The environmental processes and conditions controlling productivity and organic matter (OM) accumulation/preservation as well as bottom–water redox conditions in the lower black shale (LBS) and upper black shale (UBS) members of the Devonian-Mississippian (D–M) Bakken Formation were evaluated utilizing trace metal (TM) concentrations, degree of pyritization (DOPT), enrichment factors (EF) of TMs, bi–metal ratios (V/Cr, V/(V+Ni), Ni/Co, U/Th), total sulfur (ST) vs. iron (Fe), total organic carbon (TOC), carbon–sulfur–iron relationships (C–S–Fe), as well as Mo–TOC and Mo EF–U EF relationships. High-resolution (1- to 3-cm scale) chemostratigraphic records were generated for twelve drill cores, four of which closely flank the N–S-trending axis of the Nesson Anticline, proximal to the center of the Williston Basin in northwest North Dakota, USA. Furthermore, five of the twelve drill cores were selected (sample selection was based on down–core spacing and TM concentrations) for petrographic and Rock-Eval analysis to assess variations in kerogen type, quantity, quality, and thermal maturity (based on solid bitumen reflectance (%SBRo), vitrinite reflectance equivalence (%VRE), Rock–Eval Tmax–derived vitrinite reflectance (%Ro)) from immature to condensate, wet gas hydrocarbon generation windows. Degree of pyritization (DOPT) values (0.25 to 1.0) indicate that bottom waters were frequently dysoxic (> 60%) with intermittent aerobic and anoxic/euxinic conditions which is in agreement with C–S–Fe and total ST vs. Fe assessments of paleoredox conditions and sedimentological evidence. Furthermore, using published Mo–TOC relationships from modern anoxic-euxinic basins, it is estimated that renewal time of the sub-chemoclinal water mass during accumulation of the LBS and UBS approximated 10 and 30 yrs., respectively. Agreement is also seen between Mo/TOC and Mo EF/U EF where both suggest the Bakken shales were deposited under relatively unrestricted water mass conditions resulting in consistent renewal of TMs into the basin. However, bi–metal ratios suggest > 80% of samples were deposited under suboxic to anoxic/euxinic conditions. Trace metal concentrations for the Bakken Fm. show considerable range for Co (0–10324 ppm), Mo (0–2018 ppm), Ni (0–1574 ppm), U (0–1604 ppm), and V (0–3194 ppm), and bi–metal ratios for the Bakken Fm. are up to 5x greater than those reported for other D–M black shale formations. The Bakken black shales represent a unique sedimentary system where the EF of various TMs such as Cu (6.2–7.7), Mo (219.7–237.8), Ni (9.4–10.2), U (20.6–29.3), V (9.9–14.2), and Zn (10.4–12.2) as well as total organic carbon contents (LBS = 10.80 and UBS = 11.80 avg. wt.%) are considerably higher than other Devonian–Mississippian black shales. In this study, raw distributions of elemental concentrations combined with bivariate and principal component analysis (PCA) were used to elucidate the processes that could have contributed to the high EF of TMs in the Bakken shales. Total organic carbon shares heavier PCA component loadings (>0.445) and stronger correlation coefficients (r) with Cu, Mo, Ni, U, V, and Zn rather than with pyrite-associated (As, Co, Fe, and S) elements, suggesting that TOC played a primary role in the scavenging and accumulation of TMs in the sediments. Reducing conditions within bottom waters or sediment pore waters may have accelerated the accumulation of redox-sensitive Cu, Mo, Ni, V, and Zn introduced into the sediments via primarily an organic matter (OM) detritus host and most likely played a secondary role in the enrichment of TMs. The high EF of TMs observed in the Bakken shales may be the result of the frequent resupply of TMs into basin waters, enhanced primary productivity that is necessary in scavenging TMs from the water column, the presence of H2S within sediment pore or bottom waters, or possibly secondary processes associated with basin-wide fluid and hydrocarbon migration. Factors controlling TM accumulation during time of deposition (e.g., TM availability, bottom-water redox conditions, adsorption onto organic matter) and during diagenesis and catagenesis (e.g., alteration and break down of organic matter, movement of fluid hydrocarbons or other basinal fluids) likely contribute to the lack of agreement between redox proxies, and subsequently, the lack of applicability of bi–metal ratios (i.e., V/Cr, V/(V+Ni), Ni/Co, U/Th) in assessing bottom–water conditions for the Bakken shales. Solid bitumen (SB), a secondary organic matter formed as a residue after hydrocarbon generation (through either sufficient thermal maturation or microbial degradation) and expulsion, is primarily dispersed within the mineral matrix and increases in quantity with increasing thermal maturity. Rock-Eval II and HAWK analyzers were used to measure and estimate the hydrogen index (HI; avg. 201 mg HC/g TOC), oxygen index (OI; avg. 7mg CO2/g TOC), S1 (free hydrocarbons; avg. 8.0 mg HC/g rock), S2 (hydrocarbons generated after cracking kerogen; avg. 24.3 mg HC/g rock), and %Ro (0.60–1.03%; estimated from Tmax). The HI and OI values are calculated from TOC as well as S2 and S3 (oxygen bonded to hydrocarbons). Plots of HI vs. Tmax (ºC) and HI vs. OI as well as S2 vs. S3 ratio were utilized to determine the type of kerogen, primary OM that is insoluble in organic solvents. However, these relationships are not in agreement with kerogen typing based on petrographic observations, where samples from more thermally mature cores plot as Type III (vitrinite) kerogen instead of observed Type I/II (marine algae) kerogen. This is largely due to the abundant presence of SB in the more thermally mature section of the Bakken (Rock-Eval Ro = 0.83–1.03%) as SB is known to have a lower HI content than Type II kerogen. Petrographic evidence shows greater abundance of alginite and amorphous organic matter (AOM or bituminite) in the thermally less mature (Rock-Eval Ro = 0.60–0.83%) section of the Bakken compared to the greater abundance of dispersed SB in the more thermally mature section where AOM is absent. Early research on the Bakken Fm. reported lower than expected vitrinite reflectance values attributed to vitrinite “suppression". The overall lack of vitrinite and abundance of solid bitumen in these shales suggests that these early attempts likely reported solid bitumen reflectance rather than vitrinite reflectance. More recent attempts to assess the thermal maturity of the Bakken Fm. black shales have measured and converted SBRo to vitrinite reflectance equivalent (VRE). However, samples selected for SBRo by some previous workers have included heterogenous, granular as well as high reflecting SB samples, which introduce error in the measurements. As such, reported reflectance values are most likely lower than they would be if smooth, homogenous solid bitumen with no inclusions were measured. For this project, smooth and homogenous SB was measured to produce consistent and reliable VRE values to assess the thermal maturity gradient from the Bakken Fm. basin margins to the depocenter. Blue-light fluorescence petrography was done to support thermal maturity assessments. Results from SBRo, Rock-Eval Ro, VRE, and blue-light fluorescence observations suggest that cores from the current study range from early oil window into condensate, wet gas.

DNA methylation is an epigenetic mechanism that usually occurs at CpG sites in the genome. Both sequencing and array-based techniques are available to detect methylation patterns. Whole-genome bisulfite sequencing is the most comprehensive but cost-prohibitive approach, and microarrays represent an affordable alternative approach. Array-based methods are generally cheaper but assess a specific number of genomic loci, such as Illumina methylation arrays. Differentially methylated regions (DMRs) are genomic regions with specific methylation patterns across multiple CpG sites that associate with a phenotype. Methylation at nearby sites tends to be correlated, therefore it may be more powerful to study sets of sites to detect methylation differences as well as reduce the multiple testing burden, compared to utilizing individual sites. Several statistical approaches exist for identifying DMRs, and a few prior publications compared the performance of several commonly used DMR methods. However, as far as we know, no comprehensive comparisons have been made based on genome-wide simulation studies. This dissertation provides some comprehensive suggestions for DMR analysis based on genome-wide evaluations of existing DMR tools and presents the development of a novel approach to increase the power to identify DMRs with clinical value in genomic research. The second chapter presents genome-wide null simulations to compare five commonly used array-based DMR methods (Bumphunter, comb-p, DMRcate, mCSEA and coMethDMR) and identifies coMethDMR as the only approach that consistently yields appropriate Type I error control. We suggest that a genome-wide evaluation of false positive (FP) rates is critical for DMR methods. The third chapter develops a novel Principal Component Analysis based DMR method (denoted as DMRPC), which demonstrates its ability to identify DMRs using genome-wide methylation arrays with well-controlled FP rates at the level of 0.05. Compared to coMethDMR, DMRPC is a robust and powerful novel DMR tool that can examine more genomic regions and extract signals from low-correlation regions. The fourth chapter applies the new DMR approach DMRPC in two “real-world” datasets and identifies novel DMRs that are associated with several inflammatory markers.

Content- and semantic-based interactive mining systems describe remote sensing images by means of relevant features. Region-based retrieval systems have been proposed to capture the local properties of an image. Existing systems use computationally extensive methods to extract primitive features based on color, texture (spatial gray level dependency - SGLD matrices), and shape from the segmented homogenous region. The use of wavelet transform techniques has recently gained momentum in multimedia image archives to expedite the retrieval process. However, the current semantic-enabled framework for the geospatial data uses computationally extensive methods for feature extraction and image segmentation. Hence, this dissertation presents the use of a wavelet-based feature extraction in a semantics-enabled framework to expedite the knowledge discovery in geospatial data archives. Geospatial data has different characteristics than multimedia images and poses more challenges. The experimental assumptions, such as the selection of the wavelet decomposition level and mother wavelet used for multimedia data archives, might not prove to be efficient for the retrieval of geospatial data. Discrete wavelet transforms (DWT) introduce aliasing effects due to subband decimation at a certain decomposition level. This dissertation addresses the issue of selecting a suitable wavelet decomposition level, and a systematic selection process is developed for image segmentation. To validate the applicability of this method, a synthetic image is generated to assess the performance qualitatively and quantitatively. In addition, results for a Landsat7 ETM+ imagery archive are illustrated, and the F-measure is used to assess the feasibility of this method for retrieval of different classes. This dissertation also introduces a new feature set obtained by coalescing wavelet and independent component analysis for image information mining. Feature-level fusion is performed to include the missing high detail information from the panchromatic image. Results show that the presented feature set is computationally less expensive and more efficient in capturing the spectral and spatial texture information when compared to traditional approaches. After extensive experimentation with different types of mother wavelets, it can be concluded that reverse Biorthogonal wavelets of shorter length and the simple Haar filter provided better results for the image information mining from the database used in this study.

Because of the vast data volume of hyperspectral imagery, compression becomes a necessary process for hyperspectral data transmission, storage, and analysis. Three-dimensional discrete wavelet transform (DWT) based algorithms are particularly of interest due to their excellent rate-distortion performance. This thesis investigates several issues surrounding efficient compression using JPEG2000. Firstly, the rate-distortion performance is studied when Principal Component Analysis (PCA) replaces DWT for spectral decorrelation with the focus on the use of a subset of principal components (PCs) rather than all the PCs. Secondly, the algorithms are evaluated in terms of data analysis performance, such as anomaly detection and linear unmixing, which is directly related to the useful information preserved. Thirdly, the performance of compressing radiance and reflectance data with or without bad band removal is compared, and instructive suggestions are provided for practical applications. Finally, low-complexity PCA algorithms are presented to reduce the computational complexity and facilitate the future hardware design.

Abiotic stresses cause extensive loss to agriculture production worldwide. Cowpea is an important legume crop grown widely in tropical and subtropical regions where high temperature, ultraviolet-B (UVB) radiation and drought are the common stress factors limiting production. Various vegetative, physiological, biochemical and reproductive plant attributes were assessed under a range of UVB radiation levels in Experiment I and in a combination with two doses of each carbon dioxide concentration [CO2], temperature, and UVB radiation and their interactions in Experiment II by using six cowpea genotypes and sunlit plant growth chambers. The dynamics of photosynthesis and fluorescence processes were assessed in 15 cowpea genotypes under drought condition in Experiment III in pot-grown plants under sunlit conditions. A distinct response pattern was not observed in cowpea in response to UVB radiation form 0 to 15 kJ; however, plants grown under elevated UVB showed reduced photosynthesis resulting in shorter plants and produced smaller flowers and lower seed yield. Increased phenolic compounds appeared to be a defense response to UVB radiation. The growth enhancements observed by doubling of [CO2] were not observed when plants were grown in combination with elevated UVB or temperature which also showed the most detrimental effects on plant growth and seed yield. Results form Experiment I and II revealed that cowpea reproductive traits were highly sensitive to abiotic stresses compared to the vegetative growth and development. A total stress response index (TSRI) technique, derived from all vegetative and reproductive parameters, was used to screen genotypes for their stress tolerance to UVB or combination of stresses. An increase in water use efficiency while maintaining higher rate of photosynthesis was an important drought tolerance mechanism in tolerant cowpea genotypes. Using principal component analysis technique, four groups of the genotypes were identified for their drought tolerance. Evaluating same genotypes across stress conditions revealed that no single genotype has the absolute tolerance characters to all stress conditions. The identified diversity for abiotic stress tolerance among cowpea genotypes and associated traits can be used to develop tolerant genotypes suitable for an agro-ecological niche though traditional breeding or genetic engineering methods.

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