Anthropogenic disturbance in a landscape can take various forms, including residential development, which has substantial impact on the world’s ecosystems. Exurban development, characterized by low density residential development outside urban areas, was and continues to be one of the fastest growing forms of residential development in North America. It has disproportionately large ecological impacts relative to its footprint, yet is mostly overlooked in scientific studies. Specifically, a lack of spatially explicit (disaggregate) data on exurban development at regional level has contributed to a very limited understanding of this interspersed low density development. The main goal of this dissertation is to provide an increased understanding of exurban development in terms of its location, locating factors, and conservation and ecological implications at regional level, especially to enable incorporation of exurban information in the decision making processes. For this I asked four specific questions in this dissertation: (i) Where exactly is exurban development? (ii) What are the most likely factors that influence exurban development location? (iii) How does current and future development conflict with conservation goals? And (iv) What is the extent of the exurban development’s ecological impacts? Using a heterogeneous landscape, the County of Peterborough (Ontario, Canada), as the case study this dissertation undertook a number of separate yet related analyses that collectively provided the improved understanding of exurban development. The investigation of traditionally used surrogates for development, like roads and census data, and a more direct remote sensing method, using moderate resolution SPOT/HRVIR imagery, provided insights and contributed to development of spatially explicit data on exurban development. The evaluation of several commonly hypothesized locating factors in relation to exurban development revealed some of the major influences on the location of this development, especially in the context of Ontario. This research contributed to our understanding of the future risks of land conversion and identification of potential conflict areas between development and conservation plans in the study area. Lastly, examining the ecological impact of exurban development including associated roads, in terms of functions such as barrier effects and landscape connectivity, highlighted the importance of these seldom included anthropogenic disturbances in land and conservation planning. The contributions of this research to the existing body of knowledge are threefold. First, this dissertation reveals the limitations associated with existing methods used to map exurban development and presents a relatively easy, effective, automated and operational method to delineate exurban built areas at regional level using GIS and remote sensing. Second, the analyses conducted in this dissertation repeatedly highlights the importance of incorporating fine level details on exurban development in land and conservation planning as well as ecological impact assessments and presents methods and tools that can systematically and scientifically integrate this information in decision making framework. Third, this study conducted one of a kind, comprehensive and spatially explicit study on exurban development in Canada, where there is near absence of such research. With the rarely available exurban built footprint data delineated for the study area, this study not only identified the potential locating factors, future conversion risk, and conflict areas between development and conservation plans, but also quantified ecological impact in terms of landscape function, namely barrier effects and landscape connectivity, using a relatively novel circuit theoretic approach that can directly inform land and conservation decision planning process.

Common carp (Cyprinus carpio) have been hypothesized to contribute to declines in aquatic macrophytes, waterfowl, and water clarity in Delta Marsh, an 18,500 ha freshwater coastal wetland on Lake Manitoba, Canada. Ten ponds (1-13 ha) were chosen for a two-year experimental manipulation study. Following a year of baseline monitoring, manipulations were conducted in 2002. To facilitate access by carp into isolated ponds, channels were blasted from the main marsh into two ponds. Meanwhile, to restrict or exclude carp access into ponds, channels were either screened or diked to four ponds. Two connected and two isolated ponds functioned as controls. Although common carp were the original subject of the study, it became apparent that hydrological connection to the surrounding marsh had a paramount importance on the abundance and diversity of the fish, amphibian and water-column invertebrate communities. Connectivity, or lack of connectivity, played an important role in the distribution of the fish community, and subsequently the composition and abundance of water-column invertebrates and amphibians. Ponds with direct connection had diverse, mixed-species fish assemblages, with fewer invertebrates and amphibians. Ponds with restricted connections had fish communities composed of tolerant small-sized species and increased abundance of invertebrates and amphibians. Ponds that lacked connection could freeze and lose all fish, and had higher numbers of invertebrates and amphibians. An absence of adult common carp may have been responsible for increased amphibian numbers in the screened ponds, however more study is needed. Confounding impacts of fluctuating water levels made it impossible to implicate common carp for most changes observed within ponds in Delta Marsh. / May 2006

Many digital models used in entertainment, medical visualization, material science, architecture, Geographic Information Systems (GIS), and mechanical Computer Aided Design (CAD) are defined in terms of their boundaries. These boundaries are often approximated using triangle meshes. The complexity of models, which can be measured by triangle count, increases rapidly with the precision of scanning technologies and with the need for higher resolution. An increase in mesh complexity results in an increase of storage requirement, which in turn increases the frequency of disk access or cache misses during mesh processing, and hence decreases performance. For example, in a test application involving a mesh with 55 million triangles in a machine with 4GB of memory versus a machine with 1GB of memory, performance decreases by a factor of about 6000 because of memory thrashing. To help reduce memory thrashing, we focus on decreasing the average storage requirement per triangle measured in 32-bit integer references per triangle (rpt). This thesis covers compact connectivity representation for triangle meshes and discusses four data structures: 1. Sorted Opposite Table (SOT), which uses 3 rpt and has been extended to support tetrahedral meshes. 2. Sorted Quad (SQuad), which uses about 2 rpt and has been extended to support streaming. 3. Laced Ring (LR), which uses about 1 rpt and offers an excellent compromise between storage compactness and performance of mesh traversal operators. 4. Zipper, an extension of LR, which uses about 6 bits per triangle (equivalently 0.19 rpt), therefore is the most compact representation. The triangle mesh data structures proposed in this thesis support the standard set of mesh connectivity operators introduced by the previously proposed Corner Table at an amortized constant time complexity. They can be constructed in linear time and space from the Corner Table or any equivalent representation. If geometry is stored as 16-bit coordinates, using Zipper instead of the Corner Table increases the size of the mesh that can be stored in core memory by a factor of about 8.

A drainage basins runoff response can be determined by the connectivity of generated runoff to the stream network and the connectivity of the downstream stream network. The connectivity of a drainage basin modulates its ability to produce streamflow and respond to precipitation events and is a function of the complex and variable storage capacities along the drainage network. An improved means to measure and account for the dynamics of hydrological connectivity at the basin scale is needed to improve prediction of basin scale streamflow. The overall goal of this thesis is to improve the understanding of hydrological connectivity at the basin scale by measuring hydrological connectivity at the Baker Creek Research Basin during 2009. To this end, the objectives are to 1) investigate the dynamics of hydrological connectivity during a typical water year, 2) define the relationship between the contributing stream network and contributing area, 3) investigate how hydrological connectivity influences streamflow, and 4) define how hydrological connectivity influences runoff response to rainfall events. At a 150 km2 subarctic Precambrian Shield catchment where the poorly-drained heterogeneous mosaic of lakes, exposed bedrock, and soil filled areas creates variable contributing areas, hydrological connectivity was measured between April and September 2009 in 10 sub-basins with a particular focus on three representative sub-basins. The three sub-basins, although of similar relative size, vary considerably in the dominant typology and topology of their constituent elements. At a 10 m spatial resolution, saturated areas were mapped using both multispectral satellite imagery and in situ measurements of storage according to land cover. To measure basin scale hydrological connectivity, the drainage network was treated as a graph network with stream reaches being the edges that connect sub-catchment nodes. The overall hydrological connectivity of the stream network was described as the ratio of actively flowing relative to potentially flowing stream reaches, and the hydrological connectivity of the stream network to the outlet was described as the ratio of actively flowing stream reaches that were connected to the outlet relative to the potentially flowing stream reaches. Hydrological connectivity was highest during the spring freshet but the stream network began to disintegrate with its passing. In some drainage basins, large gate keepers were able to maintain connectivity of the stream network downstream during dry periods. The length of the longest stream was found to be proportional to contributing area raised to a power of 0.605, similar to that noted in Hacks Law and modified Hacks Law relationships. The length of the contributing stream network was also found to be proportional to contributing area raised to a power of 0.851. In general, higher daily average streamflows were noted for higher states of connectivity to the outlet although preliminary investigations allude to the existence of hysteresis in these relationships. Elevated levels of hydrological connectivity were also found to yield higher basin runoff ratios but the shape of the characteristic curve for each basin was heavily influenced by key traits of its land cover heterogeneity. The implications of these findings are that accurate prediction of streamflow and runoff response in a heterogeneous drainage basin with dynamic connectivity will require both an account of the presence or absence of connections but also a differentiation of connection type and an incorporation of aspects of local function that control the flow through connections themselves. The improved understanding of causal factors for the variable streamflow response to runoff generation in this environment will serve as a first step towards developing improved streamflow prediction methods in formerly glaciated landscapes, especially in small ungauged basins.

Population-wide synchronized rhythmic bursts of electrical activity are present in a variety of neural circuits. The proposed general mechanisms for rhythmogenesis are often attributed to intrinsic and synaptic properties. For example, the recurrent excitation through excitatory synaptic connections determines burst initiation, and the slower kinetics of ionic currents or synaptic depression results in burst termination. In such theories, a slow recovery process is essential for the slow dynamics associated with bursting. This thesis presents a new hypothesis that depends on the connectivity pattern among neurons rather than a slow kinetic process to achieve the network-wide bursting. The thesis begins with an introduction of bursts of electrical activity in a purely excitatory neural network and existing theories explaining this phenomenon. It then covers the small-world approach, which is applied to modify the network structure in the simulation, and the Morris-Lecar (ML) neuron model, which is used as the component cells in the network. Simulation results of the dependence of bursting activity on network connectivity, as well as the inherent network properties explaining this dependence are described. This work shows that the network-wide bursting activity emerges in the small-world network regime but not in the regular or random networks, and this small-world bursting primarily results from the uniform random distribution of long-range connections in the network, as well as the unique dynamics in the ML model. Both attributes foster progressive synchronization in firing activity throughout the network during a burst, and this synchronization may terminate a burst in the absence of an obvious slow recovery process. The thesis concludes with possible future work.

Functional MRI is a method of imaging changes in blood oxygenation that accompany neural activity in the brain. A specific area within fMRI studies investigates what the brain is doing when it is not being stimulated. It is postulated that there are distinctly separate regions of the brain that are connected based upon functional relations and that these connected regions synchronously communicate even during rest. Resting state connectivity has become a tool to investigate neurological disorders in humans without specific knowledge of the mechanisms that correlate neural activity with brain metabolism and blood flow. This work attempts to characterize resting state connectivity in the rat brain to establish a model that will help elucidate the relationship between functional connectivity, as measured with fMRI, and brain function. Four analysis techniques, power spectrum estimation, cross correlation analysis, principle component analysis, and independent component analysis, are employed to examine data acquired during a non-stimulation, single-slice, gradient echo EPI sequence in search of functionally connected, spatially distant regions of the rat brain.

The disulfide bond in a protein is a single covalent bond formed from the oxidation of two cysteines. It plays an important role in the folding and structure stability, and may regulate protein functions. The connectivity prediction problem is difficult because the number of possible patterns grows rapidly with respect to the number of cysteines. We discover some rules to discriminate the patterns with high accuracy in many methods. We implement multiple SVM methods, and utilize the BKS to fuse these classifiers. We apply the hybrid method to SP39 dataset with 4-fold cross-validation for the comparison with the previous works. We raise the accuracy to 71.5%, which improves significantly that of the best previous work, 65.9%.

The American alligator (Alligator mississippiensis) has been frequently studied in large reservoirs and coastal marshes. Large ontogenetic shifts in their diet and morphology have been linked with changes in habitat use, with adult males using deep, open water and juveniles and nesting females relying on vegetated marsh. In certain regions of the inland portion of the alligator’s range, these different aquatic habitats are represented by seasonal wetlands and riverine systems that are separated by a terrestrial matrix. Ontogenetic habitat shifts, therefore, would require overland movements between systems, which has important implications for conservation of the species. I tested several commonly used methods of surveying alligator populations to determine the most effective method of studying alligators in seasonal wetlands. I then used systematic trapping, nest surveys and radio telemetry to determine habitat use and overland movement rates by different sex and size classes. I found that seasonal wetlands provided nesting and nursery sites for these inland alligator populations, but that both juveniles undergoing an ontogenetic shift and nesting females move between the wetlands and riverine systems. Overland movements by alligators between the wetland and riverine habitats establish a level of functional connectivity between these aquatic ecosystems. I constructed a habitat suitability index of both the wetlands and the surrounding landscape to determine which patch and landscape characteristics were important to wetland use by alligators. I found that both descriptive wetland characteristics and the spatial relationships between wetlands were important predictors of alligator use. Overland movement was related to upland landuse as well as distance between aquatic habitats. Conserving a variety of wetland sizes and types within an intact upland matrix is critical to maintaining connectivity across the landscape. Furthermore, understanding how species may act as mobile links between ecosystems, particularly those with ontogenetic niche shifts, illustrates the importance of approaching conservation from a landscape perspective.

Recently, there has been much interest in the resilience of complex networks to random failures and intentional attacks. The study of the network robustness is particularly important by several occasions. In one hand a higher degree of robustness to errors and attacks may be desired for maintaining the information flow in communication networks under attacks. On the other hand planning a very limited attack aimed at fragmenting a network by removal of minimum number of the most important nodes might have significant usage in drug design. Many real world networks were found to display scale free topology including WWW, the internet, social networks or regulatory gene and protein networks. In the recent studies it was shown that while these networks have a surprising error tolerance, their scale-free topology makes them fragile under intentional attack, leaving the scientists a challenge on how to improve the networks robustness against attacks. In this thesis, we studied the protein domain co-occurrence network of yeast which displays scale free topology generated with data from Biomart which links to Pfam database. Several networks obtained from protein domain co-occurrence network having exactly the same connectivity distribution were compared under attacks to investigate the assumption that the different networks with the same connectivity distribution do not need to have the same attack tolerances. In addition to this, we considered that the networks with the same connectivity distribution have higher attack tolerance as we organize the same resources in a better way. Then, we checked for the variations of attack tolerance of the networks with the same connectiviy distributions. Furthermore, we investigated whether there is an evolutionary mechanism for having networks with higher or lower attack tolerances for the same connectivity distribution. As a result of these investigations, the different networks with the same connectivity distribution do not have the same attack tolerances under attack. In addition to this, it was observed that the networks with the same connectivity distribution have higher attack tolerances as organizing the same resources in a better way which implies that there is an evolutionary mechanism for having networks with higher attack tolerance for the same connectivity distribution.

The demand for oil and gas is increasing yearly, whereas proven oil and gas reserves are being depleted. The potential of stripper oil and gas fields to supplement the national energy supply is large. In 2006, stripper wells accounted for 15% and 8% of US oil and gas production, respectively. With increasing energy demand and current high oil and gas prices, integrated reservoir studies, secondary and tertiary recovery methods, and infill drilling are becoming more common as operators strive to increase recovery from stripper oil and gas fields. The primary objective of this research was to support optimized production of oil and gas from stripper well fields by evaluating one stripper gas field and one stripper oil field. For the stripper gas field, I integrated geologic and engineering data to build a detailed reservoir characterization model of the Second White Specks (SSPK) reservoir in Garden Plains field, Alberta, Canada. The objectives of this model were to provide insights to controls on gas production and to validate a simulation-based method of infill drilling assessment. SSPK was subdivided into Units A ? D using well-log facies. Units A and B are the main producing units. Unit A has better reservoir quality and lateral continuity than Unit B. Gas production is related primarily to porosity-netthickness product and permeability and secondarily to structural position, minor structural features, and initial reservoir pressure. For the stripper oil field, I evaluated the Green River formation in the Wells Draw area of Monument Butte field, Utah, to determine interwell connectivity and to assess optimal recovery strategies. A 3D geostatistical model was built, and geological realizations were ranked using production history matching with streamline simulation. Interwell connectivity was demonstrated for only major sands and it increases as well spacing decreases. Overall connectivity is low for the 22 reservoir zones in the study area. A water-flood-only strategy provides more oil recovery than a primary-then-waterflood strategy over the life of the field. For new development areas, water flooding or converting producers to injectors should start within 6 months of initial production. Infill drilling may effectively produce unswept oil and double oil recovery. CO2 injection is much more efficient than N2 and CH4 injection. Water-alternating-CO2 injection is superior to continuous CO2 injection in oil recovery. The results of this study can be used to optimize production from Garden Plains and Monument Butte fields. Moreover, these results should be applicable to similar stripper gas and oil field fields. Together, the two studies demonstrate the utility of integrated reservoir studies (from geology to engineering) for improving oil and gas recovery.