concentrations. In support of these modeling insights, I experimentally demonstrated both the optimality in programmed death rate and the Eagle effect using our engineered system. These findings fill a critical conceptual gap in the analysis of the evolution of bacterial programmed death, and have implications for a design of antibiotic treatment.</p> / Dissertation

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There has been much discussion regarding whether the capability to perceive speech is uniquely human. The “Speech is Special” (SiS) view proposes that humans possess a specialized cognitive module for speech perception (Mann & Liberman, 1983). In contrast, the “Auditory Hypothesis” (Kuhl, 1988) suggests spoken-language evolution took advantage of existing auditory-system capabilities. In support of the Auditory Hypothesis, there is evidence that Panzee, a language-trained chimpanzee (Pan troglodytes), perceives speech in synthetic “sine-wave” and “noise-vocoded” forms (Heimbauer, Beran, & Owren, 2011). Human comprehension of these altered forms of speech has been cited as evidence for specialized cognitive capabilities (Davis, Johnsrude, Hervais-Adelman, Taylor, & McGettigan, 2005). In light of Panzee’s demonstrated abilities, three experiments extended these investigations of the cognitive processes underlying her speech perception. The first experiment investigated the acoustic cues that Panzee and humans use when identifying sine-wave and noise-vocoded speech. The second experiment examined Panzee’s ability to perceive “time-reversed” speech, in which individual segments of the waveform are reversed in time. Humans are able to perceive such speech if these segments do not much exceed average phoneme length. Finally, the third experiment tested Panzee’s ability to generalize across both familiar and novel talkers, a perceptually challenging task that humans seem to perform effortlessly. Panzee’s performance was similar to that of humans in all experiments. In Experiment 1, results demonstrated that Panzee likely attends to the same “spectro-temporal” cues in sine-wave and noise-vocoded speech that humans are sensitive to. In Experiment 2, Panzee showed a similar intelligibility pattern as a function of reversal-window length as found in human listeners. In Experiment 3, Panzee readily recognized words not only from a variety of familiar adult males and females, but also from unfamiliar adults and children of both sexes. Overall, results suggest that a combination of general auditory processing and sufficient exposure to meaningful spoken language is sufficient to account for speech-perception evidence previously proposed to require specialized, uniquely human mechanisms. These findings in turn suggest that speech-perception capabilities were already present in latent form in the common evolutionary ancestors of modern chimpanzees and humans.

DNA-based vaccines represent a novel method of immunization that has been demonstrated to induce immune responses in animals against a variety of plasmid encoded antigens and following a number of different methods of vaccine delivery. We characterized the immune response to DNA-based vaccines encoding intracellular, membrane anchored (cell associated) and extracellular (secreted) forms of glycoprotein D (gD), an antigen from the viral envelope of the bovine herpesvirus-1 (BHV-1). Intramuscular injection of mice with plasmids encoding secreted or cell associated forms of this antigen led to seroconversion and a predominance of splenic IFN ã. Mice receiving plasmids encoding cell associated or secreted antigens displayed a predominance of IgG2a and IgG 1, respectively. The predominant serum isotype correlated with the cytokine and antibody isotype profiles within the draining lymph node. We demonstrated modulation of immune responses in mice following co-delivery of plasmids encoding a secreted form of gD and each of eight different murine cytokines (IL-1á, IL-12, IL-4, IL-6, IL-10, GM-CSF, IFN ã, TNF á). Plasmids encoding GM-CSF, TNF á, IL-4 and IL-6 demonstrated the capacity to enhance serum IgG titers and seroconversion efficiency. Plasmids encoding IFN ã and TNF á increased levels of serum IgG2a in mice. Varying the dose of plasmids encoding GM-CSF enhanced (10 [mu]g) or suppressed (50 [mu]g) serum antibody levels and induced significant increases in IL-4 levels in the spleen and draining lymph nodes. High doses of GM-CSF (50 [mu]g) increased the levels of serum IgG2a after boosting. Co-administration of plasmids encoding IFN ã either reduced (10 [mu]g) or enhanced (50 [mu]g) serum antibody levels and elevated mean serum IgG 2a levels. Finally, we investigated the potential for plasmids encoding the secreted form of gD to elicit immune responses in passively immune mice. We demonstrated that a single intramuscular immunization of passively immune C3H.HeN or C57BL/6 mice with plasmids encoding the secreted form of BHV-1 gD resulted in the development of both cell-mediated and humoral immunity.

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