Matching Items (83)
Description

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

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.

ContributorsConnors, John Patrick (Author) / Turner, Billie Lee (Thesis advisor) / Eakin, Hallie (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2015
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Description
The manipulation of biological targets using synthetic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that act either as probes for studying protein conformational changes or DNA–protein interaction, or as multifunctional radical quenchers.

Fluorescent labeling is of paramount

The manipulation of biological targets using synthetic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that act either as probes for studying protein conformational changes or DNA–protein interaction, or as multifunctional radical quenchers.

Fluorescent labeling is of paramount importance to biological studies of proteins. For the development of new extrinsic small fluorophores, a series of tryptophan analogues has been designed and synthesized. Their pdCpA derivatives have been synthesized for tRNA activation and in vitro protein synthesis. The photophysical properties of the tryptophan (Trp) analogues have been examined, some of which can be selectively monitored even in the presence of multiple native tryptophan residues. Further, some of the Trp analogues form efficient FRET pairs with acceptors such as acridon-2-ylalanine (Acd) or L-(7-hydroxycoumarin-4-yl)ethylglycine (HCO) for the selective study of conformational changes in proteins.

Molecules which can bind with high sequence selectivity to a chosen target in a gene sequence are of interest for the development of gene therapy, diagnostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Stereoselective synthesis of different alanyl nucleobase amino acids is described. Their pdCpA derivatives have been synthesized for tRNA activation and site-specific incorporation into the DNA-binding protein RRM1 of hnRNP LL. It is proposed that the nucleobase moieties in the protein may specifically recognize base sequence in the i-motif DNA through H-bonding and base-stacking interactions.

The mitochondrial respiratory chain accumulates more oxidative damage than any other organelle within the cell. Dysfunction of this organelle is believed to drive the progression of many diseases, thus mitochondria are an important potential drug target. Reactive oxygen species (ROS) are generated when electrons from the respiratory chain escape and interact with oxygen. ROS can react with proteins, lipids or DNA causing cell death. For the development of effective neuroprotective drugs, a series of N-hydroxy-4-pyridones have been designed and synthesized as CoQ10 analogues. All the analogues synthesized were evaluated for their ability to quench lipid peroxidation and reactive oxygen species (ROS).
ContributorsTalukder, Poulami (Author) / Hecht, Sidney M. (Thesis advisor) / Woodbury, Neal (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016
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Description
The quality of real-world visual content is typically impaired by many factors including image noise and blur. Detecting and analyzing these impairments are important steps for multiple computer vision tasks. This work focuses on perceptual-based locally adaptive noise and blur detection and their application to image restoration.

In the context of

The quality of real-world visual content is typically impaired by many factors including image noise and blur. Detecting and analyzing these impairments are important steps for multiple computer vision tasks. This work focuses on perceptual-based locally adaptive noise and blur detection and their application to image restoration.

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.
ContributorsZhu, Tong (Author) / Karam, Lina (Thesis advisor) / Li, Baoxin (Committee member) / Bliss, Daniel (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2016
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Description
The combination of rapid urban growth and climate change places stringent constraints on multisector sustainability of cities. Green infrastructure provides a great potential for mitigating anthropogenic-induced urban environmental problems; nevertheless, studies at city and regional scales are inhibited by the deficiency in modelling the complex transport coupled water and energy

The combination of rapid urban growth and climate change places stringent constraints on multisector sustainability of cities. Green infrastructure provides a great potential for mitigating anthropogenic-induced urban environmental problems; nevertheless, studies at city and regional scales are inhibited by the deficiency in modelling the complex transport coupled water and energy inside urban canopies. This dissertation is devoted to incorporating hydrological processes and urban green infrastructure into an integrated atmosphere-urban modelling system, with the goal to improve the reliability and predictability of existing numerical tools. Based on the enhanced numerical tool, the effects of urban green infrastructure on environmental sustainability of cities are examined.

Findings indicate that the deployment of green roofs will cool the urban environment in daytime and warm it at night, via evapotranspiration and soil insulation. At the annual scale, green roofs are effective in decreasing building energy demands for both summer cooling and winter heating. For cities in arid and semiarid environments, an optimal trade-off between water and energy resources can be achieved via innovative design of smart urban irrigation schemes, enabled by meticulous analysis of the water-energy nexus. Using water-saving plants alleviates water shortage induced by population growth, but comes at the price of an exacerbated urban thermal environment. Realizing the potential water buffering capacity of urban green infrastructure is crucial for the long-term water sustainability and subsequently multisector sustainability of cities. Environmental performance of urban green infrastructure is determined by land-atmosphere interactions, geographic and meteorological conditions, and hence it is recommended that analysis should be conducted on a city-by-city basis before actual implementation of green infrastructure.
ContributorsYang, Jiachuan (Author) / Wang, Zhihua (Thesis advisor) / Kaloush, Kamil (Committee member) / Myint, Soe (Committee member) / Huang, Huei-Ping (Committee member) / Mascaro, Giuseppe (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Sunlight, the most abundant source of energy available, is diffuse and intermittent; therefore it needs to be stored in chemicals bonds in order to be used any time. Photosynthesis converts sunlight into useful chemical energy that organisms can use for their functions. Artificial photosynthesis aims to use the essential chemistry

Sunlight, the most abundant source of energy available, is diffuse and intermittent; therefore it needs to be stored in chemicals bonds in order to be used any time. Photosynthesis converts sunlight into useful chemical energy that organisms can use for their functions. Artificial photosynthesis aims to use the essential chemistry of natural photosynthesis to harvest solar energy and convert it into fuels such as hydrogen gas. By splitting water, tandem photoelectrochemical solar cells (PESC) can produce hydrogen gas, which can be stored and used as fuel. Understanding the mechanisms of photosynthesis, such as photoinduced electron transfer, proton-coupled electron transfer (PCET) and energy transfer (singlet-singlet and triplet-triplet) can provide a detailed knowledge of those processes which can later be applied to the design of artificial photosynthetic systems. This dissertation has three main research projects. The first part focuses on design, synthesis and characterization of suitable photosensitizers for tandem cells. Different factors that can influence the performance of the photosensitizers in PESC and the attachment and use of a biomimetic electron relay to a water oxidation catalyst are explored. The second part studies PCET, using Nuclear Magnetic Resonance and computational chemistry to elucidate the structure and stability of tautomers that comprise biomimetic electron relays, focusing on the formation of intramolecular hydrogen bonds. The third part of this dissertation uses computational calculations to understand triplet-triplet energy transfer and the mechanism of quenching of the excited singlet state of phthalocyanines in antenna models by covalently attached carotenoids.
ContributorsTejeda Ferrari, Marely (Author) / Moore, Ana (Thesis advisor) / Mujica, Vladimiro (Thesis advisor) / Gust, John (Committee member) / Woodbury, Neal (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Ephemeral streams in Arizona that are perpendicularly intersected by the Central Arizona Project (CAP) canal have been altered due to partial or complete damming of the stream channel. The dammed upstream channels have experienced decades long cycles of sediment deposition and waterlogging during storm events causing the development of "green-up"

Ephemeral streams in Arizona that are perpendicularly intersected by the Central Arizona Project (CAP) canal have been altered due to partial or complete damming of the stream channel. The dammed upstream channels have experienced decades long cycles of sediment deposition and waterlogging during storm events causing the development of "green-up" zones. This dissertation examines the biogeomorphological effects of damming ephemeral streams caused by the CAP canal by investigating: (1) changes in the preexisting spatial cover of riparian vegetation and how these changes are affected by stream geometry; (2) green-up initiation and evolution; and (3) changes in plant species and community level changes. To the author's knowledge, this is the only study that undertakes an interdisciplinary approach to understanding the environmental responses to anthropogenically-altered ephemeral stream channels. The results presented herein show that vegetation along the upstream section increased by an average of 200,872 m2 per kilometer of the CAP canal over a 28 year period. Vegetation growth was compared to channel widths which share a quasi-linear relationship. Remote sensing analysis of Landsat TM images using an object-oriented approach shows that riparian vegetation cover gradually increased over 28 years. Field studies reveal that the increases in vegetation are attributed to the artificial rise in local base-level upstream created by the canal, which causes water to spill laterally onto the desert floor. Vegetation within the green-up zone varies considerably in comparison to pre-canal construction. Changes are most notable in vegetation community shifts and abundance. The wettest section of the green-up zone contains the greatest density of woody plant stems, the greatest vegetation volume, and a high percentage of herbaceous cover. Vegetation within wetter zones changed from a tree-shrub to a predominantly tree-herb assemblage, whereas desert shrubs located in zones with intermediate moisture have developed larger stems. Results from this study lend valuable insight to green-up processes associated with damming ephemeral streams, which can be applied to planning future canal or dam projects in drylands. Also, understanding the development of the green-up zones provide awareness to potentially avoiding flood damage to infrastructure that may be unknowingly constructed within the slow-growing green-up zone.
ContributorsHamdan, Abeer (Author) / Schmeeckle, Mark (Thesis advisor) / Myint, Soe (Thesis advisor) / Dorn, Ronald (Committee member) / Stromberg, Juliet (Committee member) / Arizona State University (Publisher)
Created2014
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Description
The healthcare system in this country is currently unacceptable. New technologies may contribute to reducing cost and improving outcomes. Early diagnosis and treatment represents the least risky option for addressing this issue. Such a technology needs to be inexpensive, highly sensitive, highly specific, and amenable to adoption in a clinic.

The healthcare system in this country is currently unacceptable. New technologies may contribute to reducing cost and improving outcomes. Early diagnosis and treatment represents the least risky option for addressing this issue. Such a technology needs to be inexpensive, highly sensitive, highly specific, and amenable to adoption in a clinic. This thesis explores an immunodiagnostic technology based on highly scalable, non-natural sequence peptide microarrays designed to profile the humoral immune response and address the healthcare problem. The primary aim of this thesis is to explore the ability of these arrays to map continuous (linear) epitopes. I discovered that using a technique termed subsequence analysis where epitopes could be decisively mapped to an eliciting protein with high success rate. This led to the discovery of novel linear epitopes from Plasmodium falciparum (Malaria) and Treponema palladium (Syphilis), as well as validation of previously discovered epitopes in Dengue and monoclonal antibodies. Next, I developed and tested a classification scheme based on Support Vector Machines for development of a Dengue Fever diagnostic, achieving higher sensitivity and specificity than current FDA approved techniques. The software underlying this method is available for download under the BSD license. Following this, I developed a kinetic model for immunosignatures and tested it against existing data driven by previously unexplained phenomena. This model provides a framework and informs ways to optimize the platform for maximum stability and efficiency. I also explored the role of sequence composition in explaining an immunosignature binding profile, determining a strong role for charged residues that seems to have some predictive ability for disease. Finally, I developed a database, software and indexing strategy based on Apache Lucene for searching motif patterns (regular expressions) in large biological databases. These projects as a whole have advanced knowledge of how to approach high throughput immunodiagnostics and provide an example of how technology can be fused with biology in order to affect scientific and health outcomes.
ContributorsRicher, Joshua Amos (Author) / Johnston, Stephen A. (Thesis advisor) / Woodbury, Neal (Committee member) / Stafford, Phillip (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Glycans are monosaccharide-based heteropolymers that are found covalently attached to many different proteins and lipids and are ubiquitously displayed on the exterior surfaces of cells. Serum glycan composition and structure are well known to be altered in many different types of cancer. In fact, glycans represent a promising but only

Glycans are monosaccharide-based heteropolymers that are found covalently attached to many different proteins and lipids and are ubiquitously displayed on the exterior surfaces of cells. Serum glycan composition and structure are well known to be altered in many different types of cancer. In fact, glycans represent a promising but only marginally accessed source of cancer markers. The approach used in this dissertation, which is referred to as “glycan node analysis”, is a molecularly bottom-up approach to plasma/serum (P/S) glycomics based on glycan linkage analysis that captures features such as α2-6 sialylation, β1-6 branching, and core fucosylation as single analytical signals.

The diagnostic utility of this approach as applied to lung cancer patients across all stages as well as prostate, serous ovarian, and pancreatic cancer patients compared to certifiably healthy individuals, nominally healthy individuals and/or risk-matched controls is reported. Markers for terminal fucosylation, α2-6 sialylation, β1-4 branching, β1-6 branching and outer-arm fucosylation were most able to differentiate cases from controls. These markers behaved in a stage-dependent manner in lung cancer as well as other types of cancer. Using a Cox proportional hazards regression model, the ability of these markers to predict progression and survival in lung cancer patients was assessed. In addition, the potential mechanistic role of aberrant P/S glycans in cancer progression is discussed.

Plasma samples from former bladder cancer patients with currently no evidence of disease (NED), non-muscle invasive bladder cancer (NMIBC), and muscle invasive bladder cancer (MIBC) along with certifiably healthy controls were analyzed. Markers for α2-6 sialylation, β1-4 branching, β1-6 branching, and outer-arm fucosylation were able to separate current and former (NED) cases from controls; but NED, NMIBC, and MIBC were not distinguished from one another. Markers for α2-6 sialylation and β1-6 branching were able to predict recurrence from the NED state using a Cox proportional hazards regression model adjusted for age, gender, and time from cancer. These two glycan features were found to be correlated to the concentration of C-reactive protein, a known prognostic marker for bladder cancer, further strengthening the link between inflammation and abnormal plasma protein glycosylation.
ContributorsRoshdiferdosi, Shadi (Author) / Borges, Chad R (Thesis advisor) / Woodbury, Neal (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Though DNA nanostructures (DNs) have become interesting subjects of drug delivery, in vivo imaging and biosensor research, however, for real biological applications, they should be ‘long circulating’ in blood. One of the crucial requirements for DN stability is high salt concentration (like ~5–20 mM Mg2+) that is unavailable in a

Though DNA nanostructures (DNs) have become interesting subjects of drug delivery, in vivo imaging and biosensor research, however, for real biological applications, they should be ‘long circulating’ in blood. One of the crucial requirements for DN stability is high salt concentration (like ~5–20 mM Mg2+) that is unavailable in a cell culture medium or in blood. Hence DNs denature promptly when injected into living systems. Another important factor is the presence of nucleases that cause fast degradation of unprotected DNs. The third factor is ‘opsonization’ which is the immune process by which phagocytes target foreign particles introduced into the bloodstream. The primary aim of this thesis is to design strategies that can improve the in vivo stability of DNs, thus improving their pharmacodynamics and biodistribution.

Several strategies were investigated to address the three previously mentioned limitations. The first attempt was to study the effect length and conformation of polyethylene glycol (PEG) on DN stability. DNs were also coated with PEG-lipid and human serum albumin (HSA) and their stealth efficiencies were compared. The findings reveal that both PEGylation and albumin coating enhance low salt stability, increase resistance towards nuclease action and reduce uptake of DNs by macrophages. Any protective coating around a DN increases its hydrodynamic radius, which is a crucial parameter influencing their clearance. Keeping this in mind, intrinsically stable DNs that can survive low salt concentration without any polymer coating were built. Several DNA compaction agents and DNA binders were screened to stabilize DNs in low magnesium conditions. Among them arginine, lysine, bis-lysine and hexamine cobalt showed the potential to enhance DN stability.

This thesis also presents a sensitive assay, the Proximity Ligation Assay (PLA), for the estimation of DN stability with time. It requires very simple modifications on the DNs and it can yield precise results from a very small amount of sample. The applicability of PLA was successfully tested on several DNs ranging from a simple wireframe tetrahedron to a 3D origami and the protocol to collect in vivo samples, isolate the DNs and measure their stability was developed.
ContributorsBanerjee, Saswata (Author) / Yan, Hao (Thesis advisor) / Angell, Austen (Committee member) / Woodbury, Neal (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Deforestation is a common phenomenon in Bangladesh, leaving the country under a great threat of losing its natural habitat. The increasing rate of natural habitat loss has raised questions regarding the country’s forest resource management practices. These practices were originally adopted to protect the forest ecosystem and secure the livelihood

Deforestation is a common phenomenon in Bangladesh, leaving the country under a great threat of losing its natural habitat. The increasing rate of natural habitat loss has raised questions regarding the country’s forest resource management practices. These practices were originally adopted to protect the forest ecosystem and secure the livelihood of the people dependent on forest resources. Despite the support from development partners like the United States Agency for International Development (USAID), the country is still struggling to protect its forest resources from human encroachment. One of the major problems is the lack of inconclusiveness in current approaches. Most initiatives are not evidence-based and are project-based for only a certain period of time. This has failed to ensure sustainable outcomes. This study looks at Bangladesh’s Himchari National Park forest management system to generate evidence regarding deforestation from 1991-2018 and highlight existing gaps. To identify and analyze the gaps, the study uses a social-ecological system (SES) lens. Results reveal deforestation across different time periods, articulates the overall governance structure regarding forest resource management, and provides an overview of the major gaps within the system. The study also offers a set of recommendations for improving the existing management system and policy implications.
ContributorsMahid, Yousuf (Author) / Pijawka, David (Thesis advisor) / Myint, Soe (Thesis advisor) / Liao, Chuan (Committee member) / Arizona State University (Publisher)
Created2020