Extended principal component analysis and its applications to image analysis

The objectives of this research are to analyze and develop a modified Principal Component Analysis (PCA) and to develop a two-dimensional PCA with applications in image processing. PCA is a classical multivariate technique where its mathematical treatment is purely based on the eigensystem of positive-definite symmetric matrices. Its main function is to statistically transform a set of correlated variables to a new set of uncorrelated variables over $\IR\sp{n}$ by retaining most of the variations present in the original variables.^ The variances of the Principal Components (PCs) obtained from the modified PCA form a correlation matrix of the original variables. The decomposition of this correlation matrix into a diagonal matrix produces a set of orthonormal basis that can be used to linearly transform the given PCs. It is this linear transformation that reproduces the original variables. The two-dimensional PCA can be devised as a two successive of one-dimensional PCA. It can be shown that, for an $m\times n$ matrix, the PCs obtained from the two-dimensional PCA are the singular values of that matrix.^ In this research, several applications for image analysis based on PCA are developed, i.e., edge detection, feature extraction, and multi-resolution PCA decomposition and reconstruction. ^

Correlation of detector dog alerts to cocaine decomposition products found in illicit forensic specimens

The volatile chemicals which comprise the odor of the illicit drug cocaine have been analyzed by adsorption onto activated charcoal followed by solvent elution and GC/MS analysis. A series of field tests have been performed to determine the dominant odor compound to which dogs alert. All of our data to date indicate that the dominant odor is due to the presence of methyl benzoate which is associated with the cocaine, rather than the cocaine itself. When methyl benzoate and cocaine are spiked onto U.S. currency, the threshold level of methyl benzoate required for a canine to signal an alert is typically 1-10 $\mu$g. Humans have been shown to have a sensitivity similar to dogs for methyl benzoate but with poorer selectivity/reliability. The dominant decomposition pathway for cocaine has been evaluated at elevated temperatures (up to 280$\sp\circ$C). Benzoic acid, but no detectable methyl benzoate, is formed. Solvent extraction and SFE were used to study the recovery of cocaine from U.S. currency. The amount of cocaine which could be recovered was found to decrease with time. ^

American Alligator Digestion Rate of Blue Crabs and Its Implications for Stomach Contents Analysis

Stomach contents analysis (SCA) provides a snap-shot observation of a consumer's diet. Interpretation of SCA data can be complicated by many factors, including variation in gastric residence times and digestion rates among prey taxa. Although some SCA methods are reported to efficiently remove all stomach contents, the effectiveness of these techniques has rarely been tested for large irregular shaped prey with hard exoskeletons. We used a controlled feeding trial to estimate gastric residency time and decomposition rate of a large crustacean prey item, the Blue Crab (Callinectes sapidus), which is consumed by American Alligators (Alligator mississippiensis), an abundant apex predator in coastal habitats of the southeastern United States. The decomposition rate of C. sapidus in the stomachs of A. mississippiensis followed a predictable pattern, and some crab pieces remained in stomachs for at least 14 days. We also found that certain portions of C. sapidus were prone to becoming caught within the stomach or esophagus, meaning not all crab parts are consistently recovered using gastric lavage techniques. However, because the state of decomposition of crabs was predictable, it is possible to estimate time since consumption for crabs recovered from wild alligators. This information, coupled with a detailed understanding of crab distributions and alligator movement tactics could help elucidate patterns of cross-ecosystem foraging by the American Alligator in coastal habitats.

Hydroperiod and seasonal effects on fish decomposition in an oligotrophic Everglades marsh

In the Everglades, the majority of fish detrital inputs occur during the dry scason, when waterlevel drawdown reduces aquatic habitat. While these mortality events are highly seasonal, the remineralization and recycling of fish detrital nutrients may represent an important stimulus to the ecosystem in the following wet season. The goal of this study was to quantify the rate of detrital fish decomposition during three periods of the year to determine seasonal variations in decomposition patterns in this ecosystem. A multiple regression analysis showed that hydroperiod and water depth both played a role in determining fish decomposition rates within this ecosystem. Decomposition rates ranged from a low of 13% day−1 in December 2000 to a high of 50% day−1 in April 2001, the height of the dry season. Phosphorus analysis showed that Gambusia holbrooki, the dominant small fish species in the Everglades, contains 7.169±1.46 mg P g−1 wet fish weight. Based on the observed decomposition rates and the average biomass added, the estimafed daily flux of phosphorus from the experimental detrital loading ranged from a low of 27.04 mg P day−1 to a high of 108.14 mg P day−1 during the decomposition period. We estimated that these inputs could represent an input of 43 μg P m−2 day−1 to the total temporal Everglades phosphorus budget. Although much of this phosphorus is likely incorporated into the macroinvertebrate pool, detrital inputs peak during the dry season when nutrients are most likely to be incorporated into the soil and occur when decomposition of vegetative material is moisture-limited. These inputs may therefore play an important role in stimulating vegetative production during the early wet season.

Critical Analysis on the Structural and Magnetic Properties of Bulk and Nanocrystalline Cu-Fe-O

Nanocrystalline and bulk samples of “Fe”-doped CuO were prepared by coprecipitation and ceramic methods. Structural and compositional analyses were performed using X-ray diffraction, SEM, and EDAX. Traces of secondary phases such as CuFe2O4, Fe3O4, and α-Fe2O3 having peaks very close to that of the host CuO were identified from the Rietveld profile analysis and the SAED pattern of bulk and nanocrystalline Cu0.98Fe0.02O samples. Vibrating Sample Magnetometer (VSM) measurements show hysteresis at 300 K for all the samples. The ferrimagnetic Neel transition temperature () was found to be around 465°C irrespective of the content of “Fe”, which is close to the value of cubic CuFe2O4. High-pressure X-Ray diffraction studies were performed on 2% “Fe”-doped bulk CuO using synchrotron radiation. From the absence of any strong new peaks at high pressure, it is evident that the secondary phases if present could be less than the level of detection. Cu2O, which is diamagnetic by nature, was also doped with 1% of “Fe” and was found to show paramagnetic behavior in contrast to the “Fe” doped CuO. Hence the possibility of intrinsic magnetization of “Fe”-doped CuO apart from the secondary phases is discussed based on the magnetization and charge state of “Fe” and the host into which it is substituted.

Method development for the analysis of smokeless powders and organic gunshot residue by ultra performance liquid chromatography with tandem mass spectrometry

The goal of this project was to develop a rapid separation and detection method for analyzing organic compounds in smokeless powders and then test its applicability on gunshot residue (GSR) samples. In this project, a total of 20 common smokeless powder additives and their decomposition products were separated by ultra performance liquid chromatography (UPLC) and confirmed by tandem mass spectrometry (MS/MS) using multiple reaction monitoring mode (MRM). Some of the targeted compounds included diphenylamines, centralites, nitrotoluenes, nitroglycerin, and various phthalates. The compounds were ionized in the MS source using simultaneous positive and negative electrospray ionization (ESI) with negative atmospheric pressure chemical ionization (APCI) in order to detect all compounds in a single analysis. The developed UPLC/MS/MS method was applied to commercially available smokeless powders and gunshot residue samples recovered from the hands of shooters, spent cartridges, and smokeless powder retrieved from unfired cartridges. Distinct compositions were identified for smokeless powders from different manufacturers and from separate manufacturing lots. The procedure also produced specific chemical profiles when tested on gunshot residues from different manufacturers. Overall, this thesis represents the development of a rapid and reproducible procedure capable of simultaneously detecting the widest possible range of components present in organic gunshot residue.^

Identification of characteristic volatile organic compounds released during the decomposition process of human remains and analogues

The manner in which remains decompose has been and is currently being researched around the world, yet little is still known about the generated scent of death. In fact, it was not until the Casey Anthony trial that research on the odor released from decomposing remains, and the compounds that it is comprised of, was brought to light. The Anthony trial marked the first admission of human decomposition odor as forensic evidence into the court of law; however, it was not "ready for prime time" as the scientific research on the scent of death is still in its infancy. This research employed the use of solid-phase microextraction (SPME) with gas chromatography-mass spectrometry (GC-MS) to identify the volatile organic compounds (VOCs) released from decomposing remains and to assess the impact that different environmental conditions had on the scent of death. Using human cadaver analogues, it was discovered that the environment in which the remains were exposed to dramatically affected the odors released by either modifying the compounds that it was comprised of or by enhancing/hindering the amount that was liberated. In addition, the VOCs released during the different stages of the decomposition process for both human remains and analogues were evaluated. Statistical analysis showed correlations between the stage of decay and the VOCs generated, such that each phase of decomposition was distinguishable based upon the type and abundance of compounds that comprised the odor. This study has provided new insight into the scent of death and the factors that can dramatically affect it, specifically, frozen, aquatic, and soil environments. Moreover, the results revealed that different stages of decomposition were distinguishable based upon the type and total mass of each compound present. Thus, based upon these findings, it is suggested that the training aids that are employed for human remains detection (HRD) canines should 1) be characteristic of remains that have undergone decomposition in different environmental settings, and 2) represent each stage of decay, to ensure that the HRD canines have been trained to the various odors that they are likely to encounter in an operational situation.

Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.