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.

No description available.

<p>Bistable switches are commonly observed in the regulation of critical processes such as cell cycles and differentiation. The switches possess two fundamental properties: memory and bimodality. Once switched ON, the switches can remember their ON state despite a drastic drop in stimulus levels. Furthermore, at intermediate stimulus levels with cellular noise, the switches can cause a population to exhibit bimodal distribution of cell states. Till date, experimental studies have focused primarily on cellular mechanisms that generate bistable switches and their impact on cellular dynamics. </p><p>Here, I study emergent bistability due to bacterial interactions with either synthetic gene circuits or antibiotics. A synthetic gene circuit is often engineered by considering the host cell as an invariable "chassis". Circuit activation, however, may modulate host physiology, which in turn can drastically impact circuit behavior. I illustrate this point by a simple circuit consisting of mutant T7 RNA polymerase (T7 RNAP*) that activates its own expression in bacterium Escherichia coli. Although activation by the T7 RNAP* is noncooperative, the circuit caused bistable gene expression. This counterintuitive observation can be explained by growth retardation caused by circuit activation, which resulted in nonlinear dilution of T7 RNAP* in individual bacteria. Predictions made by models accounting for such effects were verified by further experimental measurements. The results reveal a novel mechanism of generating bistability and underscore the need to account for host physiology modulation when engineering gene circuits.</p><p>In the context of antibiotic treatment, I investigate bistability as the underlying mechanism of inoculum effect. The inoculum effect refers to the decreasing efficacy of an antibiotic with increasing bacterial density. Despite its implication for the design of antibiotic treatment strategies, its mechanism remains poorly understood. Here I show that, for antibiotics that target the core replication machinery, the inoculum effect can be explained by bistable bacterial growth. My results suggest that a critical requirement for this bistability is sufficiently fast turnover of the core machinery induced by the antibiotic via the heat shock response. I further show that antibiotics that exhibit the inoculum effect can cause a "band-pass" response of bacterial growth on the frequency of antibiotic treatment, whereby the treatment efficacy drastically diminishes at intermediate frequencies. The results have implications on optimal design of antibiotic treatment.</p> / Dissertation

<p>The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation.</p><p>A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. </p><p>We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible.</p><p>We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. </p><p>We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software.</p><p>We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. </p><p>We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.</p> / Dissertation

In order to extend fluid-based flow control techniques that have been demonstrated at low subsonic speeds to high speed flows, it is necessary to develop actuators having sufficient momentum to control and manipulate high speed flows. Two fluidic actuation approaches are developed where the control jet may reach supersonic velocities and their performance is characterized. The first actuator is a compressible synthetic (zero net mass flux) jet. This is an extension of previous work on synthetic jets with an increase in driver power yielding substantial pressurization of the cavity such that the flow is compressible. The jet is generated using a piston/cylinder actuator, and the effects of variation of the orifice diameter, actuation frequency, and compression ratio are investigated. Operation in the compressible regime uniquely affects the time-dependent cylinder pressure in that the duty cycle of the system shifts such that the suction phase is longer than the blowing phase. The structure of the jet in the near-field is documented using particle image velocimetry and Schlieren flow visualization. In the range investigated, the stroke length is sufficiently long that the jet flow is dominated by a starting jet rather than a starting vortex (which is typical of low-speed synthetic jets). A simple, quasi-static numerical model of the cylinder pressure is developed and is in generally good agreement with the experimental results. This model is used to assess system parameters which could not be measured directly (e.g., the dynamic gas temperature and mass within the cylinder) and for predictions of the actuator performance beyond the current experimental range. Finally, an experiment is described with self-actuated valves mounted into the cylinder head which effectively icrease the orifice area in suction and overcome some of the limitations inherent to compressible operation. The second actuation concept is the combustion-driven jet actuator. This device consists of a small-scale (nominally 1 cc) combustion chamber which is filled with premixed fuel and oxidizer. The mixture is ignited using an integrated spark gap, creating a momentary high pressure burst within the combustor that drives a high-speed jet from an exhaust orifice. At these scales, the entire combustion process is complete within several milliseconds and the cycle resumes when fresh fuel/oxidizer is fed into the chamber and displaces the remaining combustion products. The actuator performance is characterized by using dynamaic measurements of the combustor pressure along with Schlieren flow visualization, limited dynamic thrust measurements, and flame photography. The effects of variation in the following system parameters are investigated: fuel type and mixture ratio, exhaust orifice diameter, chamber aspect ratio, chamber volume, fuel/air flow rate, ignition/combustion frequency, and spark ignition energy. The resulting performance trends are documented and the basis for each discussed. Finally, a proof-of-concept experiment demonstrates the utility of teh combustion-driven jet actuators at low-speed for transitory reattachment of a separated flow over an airfoil at high angles of attack.

In Taiwan, the rubber industry began to bloom from the Japanese Colonial Era, and most of the rubber technologies were originated from Japan. Its evolution began from the rubber parts to the synthetic rubber manufacturing. The most of synthetic rubber manufacturers are cooperated with companies from Japan and US, the rubber industry was allowed to develop vigorously in a short period of time. In contrary to Taiwan, China could only obtain the obsolete rubber technologies and management skills from the Former USSR due to economy sanction during the Cold War period. The rubber industries lagged behind in terms of quality, production efficiency, and management. As China embraced the Socialist Planned Economy after the Communist Victory in Civil War, the marketing and sales made subject to state control and development was being dragged. After the Reform and Opening-Up, although there were a bunch of rubber manufacturers from Japan and western countries started to establish local production activities in China, the foreign investment bogged down after the Tiananman Square Protest in 1989. Only the Taiwanese manufacturers moved their steps to China against the tide with modern production technologies and management skills. The complementary development brought by Taiwan and China contributed significant improvement in quality of Chinese rubber goods and became a story on everybody¡¦s lips on the cooperation of the rubber industries between two sides of Taiwan Strait. Rubber industries are closely related to national defense and consumer goods, which makes themselves equally import to plastic industries. However, due to the labor-intensive nature of rubber industries and the serious lack of labor force in Taiwan in 1990¡¦s, the Taiwanese rubber industries began to move their production sites to China and accelerated the inosculation of the rubber industries in Taiwan and China. As the main raw material of rubber industries, the synthetic rubber is no exceptional either. In the end of 20th Century, China has successfully become the ¡§World Factory¡¨ and the consumption and capacity of synthetic rubber became the top of the world. Then the financial crisis in 2008 turned the China¡¦s policies to concentrate the development of the domestic demand, which made China the ¡§World Market¡¨. In recent years, the relationships between Taiwan and China have been substantially improved. The Economy Cooperation Framework Agreement (ECFA) is officially signed and taking effects, the economical activities and relationships between both sides are expected to be more liberalized than the past. The study is specially focused on the evolution of the marketing channel of the synthetic rubber between Taiwan and China, and how ECFA is going to possibly affect the synthetic rubber industries. The study will integrate the writer¡¦s points of view and the various ideas abstracted from the interviews with the several Associations and main agents/distributors in Taiwan and China in order to infer the trends of future development of rubber industries. With this study, the readers who are in the business are allowed to be more clear about the evolution of the marketing channel of the synthetic rubber industries and the trends of future development, so that the readers can take the initiatives to prepare for the future.