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This dissertation presents several works on developing novel plasmonic based techniques for protein detections on the last two aspects to extend the application field. A fast electrochemically controlled plasmonic detection technique is first developed with the capability of monitoring electrochemical signal with nanosecond response time. The study reveals that the conformational gating of electron transfer in a redox protein (cytochrome c) takes place over a broad range of time scales (sub-µs to ms). The second platform integrates ultra-low volume piezoelectric liquid dispensing and plasmonic imaging detection to monitor different protein binding processes simultaneously with low sample cost. Experiment demonstrates the system can observe binding kinetics in 10×10 microarray of 6 nL droplet, with variations of kinetic rate constants among spots less than ±5%. A focused plasmonic imaging system with bi-cell algorithm is also proposed for spatial resolution enhancement. The two operation modes, scanning mode and focus mode, can be applied for different purposes. Measurement of bacterial aggregation demonstrates the higher spatial resolution. Detections of polystyrene beads binding and 50 nm gold nanoparticles oscillation show a high signal to noise ratio of the system.
The real properties of protein rely on its dynamic personalities. The above works shed light upon fast and high throughput detection of protein kinetics, and enable more applications for plasmonic imaging techniques. It is anticipated that such methods will help to invoke a new surge to unveil the mysteries of biological activities and chemical process.
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Three novel image-based methods for quantitative real time environmental monitoring were introduced and the sensing principle, sensor performances were evaluated through simulation and field tests. The first sensing principle uses surface plasmon resonance (SPR) image and home-made molecular sieve (MS) column to realize real time chemical separation and detection. SPR is sensitive and non-specific, which makes it a desirable optical method for sensitive biological and chemical sensing, the miniaturized MS column provides small area footprint and makes it possible for SPR to record images of the whole column area. The innovative and system level integration approach provide a new way for simultaneous chemical separation and detection. The second sensor uses scattered laser light, Complementary metal-oxide-semiconductor (CMOS) imager and image processing to realize real-time particulate matter (PM) sensing. Complex but low latency algorithm was developed to obtain real time information for PM including PM number, size and size distribution. The third sensor uses gradient based colorimetric sensor, absorbance light signal and image processing to realize real-time Ozone sensing and achieved high sensitivity and substantially longer lifetime compared to conventional colorimetric sensors. The platform provides potential for multi-analyte integration and large-scale consumer use as wearable device.
The three projects provide novel, state-of-the-art and sensitive solutions for environmental and personal exposure monitoring. Moreover, the sensing platforms also provide tools for clinicians and epidemiologists to conduct large scale clinical studies on the adverse health effects of pollutants on various kinds of diseases.
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This dissertation presents a work to develop optical methods for studying cell mechanics which encompasses four applications. Surface plasmon resonance microscopy based optical method has been applied to image intracellular motions and cell mechanical motion. This label-free technique enables ultrafast imaging with extremely high sensitivity in detecting cell deformation. The technique was first applied to study intracellular transportation. Organelle transportation process and displacement steps of motor protein can be tracked using this method. The second application is to study heterogeneous subcellular membrane displacement induced by membrane potential (de)polarization. The application can map the amplitude and direction of cell deformation. The electromechanical coupling of mammalian cells was also observed. The third application is for imaging electrical activity in single cells with sub-millisecond resolution. This technique can fast record actions potentials and also resolve the fast initiation and propagation of electromechanical signals within single neurons. Bright-field optical imaging approach has been applied to the mechanical wave visualization that associated with action potential in the fourth application. Neuron-to-neuron viability of membrane displacement was revealed and heterogeneous subcellular response was observed.
All these works shed light on the possibility of using optical approaches to study millisecond-scale and sub-nanometer-scale mechanical motions. These studies revealed ultrafast and ultra-small mechanical motions at the cellular level, including motor protein-driven motions and electromechanical coupled motions. The observations will help understand cell mechanics and its biological functions. These optical approaches will also become powerful tools for elucidating the interplay between biological and physical functions.
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Fourteen native lizard species inhabit the desert surrounding Phoenix, AZ, USA, but only two species persist within heavily developed areas. This pattern is best explained by a combination of socioeconomic status, land cover, and location. Lizard diversity is highest in affluent areas and lizard abundance is greatest near large patches of open desert. The percentage of building cover has a strong negative impact on both diversity and abundance. Despite Phoenix's intense urban heat island effect, which strongly constrains the potential activity and microhabitat use of lizards in summer, thermal patterns have not yet impacted their distribution and relative abundance at larger scales.
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The study finds that urbanization in Las Vegas produces a classic urban heat island (UHI) at night but a minor cooling during the day. A further analysis of the surface energy balance shows that the decrease in surface Albedo and increase effective emissivity play an important role in shaping the local climate change over urban areas. The emerging urban structures slow down the diurnal wind circulation over the city due to an increased effective surface roughness. This leads to a secondary modification of temperature due to the interaction between the mechanical and thermodynamic effects of urbanization.
The simulations for the five desert cities for 1985 and 2010 further confirm a common pattern of the climatic effect of urbanization with significant nighttime warming and moderate daytime cooling. This effect is confined to the urban area and is not sensitive to the size of the city or the detail of land cover in the surrounding areas. The pattern of nighttime warming and daytime cooling remains robust in the simulations for the future climate of the five cities using the projected 2030 land-use maps. Inter-city differences among the five urban areas are discussed.
The Kilombero Valley lies at the intersection of a network of protected areas that cross Tanzania. The wetlands and woodlands of the Valley, as well as the forest of surrounding mountains are abundant in biodiversity and are considered to be critical areas for conservation. This area, however, is also the home to more than a half million people, primarily poor smallholder farmers. In an effort to support the livelihoods and food security of these farmers and the larger Tanzanian population, the country has recently targeted a series of programs to increase agricultural production in the Kilombero Valley and elsewhere in the country. Bridging concepts and methods from land change science, political ecology, and sustainable livelihoods, I present an integrated assessment of the linkages between development and conservation efforts in the Kilombero Valley and the implications for food security.
This dissertation uses three empirical studies to understand the process of development in the Kilombero Valley and to link the priorities and perceptions of conservation and development efforts to the material outcomes in food security and land change. The first paper of this dissertation examines the changes in land use in the Kilombero Valley between 1997 and 2014 following the privatization of agriculture and the expansion of Tanzania’s Kilimo Kwanza program. Remote sensing analysis reveals a two-fold increase in agricultural area during this short time, largely at the expense of forest. Protected areas in some parts of the Valley appear to be deterring deforestation, but rapid agricultural growth, particularly surrounding a commercial rice plantation, has led to loss of extant forest and sustained habitat fragmentation. The second paper focuses examines livelihood strategies in the Valley and claims regarding the role of agrobiodiversity in food security.
The results of household survey reveal no difference or lower food security among households that diversify their agricultural activities. Some evidence, however, emerges regarding the importance of home gardens and crop diversification for dietary diversity. The third paper considers the competing discourses surrounding conservation and development in the Kilombero Valley. Employing q-method, this paper discerns four key viewpoints among various stakeholders in the Valley. While there are some apparently intractable distinctions between among these discourses, consensus regarding the importance of wildlife corridors and the presence of boundary-crossing individuals provide the promise of collaboration and compromise.
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In the context of noise detection, this work proposes perceptual-based full-reference and no-reference objective image quality metrics by integrating perceptually weighted local noise into a probability summation model. Results are reported on both the LIVE and TID2008 databases. The proposed metrics achieve consistently a good performance across noise types and across databases as compared to many of the best very recent quality metrics. The proposed metrics are able to predict with high accuracy the relative amount of perceived noise in images of different content.
In the context of blur detection, existing approaches are either computationally costly or cannot perform reliably when dealing with the spatially-varying nature of the defocus blur. In addition, many existing approaches do not take human perception into account. This work proposes a blur detection algorithm that is capable of detecting and quantifying the level of spatially-varying blur by integrating directional edge spread calculation, probability of blur detection and local probability summation. The proposed method generates a blur map indicating the relative amount of perceived local blurriness. In order to detect the flat
ear flat regions that do not contribute to perceivable blur, a perceptual model based on the Just Noticeable Difference (JND) is further integrated in the proposed blur detection algorithm to generate perceptually significant blur maps. We compare our proposed method with six other state-of-the-art blur detection methods. Experimental results show that the proposed method performs the best both visually and quantitatively.
This work further investigates the application of the proposed blur detection methods to image deblurring. Two selective perceptual-based image deblurring frameworks are proposed, to improve the image deblurring results and to reduce the restoration artifacts. In addition, an edge-enhanced super resolution algorithm is proposed, and is shown to achieve better reconstructed results for the edge regions.
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First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory.
Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations.
Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases.