Imaging instruments are required for accurate tumor resection during neurosurgery, especially in the case of glioblastoma multiforme (GBM) - the most common and aggressive malignant glioma. However, current intraoperative imaging techniques for detection of glioma either suffer low sensitivity and low specificity or require a significant capital cost. Advances in diffuse reflectance spectroscopy and fluorescence spectroscopy have offered high sensitivity and high specificity in differentiating tumors from normal tissues with much lower capital cost. Whereas diffuse reflectance spectroscopy alone and fluorescence spectroscopy alone has been used in limited studies to differentiate normal brain tissues from brain tumors with moderate sensitivity and specificity, low specificity and sensitivity were usually observed when studying high grade glioma (HGG) such as GBM. Furthermore, optical properties and diffuse reflectance signal of HGG and low grade glioma (LGG) have not been observed separately, and thus a relation between optical properties and glioma progression has not been established. Intraoperative differentiation of GBM and LGG can be helpful in making treatment plan at the first surgery. This thesis focuses on characterizing a previous integrated system of diffuse reflectance spectroscopy and fluorescence spectroscopy to extract optical properties and fluorescence properties of LGG and GBM. First, tissue-simulating phantom models were developed to calibrate the integrated system. The direct method and Mie theory were used to calculate optical scattering of the phantoms while Beer-Lambert’s law was used to calculate optical absorption. Second, an experimental method was introduced to recover intrinsic fluorescence because the measured fluorescence signal is likely distorted by the presence of scatterers and absorbers in tissue (i.e. hemoglobin). Third, an experimental method was developed to recover optical properties of both GBM and LGG. In addition, the sensitivity and specificity of the integrated system was optimized. / Thesis / Doctor of Philosophy (PhD)

Condoms have been used in sexual assaults as a means of preventing the transmission of biological fluids. Current sexual assault evidence collection kit processing protocols do not regularly take advantage of the information that can be gathered by examining residues left by condoms during intercourse. A biphasic liquid-liquid extraction technique was developed to separate polar and non-polar condom residues, which had been collected on cotton tipped swabs. This research involved the examination of twenty condom brands by Diffuse Reflectance Infrared Fourier Transform Spectroscopy. Five brands were selected to examine the consistency of this technique when the lubricants were exposed to body and storage temperature conditions for various times and in the presence of oral, vaginal, and blood samples. Additionally, starches collected from the condoms under each of the above conditions were examined. Although all lubricants were identifiable using this IR technique, the nonoxynol-9 (spermicide) containing samples produced spectra which were not identical to those produced by nonoxynol-9 standards. Although there was a decrease in the percent transmittance within IR spectra as the time between the collection and the extraction of the swabs increased, the condom residues of interest remained identifiable at all time points examined. The use of vaginal and oral swabs in the collection caused a negligible amount of background interference, which could be eliminated through spectral subtraction of the swab.

Golf courses can expand hundreds of acres, making scouting for both pests and beneficial insect populations a time-consuming task. Scouting for insects is labor-intensive, potentially damaging, but is an integral part of an integrated pest and pollinator management (IPPM) plan. Virginia golf courses are currently using remote sensing and light reflectance to detect non-insect pests in turfgrass. This thesis aims to develop remote sensing and light reflectance methods to aid in a turfgrass IPPM plan, to document the phenology of ABW weevil (Listronotus maculicollis Kirby, Coleoptera: Curculionidae, ABW), and to catalogue pollinator-friendly out-of-play areas. Light reflectance, the measurement of the amount of light reflected, of plants can be used as a proxy for the health of a plant. The light reflectance of turfgrass affected by ABW stress and plants in the out-of-play areas of golf courses was collected proximally and remotely, using a backpack spectrometer and an unmanned aerial vehicle (UAV), respectively. Mathematical light reflectance indices were applied and compared to insect populations in both areas to determine the correlation. The Normalized Difference Vegetation Index (NDVI), which uses red and near-infrared wavelengths to indicate stress, was found to highlight ABW stressed turfgrass. The Structure Intensive Vegetation Pigment Index (SIPI), which uses red and green wavelengths to highlight flowering plants, was found to highlight potential pollinator- friendly habitats in out-of-play areas. When applied to flights, NDVI could help in the targeted application of insecticides to combat the annual bluegrass weevil, therefore reducing their presence in the environment. The use of SIPI could highlight potential pollinator friendly habitats and therefore assist superintendents in the development of their IPPM plan. / Master of Science in Life Sciences / Scouting, such as completing visual monitoring or taking soil core samples, is an important part in the development of an integrated pest and pollinator management (IPPM) plan for Virginia golf courses; an IPPM plan focuses on control of a pest, while considering the needs of pollinators. The size of golf courses makes scouting for insect pests and beneficial insects a time-consuming task. Golf courses are currently using remote sensing, the use of drones in combination with other technology, to scout for other pests or disease. Light reflectance, the measurement of the amount of light reflected, is often used in combination with remote sensing as a proxy for the health of plants. This thesis developed remote sensing and light reflectance techniques not only to detect a common turfgrass pest, the annual bluegrass weevil (Listronotus maculicollis Kirby, Coleoptera: Curculionidae, ABW), but to also predict the presence of potential pollinator habitats in the out-of-play areas of Virginia golf courses. Instruments such as a spectrometer and a drone were used to collect light reflectance at the ground level and aerially, respectively. Ground data was collected through soap water flushes to detect adult ABW, and visual monitoring of potentially pollinating bees, beetles, butterflies, and flies. The light reflectance and ground data were compared using mathematical indices to determine if there was a relationship between the presence of insects and a particular index. Indices could be applied to drone flights that golf course superintendents are already performing, and they can use this information to highlight potential areas of insect presence. This will help them to take care not to apply insecticides in areas with pollinators or to only apply necessary insecticides where there is likely a presence of ABW. This will reduce the labor, other costs, and the environmental impact of insecticides.

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.

Whole genome duplication, or polyploidy, is a common process in plants by which failures in meiosis or fertilization result in offspring with twice the number of chromosomes. This doubles the number of copies of every gene, an effect thought to generate new ‘raw material' upon which natural selection can act. Few studies exist examining the consequences of polyploidy for plant physiological traits. Doubling the number of gene copies may have unknown effects on leaf structure and function. In this study, I compare diploid, tetraploid, and hexaploid species within the genus Helianthus (wild sunflowers). Forty different accessions of wild sunflowers were grown under standardized greenhouse conditions and phenotyped for both leaf functional traits and leaf hyperspectral reflectance. Interestingly, I find that whole genome duplication can have effects on leaf functional traits relevant to both size and ecophysiology, and thus that polyploidy may lead to functional trait differentiation between polyploids and their diploid progenitors.

No description available.

No description available.

No description available.

No description available.

No description available.