Exploratory data analysis with non-linear and missing data in geochemistry

Exploratory analysis of data seeks to find common patterns to gain insights into the structure and distribution of the data. In geochemistry it is a valuable means to gain insights into the complicated processes making up a petroleum system. Typically linear visualisation methods like principal components analysis, linked plots, or brushing are used. These methods can not directly be employed when dealing with missing data and they struggle to capture global non-linear structures in the data, however they can do so locally. This thesis discusses a complementary approach based on a non-linear probabilistic model. The generative topographic mapping (GTM) enables the visualisation of the effects of very many variables on a single plot, which is able to incorporate more structure than a two dimensional principal components plot. The model can deal with uncertainty, missing data and allows for the exploration of the non-linear structure in the data. In this thesis a novel approach to initialise the GTM with arbitrary projections is developed. This makes it possible to combine GTM with algorithms like Isomap and fit complex non-linear structure like the Swiss-roll. Another novel extension is the incorporation of prior knowledge about the structure of the covariance matrix. This extension greatly enhances the modelling capabilities of the algorithm resulting in better fit to the data and better imputation capabilities for missing data. Additionally an extensive benchmark study of the missing data imputation capabilities of GTM is performed. Further a novel approach, based on missing data, will be introduced to benchmark the fit of probabilistic visualisation algorithms on unlabelled data. Finally the work is complemented by evaluating the algorithms on real-life datasets from geochemical projects.

Addressing missing data in geochemistry: a non-linear approach

Exploratory analysis of petroleum geochemical data seeks to find common patterns to help distinguish between different source rocks, oils and gases, and to explain their source, maturity and any intra-reservoir alteration. However, at the outset, one is typically faced with (a) a large matrix of samples, each with a range of molecular and isotopic properties, (b) a spatially and temporally unrepresentative sampling pattern, (c) noisy data and (d) often, a large number of missing values. This inhibits analysis using conventional statistical methods. Typically, visualisation methods like principal components analysis are used, but these methods are not easily able to deal with missing data nor can they capture non-linear structure in the data. One approach to discovering complex, non-linear structure in the data is through the use of linked plots, or brushing, while ignoring the missing data. In this paper we introduce a complementary approach based on a non-linear probabilistic model. Generative topographic mapping enables the visualisation of the effects of very many variables on a single plot, while also dealing with missing data. We show how using generative topographic mapping also provides an optimal method with which to replace missing values in two geochemical datasets, particularly where a large proportion of the data is missing.

Relationships Between Hydrology and Soils Describe Vegetation Patterns in Seasonally Flooded Tree Islands of the Southern Everglades, Florida

Tree island ecosystems are important and distinct features of Florida Everglades wetlands. We described the inter-relationships among abiotic factors describing seasonally flooded tree islands and characterized plant–soil relationships in tree islands occurring in a relatively unimpacted area of the Everglades. We used Principal Components Analysis (PCA) to reduce our multi-factor dataset, quantified forest structure and vegetation nutrient dynamics, and related these vegetation parameters to PCA summary variables using linear regression analyses. We found that, of the 21 abiotic parameters used to characterize the ecosystem structure of seasonally flooded tree islands, 13 parameters were significantly correlated with four principal components, and they described 78% of the variance among the study islands. Most variation was described by factors related to soil oxidation and hydrology, exemplifying the sensitivity of tree island structure to hydrologic conditions. PCA summary variables describing tree island structure were related to variability in Chrysobalanus icaco (L.) canopy cover, Ilex cassine (L.) and Salix caroliniana (Michx.) canopy cover, Myrica cerifera (L.) plot frequency, litter turnover, % phosphorus resorption of co-dominant species, and nitrogen nutrient-use efficiency. This study supported findings that vegetation characteristics can be sensitive indicators of variability in tree island ecosystem structure. This study produced valuable, information which was used to recommend ecological targets (i.e. restoration performance measures) for seasonally flooded tree islands in more impacted regions of the Everglades landscape.

Switching patterns and steady-state analysis of grid-connected and stand-alone single-stage boost-inverters for PV applications

Renewable or sustainable energy (SE) sources have attracted the attention of many countries because the power generated is environmentally friendly, and the sources are not subject to the instability of price and availability. This dissertation presents new trends in the DC-AC converters (inverters) used in renewable energy sources, particularly for photovoltaic (PV) energy systems. A review of the existing technologies is performed for both single-phase and three-phase systems, and the pros and cons of the best candidates are investigated. In many modern energy conversion systems, a DC voltage, which is provided from a SE source or energy storage device, must be boosted and converted to an AC voltage with a fixed amplitude and frequency. A novel switching pattern based on the concept of the conventional space-vector pulse-width-modulated (SVPWM) technique is developed for single-stage, boost-inverters using the topology of current source inverters (CSI). The six main switching states, and two zeros, with three switches conducting at any given instant in conventional SVPWM techniques are modified herein into three charging states and six discharging states with only two switches conducting at any given instant. The charging states are necessary in order to boost the DC input voltage. It is demonstrated that the CSI topology in conjunction with the developed switching pattern is capable of providing the required residential AC voltage from a low DC voltage of one PV panel at its rated power for both linear and nonlinear loads. In a micro-grid, the active and reactive power control and consequently voltage regulation is one of the main requirements. Therefore, the capability of the single-stage boost-inverter in controlling the active power and providing the reactive power is investigated. It is demonstrated that the injected active and reactive power can be independently controlled through two modulation indices introduced in the proposed switching algorithm. The system is capable of injecting a desirable level of reactive power, while the maximum power point tracking (MPPT) dictates the desirable active power. The developed switching pattern is experimentally verified through a laboratory scaled three-phase 200W boost-inverter for both grid-connected and stand-alone cases and the results are presented.

Theoretical Investigation of Intra- and Inter-cellular Spatiotemporal Calcium Patterns in Microcirculation

Microcirculatory vessels are lined by endothelial cells (ECs) which are surrounded by a single or multiple layer of smooth muscle cells (SMCs). Spontaneous and agonist induced spatiotemporal calcium (Ca2+) events are generated in ECs and SMCs, and regulated by complex bi-directional signaling between the two layers which ultimately determines the vessel tone. The contractile state of microcirculatory vessels is an important factor in the determination of vascular resistance, blood flow and blood pressure. This dissertation presents theoretical insights into some of the important and currently unresolved phenomena in microvascular tone regulation. Compartmental and continuum models of isolated EC and SMC, coupled EC-SMC and a multi-cellular vessel segment with deterministic and stochastic descriptions of the cellular components were developed, and the intra- and inter-cellular spatiotemporal Ca2+ mobilization was examined. Coupled EC-SMC model simulations captured the experimentally observed localized subcellular EC Ca2+ events arising from the opening of EC transient receptor vanilloid 4 (TRPV4) channels and inositol triphosphate receptors (IP3Rs). These localized EC Ca2+ events result in endothelium-derived hyperpolarization (EDH) and Nitric Oxide (NO) production which transmit to the adjacent SMCs to ultimately result in vasodilation. The model examined the effect of heterogeneous distribution of cellular components and channel gating kinetics in determination of the amplitude and spread of the Ca2+ events. The simulations suggested the necessity of co-localization of certain cellular components for modulation of EDH and NO responses. Isolated EC and SMC models captured intracellular Ca2+ wave like activity and predicted the necessity of non-uniform distribution of cellular components for the generation of Ca2+ waves. The simulations also suggested the role of membrane potential dynamics in regulating Ca2+ wave velocity. The multi-cellular vessel segment model examined the underlying mechanisms for the intercellular synchronization of spontaneous oscillatory Ca2+ waves in individual SMC. From local subcellular events to integrated macro-scale behavior at the vessel level, the developed multi-scale models captured basic features of vascular Ca2+ signaling and provide insights for their physiological relevance. The models provide a theoretical framework for assisting investigations on the regulation of vascular tone in health and disease.

Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy metabolism, link to supplementary material

Marine organisms have to cope with increasing CO2 partial pressures and decreasing pH in the oceans. We elucidated the impacts of an 8-week acclimation period to four seawater pCO2 treatments (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm) on mantle gene expression patterns in the blue mussel Mytilus edulis from the Baltic Sea. Based on the M. edulis mantle tissue transcriptome, the expression of several genes involved in metabolism, calcification and stress responses was assessed in the outer (marginal and pallial zone) and the inner mantle tissues (central zone) using quantitative real-time PCR. The expression of genes involved in energy and protein metabolism (F-ATPase, hexokinase and elongation factor alpha) was strongly affected by acclimation to moderately elevated CO2 partial pressures. Expression of a chitinase, potentially important for the calcification process, was strongly depressed (maximum ninefold), correlating with a linear decrease in shell growth observed in the experimental animals. Interestingly, shell matrix protein candidate genes were less affected by CO2 in both tissues. A compensatory process toward enhanced shell protection is indicated by a massive increase in the expression of tyrosinase, a gene involved in periostracum formation (maximum 220-fold). Using correlation matrices and a force-directed layout network graph, we were able to uncover possible underlying regulatory networks and the connections between different pathways, thereby providing a molecular basis of observed changes in animal physiology in response to ocean acidification.

Transferability of Regional Permafrost Disturbance Susceptibility Modelling Using Generalized Linear and Generalized Additive Models

To effectively assess and mitigate risk of permafrost disturbance, disturbance-p rone areas can be predicted through the application of susceptibility models. In this study we developed regional susceptibility models for permafrost disturbances using a field disturbance inventory to test the transferability of the model to a broader region in the Canadian High Arctic. Resulting maps of susceptibility were then used to explore the effect of terrain variables on the occurrence of disturbances within this region. To account for a large range of landscape charac- teristics, the model was calibrated using two locations: Sabine Peninsula, Melville Island, NU, and Fosheim Pen- insula, Ellesmere Island, NU. Spatial patterns of disturbance were predicted with a generalized linear model (GLM) and generalized additive model (GAM), each calibrated using disturbed and randomized undisturbed lo- cations from both locations and GIS-derived terrain predictor variables including slope, potential incoming solar radiation, wetness index, topographic position index, elevation, and distance to water. Each model was validated for the Sabine and Fosheim Peninsulas using independent data sets while the transferability of the model to an independent site was assessed at Cape Bounty, Melville Island, NU. The regional GLM and GAM validated well for both calibration sites (Sabine and Fosheim) with the area under the receiver operating curves (AUROC) N 0.79. Both models were applied directly to Cape Bounty without calibration and validated equally with AUROC's of 0.76; however, each model predicted disturbed and undisturbed samples differently. Addition- ally, the sensitivity of the transferred model was assessed using data sets with different sample sizes. Results in- dicated that models based on larger sample sizes transferred more consistently and captured the variability within the terrain attributes in the respective study areas. Terrain attributes associated with the initiation of dis- turbances were similar regardless of the location. Disturbances commonly occurred on slopes between 4 and 15°, below Holocene marine limit, and in areas with low potential incoming solar radiation

Patterns of Behaviour, Group Structure and Reproductive Status Predict Levels of Glucocorticoid Metabolites in Zoo-Housed Ring-Tailed Lemurs, Lemur catta

In ring-tailed lemurs, Lemur catta, the factors modulating hypothalamic-pituitaryadrenal (HPA) activity differ between wild and semi-free-ranging populations. Here we assess factors modulating HPA activity in ring-tailed lemurs housed in a third environment: the zoo. First we validate an enzyme immunoassay to quantify levels of glucocorticoid (GC) metabolites in the faeces of L. catta . We determine the nature of the femalefemale dominance hierarchies within each group by computing David's scores and examining these in relation to faecal GC (fGC). Relationships between female age and fGC are assessed to evaluate potential age-related confounds. The associations between fGC, numbers of males in a group and reproductive status are explored. Finally, we investigate the value of 7 behaviours in predicting levels of fGC. The study revealed stable linear dominance hierarchies in females within each group. The number of males in a social group together with reproductive status, but not age, influenced fGC. The 7 behavioural variables accounted for 68% of the variance in fGC. The amounts of time an animal spent locomoting and in the inside enclosure were both negative predictors of fGC. The study highlights the flexibility and adaptability of the HPA system in ring-tailed lemurs.

Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific .1. Influence of vent site distribution, bottom currents, and biological patterns

Deep-sea hydrothermal-vent habitats are typically linear, discontinuous, and short-lived. Some of the vent fauna such as the endemic polychaete family Alvinellidae are thought to lack a planktotrophic larval stage and therefore not to broadcast-release their offspring. The genetic evidence points to exchanges on a scale that seems to contradict this type of reproductive pattern. However, the rift valley may topographically rectify the bottom currents, thereby facilitating the dispersal of propagules between active vent sites separated in some cases by 10s of kilometers or more along the ridge axis. A propagule flux model based on a matrix of intersite distances, long-term current-meter data, and information on the biology and ecology of Alvinellidae was developed to test this hypothesis. Calculations of the number of migrants exchanged between two populations per generation (N-m) allowed comparisons with estimates obtained from genetic studies. N, displays a logarithmic decrease with increasing dispersal duration and reaches the critical value of 1 after 8 d when the propagule Aux model was run in standard conditions. At most, propagule traveling time cannot reasonably exceed 15-30 d, according to the model, whereas reported distances between sites would require longer lasting dispersal abilities. Two nonexclusive explanations are proposed. First, some aspects of the biology of Alvinellidae have been overlooked and long-distance dispersal does occur. Second, such dispersal never occurs in Alvinellidae, but the spatial-temporal dynamics of vent sites over geological timescales allows short-range dispersal processes to maintain gene flow.

MIGRATION PATTERNS AMONG YOUNG ADULTS IN THE UNITED STATES: ENVIRONMENTAL, SOCIAL, AND ECONOMIC EXPLANATIONS

Young adult migration is a key factor in community development. The goal of this paper is to study what kinds of places attract young adults and what kinds are losing them. Linear regression is conducted to analyze what place-specific factors explain migration patterns among young adults. These factors include economic, social, and environmental variables. This study finds that social and environmental factors are just as important as economic ones. Specifically, employment in the arts increases young adult net migration. Environmental variables, for example, natural amenities and protected federal lands are particularly important in rural settings in attracting young adults. These findings suggest that policy makers interested in attracting and retaining young adults should pay closer attention to social and environmental factors and consider creating more opportunities for arts employment in general. For rural areas, improving the attractiveness of natural amenities and better protection of federal lands is also recommended.

Switching Patterns and Steady-State Analysis of Grid-Connected and Stand-Alone Single-Stage Boost-Inverters for PV Applications

Renewable or sustainable energy (SE) sources have attracted the attention of many countries because the power generated is environmentally friendly, and the sources are not subject to the instability of price and availability. This dissertation presents new trends in the DC-AC converters (inverters) used in renewable energy sources, particularly for photovoltaic (PV) energy systems. A review of the existing technologies is performed for both single-phase and three-phase systems, and the pros and cons of the best candidates are investigated. In many modern energy conversion systems, a DC voltage, which is provided from a SE source or energy storage device, must be boosted and converted to an AC voltage with a fixed amplitude and frequency. A novel switching pattern based on the concept of the conventional space-vector pulse-width-modulated (SVPWM) technique is developed for single-stage, boost-inverters using the topology of current source inverters (CSI). The six main switching states, and two zeros, with three switches conducting at any given instant in conventional SVPWM techniques are modified herein into three charging states and six discharging states with only two switches conducting at any given instant. The charging states are necessary in order to boost the DC input voltage. It is demonstrated that the CSI topology in conjunction with the developed switching pattern is capable of providing the required residential AC voltage from a low DC voltage of one PV panel at its rated power for both linear and nonlinear loads. In a micro-grid, the active and reactive power control and consequently voltage regulation is one of the main requirements. Therefore, the capability of the single-stage boost-inverter in controlling the active power and providing the reactive power is investigated. It is demonstrated that the injected active and reactive power can be independently controlled through two modulation indices introduced in the proposed switching algorithm. The system is capable of injecting a desirable level of reactive power, while the maximum power point tracking (MPPT) dictates the desirable active power. The developed switching pattern is experimentally verified through a laboratory scaled three-phase 200W boost-inverter for both grid-connected and stand-alone cases and the results are presented.

Landscape Patterns of Permafrost Disturbance and Degradation in the Canadian High Arctic

Intensification of permafrost disturbances such as active layer detachments (ALDs) and retrogressive thaw slumps (RTS) have been observed across the circumpolar Arctic. These features are indicators of unstable conditions stemming from recent climate warming and permafrost degradation. In order to understand the processes interacting to give rise to these features, a multidisciplinary approach is required; i.e., interactions between geomorphology, hydrology, vegetation and ground thermal conditions. The goal of this research is to detect and map permafrost disturbance, predict landscape controls over disturbance and determine approaches for monitoring disturbance, all with the goal of contributing to the mitigation of permafrost hazards. Permafrost disturbance inventories were created by applying semi-automatic change detection techniques to IKONOS satellite imagery collected at the Cape Bounty Arctic Watershed Observatory (CBAWO). These methods provide a means to estimate the spatial distribution of permafrost disturbances for a given area for use as an input in susceptibility modelling. Permafrost disturbance susceptibility models were then developed using generalized additive and generalized linear models (GAM, GLM) fitted to disturbed and undisturbed locations and relevant GIS-derived predictor variables (slope, potential solar radiation, elevation). These models successfully delineated areas across the landscape that were susceptible to disturbances locally and regionally when transferred to an independent validation location. Permafrost disturbance susceptibility models are a first-order assessment of landscape susceptibility and are promising for designing land management strategies for remote permafrost regions. Additionally, geomorphic patterns associated with higher susceptibility provide important knowledge about processes associated with the initiation of disturbances. Permafrost degradation was analyzed at the CBAWO using differential interferometric synthetic aperture radar (DInSAR). Active-layer dynamics were interpreted using inter-seasonal and intra-seasonal displacement measurements and highlight the importance of hydroclimatic factors on active layer change. Collectively, these research approaches contribute to permafrost monitoring and the assessment of landscape-scale vulnerability in order to develop permafrost disturbance mitigation strategies.

Wavelengths in bioconvection patterns

Unicellular bottom-heavy swimming microorganisms are usually denser than the fluid in which they swim. In shallow suspensions, the bottom heaviness results in a gravitational torque that orients the cells to swim vertically upwards in the absence of fluid flow. Swimming cells thus accumulate at the upper surface to form a concentrated layer of cells. When the cell concentration is high enough, the layer overturns to form bioconvection patterns. Thin concentrated plumes of cells descend rapidly and cells return to the upper surface in wide, slowly moving upwelling plumes. When there is fluid flow, a second viscous torque is exerted on the swimming cells. The balance between the local shear flow viscous and the gravitational torques determines the cells' swimming direction, (gyrotaxis). In this thesis, the wavelengths of bioconvection patterns are studied experimentally as well as theoretically as follow; First, in aquasystem it is rare to find one species lives individually and when they swim they can form complex patterns. Thus, a protocol for controlled experiments to mix two species of swimming algal cells of \emph{C. rienhardtii} and \emph{C. augustae} is systematically described and images of bioconvection patterns are captured. A method for analysing images using wavelets and extracting the local dominant wavelength in spatially varying patterns is developed. The variation of the patterns as a function of the total concentration and the relative concentration between two species is analysed. Second, the linear stability theory of bioconvection for a suspension of two mixed species is studied. The dispersion relationship is computed using Fourier modes in order to calculate the neutral curves as a function of wavenumbers $k$ and $m$. The neutral curves are plotted to compare the instability onset of the suspension of the two mixed species with the instability onset of each species individually. This study could help us to understand which species contributes the most in the process of pattern formation. Finally, predicting the most unstable wavelength was studied previously around a steady state equilibrium situation. Since assuming steady state equilibrium contradicts with reality, the pattern formation in a layer of finite depth of an evolving basic state is studied using the nonnormal modes approach. The nonnormal modes procedure identifies the optimal initial perturbation that can be obtained for a given time $t$ as well as a given set of parameters and wavenumber $k$. Then, we measure the size of the optimal perturbation as it grows with time considering a range of wavenumbers for the same set of parameters to be able to extract the most unstable wavelength.

Geographical patterns of the species richness of helminth parasites of moles (Talpa spp.) in Spain: Separating the effects of sampling effort from those of other conditioning factors

We analysed the viscera of 534 moles (Ta l p a spp.) from 30 of the 47 provinces of peninsular Spain, including 255 individuals of T. europaea from eight provinces, 154 individuals of T. occidentalis from 20 provinces, and 125 unidentified Ta l p a individuals from two provinces. We identified their helminth parasites and determined parasite species richness. We related parasite species richness with sampling effort using both a linear and a logarithmic function. We then performed stepwise linear regressions to predict mole parasite species richness from a small set of selected predictor variables that included sampling effort. We applied the resulting models to forecast T. euro p a e a, T. occidentalis, and Ta l p a spp. parasite species richness in all provinces with recorded host presence, assuming different levels of sampling eff o r t . F i n a l l y, we used partial regression analysis to partition the variation explained by each of the selected variables in the models. We found that mole parasite species richness is strongly conditioned by sampling effort, but that other factors such as cropland area and environmental disturbance have significant independent effects.

From images to signs: Cretan Hieroglyphic and Linear A in context

This dissertation adopts a multidisciplinary approach to investigate graphical and formal features of Cretan Hieroglyphic and Linear A. Drawing on theories which understand inscribed artefacts as an interplay of materials, iconography, and texts, I combine archaeological and philological considerations with statistical and experimental observations. The work is formulated on three key-questions. The first deals with the origins of Cretan Hieroglyphic. After providing a fresh view on Prepalatial seals chronology, I identify a number of forerunners of Hieroglyphic signs in iconographic motifs attested among the Prepalatial glyptic and material culture. I further identified a specific style-group, i.e., the ‘Border and Leaf Complex’, as the decisive step towards the emergence of the Hieroglyphic graphic repertoire. The second deals with the interweaving of formal, iconographical, and epigraphic features of Hieroglyphic seals with the sequences they bear and the contexts of their usage. By means of two Correspondence Analyses, I showed that the iconography on seals in some materials and shapes is closer to Cretan Hieroglyphics, than that on the other ones. Through two Social Network Analyses, I showed that Hieroglyphic impressions, especially at Knossos, follow a precise sealing pattern due to their shapes and sequences. Furthermore, prisms with a high number of inscribed faces adhere to formal features of jasper ones. Finally, through experimental engravings, I showed differences in cutting rates among materials, as well as the efficiency of abrasives and tools unearthed within the Quartier Mu. The third question concerns overlaps in chronology, findspots and signaries between Cretan Hieroglyphic and Linear A. I discussed all possible earliest instances of both scripts and argued for some items datable to the MM I-IIA period. I further provide an insight into the Hieroglyphic-Linear A dubitanda and criteria for their interpretation. Finally, I suggest four different patterns in the creation and diversification of the two signaries.