Frequency-dependent earthquake coda attenuation values are often reported; however such measurements usually depend on the types of the attenuation models employed. In this thesis, I use numerical modeling of Peaceful Nuclear Explosion (PNE) codas at far regional to teleseismic distances to compare two of such models, namely the conventional frequency-dependent attenuation with parameters (Q0, ¦Ç) defined by Qcoda(f) = Q0f¦Ç and frequency-independent effective attenuation (Qe) with geometrical attenuation (¦Ã). The results favour strongly the (¦Ã, Qe) model and illustrate the mechanisms leading to apparent Qcoda(f) dependencies. Tests for variations of the crustal velocity structures show that the values of ¦Ã are stable and related to lithospheric structural types, and the inverted Qe values can be systematically mapped into the true Swave attenuation factors within the crust. Modeling also shows that ¦Ã could increase in areas where relatively thin attenuating layers are present within the crust; such areas could likely be related to younger and active tectonics. By contrast, when interpreted by using the traditional (Q0,¦Ç) approach, the synthetic coda shows a strong and spurious frequency dependence with ¦Ç ¡Ö 0.5, which is also similar to many published observations.<p> Observed Lg codas from two Peaceful Nuclear Explosions located in different areas in Russia show similar values of ¦Ã ¡Ö 0.75¡¤10-2 s-1, which are also remarkably close to the independent numerical predictions in this thesis. At the same time, coda Qe values vary strongly, from 850 in the East European Platform to 2500 within the Siberian Craton. This suggests that parameters ¦Ã and Qe could provide stable and transportable discriminants for differentiating between the lithospheric tectonic types and ages, and also for seismic coda regionalization in nuclear-test monitoring research.

Hurricanes are one of the primary threats to the Texas coastal environment and economy. They generate large wave and storm surges that have caused much damage on the Texas coast in the past. Understanding both the hydrodynamic processes that damage coastal habitats and hurricane hazard and risk are critical to preserve coastal vegetation and quantify its benefits to coastal storm protection. The goal of this project is to quantify the impact of wave attenuation and wave refraction as well as the development of coherent structures in marsh fringes and the formation of a rip current system over wetlands on storm protection. The 3D Shallow Water Wave Basin at Texas A&M University hosted a series of large-scale experiments considering an idealized wetland model to pursue this goal. Study of the marsh geometry of the Texas coast was done in order to scale the experiments to the size of the Haynes Laboratory 3D-Water Wave Basin using a Froude and a Reynolds scalings. Particularly, averaged size and idealized shape of marsh segments in the area of Dalehite Cove in Galveston Bay were considered. Three sets of different wave conditions and water levels were tested to approximate different intensities of storm surge. Identical tests with both vegetated and non-vegetated marshes were run to compare the influence of the vegetation in storm conditions, and three different spacings between marsh segments were tested. In the basin, normally incident regular waves were generated at three water circulation structures. Data analysis allows the determination of the impact of discontinuous marsh segments on wave attenuation and wave refraction. Coherent structures such as rip current and the circulation pattern were analyzed to study the change in the flow field during passage of the waves. The experimental measurements were able to describe the wave transformations over the marsh segments. The influence of coastal wetlands was identified to affect the hydrodynamic process and reduce the total wave energy which is dissipated and redistributed by vegetation. The presence of the mounds induced an important decrease in the wave height, in addition to the damping of the waves by the vegetation stems. The variation in spatial coverage of the wetland model has been shown to highly affect the flow dynamics by generating offshore directed flow in the channel and onshore directed flow on the marsh mounds. This experimental approach provides a further understanding of flow dynamics by waves and surge in wetlands, at a large scale.

Over the last decade in North America, an increasing number of microbiological drinking water regulations have been used to manage groundwater resources that are potentially influenced by surface water. Regulations such as the Ontario Ministry of Environment Regulation 505, which requires at least a 60 day groundwater travel time between surface waters and drinking water wells, have been created with limited understanding of subsurface pathogen transport processes. Groundwater Under Direct Influence studies (GUDI or GWUDI in USA) are conducted to assess the need to treat well water at an extraction point. Currently, there is a lack of knowledge regarding factors that affect the transport of pathogens through porous media at the surface water-groundwater interface. Such information is required to supply sufficient quantities of drinking water in a cost effective and safe manner. <br /><br /> Factors that affect pathogen transport through porous media include: properties of the pathogen (i. e. surface charge, size, and morphology), properties of the granular media (i. e. mineralogy, size, texture, angularity) and properties of the water (i. e. pH, ionic strength and content, and natural organic matter). This study examines the effects of ionic strength, grain size and influent virus concentrations on pathogen transport in porous media. Fourteen column tests were conducted using the bacteriophage MS2 and 1. 5 µm microspheres; two commonly used non-pathogenic surrogates representative of human viruses and bacteria, respectively. Two size distributions of crushed silica sand, with median grain diameters of 0. 7 and 0. 34 mm, and two ionic strengths of 8 and 95 mmol/L were used. A 2² partial factorial design was used with a minimum of two replicates of each combination of the parameters. <br /><br /> The results show that complete breakthrough of both viruses and microspheres occurred in medium sand at low ionic strength. It was found that increasing ionic strength by Ca²⁺ addition precluded breakthrough of MS2 in both the medium and fine sands. This represents a greater than 8 log reduction in peak effluent concentration and essentially complete attenuation. <br /><br /> In fine sand, with low ionic strength water, a 5 log reduction in peak MS2 concentrations was observed. In the same sand at high ionic strength, no MS2 broke through the column, corresponding to a greater than 8 log removal. Since complete attenuation occurred in both grain sizes at high ionic strength, the effect of higher ionic strength in the fine sand was indistinguishable from the effect observed from raising the ionic strength in the medium sand. <br /><br /> In contrast to the viruses, microsphere transport was essentially unaffected by increasing ionic strength under the conditions investigated. A 1 log reduction in peak concentration was observed in the high ionic strength water in the medium sand. In spite of this, grain size had a profound effect on the attenuation of microspheres. There was no evidence of microsphere breakthrough in any of the fine sand columns at the low or high ionic strengths, yielding a greater than 5 log reduction in microsphere concentration associated with grain size alone. The effect of varying virus concentration was also investigated. It was found that varying the concentration of viruses between 10⁵ and 10⁷ pfu/ml had no discernable effect on their observed transport characteristics; normalised peak breakthrough concentration, percent attenuation and retardation relative to a bromide tracer. <br /><br /> Based on the results from this Thesis, in a riverbank filtration environment, there is reason to expect that, at comparable water qualities and in similar porous media, multiple logarithmic reductions of viruses and bacteria would occur over the much longer (than column length) flowpaths associated with RBF. There is also reason to expect this attenuation capability to vary based on riverbank grain size and water chemistry.

Over the last decade in North America, an increasing number of microbiological drinking water regulations have been used to manage groundwater resources that are potentially influenced by surface water. Regulations such as the Ontario Ministry of Environment Regulation 505, which requires at least a 60 day groundwater travel time between surface waters and drinking water wells, have been created with limited understanding of subsurface pathogen transport processes. Groundwater Under Direct Influence studies (GUDI or GWUDI in USA) are conducted to assess the need to treat well water at an extraction point. Currently, there is a lack of knowledge regarding factors that affect the transport of pathogens through porous media at the surface water-groundwater interface. Such information is required to supply sufficient quantities of drinking water in a cost effective and safe manner. <br /><br /> Factors that affect pathogen transport through porous media include: properties of the pathogen (i. e. surface charge, size, and morphology), properties of the granular media (i. e. mineralogy, size, texture, angularity) and properties of the water (i. e. pH, ionic strength and content, and natural organic matter). This study examines the effects of ionic strength, grain size and influent virus concentrations on pathogen transport in porous media. Fourteen column tests were conducted using the bacteriophage MS2 and 1. 5 µm microspheres; two commonly used non-pathogenic surrogates representative of human viruses and bacteria, respectively. Two size distributions of crushed silica sand, with median grain diameters of 0. 7 and 0. 34 mm, and two ionic strengths of 8 and 95 mmol/L were used. A 2² partial factorial design was used with a minimum of two replicates of each combination of the parameters. <br /><br /> The results show that complete breakthrough of both viruses and microspheres occurred in medium sand at low ionic strength. It was found that increasing ionic strength by Ca²⁺ addition precluded breakthrough of MS2 in both the medium and fine sands. This represents a greater than 8 log reduction in peak effluent concentration and essentially complete attenuation. <br /><br /> In fine sand, with low ionic strength water, a 5 log reduction in peak MS2 concentrations was observed. In the same sand at high ionic strength, no MS2 broke through the column, corresponding to a greater than 8 log removal. Since complete attenuation occurred in both grain sizes at high ionic strength, the effect of higher ionic strength in the fine sand was indistinguishable from the effect observed from raising the ionic strength in the medium sand. <br /><br /> In contrast to the viruses, microsphere transport was essentially unaffected by increasing ionic strength under the conditions investigated. A 1 log reduction in peak concentration was observed in the high ionic strength water in the medium sand. In spite of this, grain size had a profound effect on the attenuation of microspheres. There was no evidence of microsphere breakthrough in any of the fine sand columns at the low or high ionic strengths, yielding a greater than 5 log reduction in microsphere concentration associated with grain size alone. The effect of varying virus concentration was also investigated. It was found that varying the concentration of viruses between 10⁵ and 10⁷ pfu/ml had no discernable effect on their observed transport characteristics; normalised peak breakthrough concentration, percent attenuation and retardation relative to a bromide tracer. <br /><br /> Based on the results from this Thesis, in a riverbank filtration environment, there is reason to expect that, at comparable water qualities and in similar porous media, multiple logarithmic reductions of viruses and bacteria would occur over the much longer (than column length) flowpaths associated with RBF. There is also reason to expect this attenuation capability to vary based on riverbank grain size and water chemistry.

Frequency-dependent earthquake coda attenuation values are often reported; however such measurements usually depend on the types of the attenuation models employed. In this thesis, I use numerical modeling of Peaceful Nuclear Explosion (PNE) codas at far regional to teleseismic distances to compare two of such models, namely the conventional frequency-dependent attenuation with parameters (Q0, ¦Ç) defined by Qcoda(f) = Q0f¦Ç and frequency-independent effective attenuation (Qe) with geometrical attenuation (¦Ã). The results favour strongly the (¦Ã, Qe) model and illustrate the mechanisms leading to apparent Qcoda(f) dependencies. Tests for variations of the crustal velocity structures show that the values of ¦Ã are stable and related to lithospheric structural types, and the inverted Qe values can be systematically mapped into the true Swave attenuation factors within the crust. Modeling also shows that ¦Ã could increase in areas where relatively thin attenuating layers are present within the crust; such areas could likely be related to younger and active tectonics. By contrast, when interpreted by using the traditional (Q0,¦Ç) approach, the synthetic coda shows a strong and spurious frequency dependence with ¦Ç ¡Ö 0.5, which is also similar to many published observations.<p> Observed Lg codas from two Peaceful Nuclear Explosions located in different areas in Russia show similar values of ¦Ã ¡Ö 0.75¡¤10-2 s-1, which are also remarkably close to the independent numerical predictions in this thesis. At the same time, coda Qe values vary strongly, from 850 in the East European Platform to 2500 within the Siberian Craton. This suggests that parameters ¦Ã and Qe could provide stable and transportable discriminants for differentiating between the lithospheric tectonic types and ages, and also for seismic coda regionalization in nuclear-test monitoring research.

Imaging based muscle density (MD) is associated with poor lower extremity performance, the development of mobility impairments, frailty, and hip fracture. These associations are all related to falls, yet no studies have investigated MD in community dwelling fallers. The primary objective of this study was to determine whether lower leg MD differed between community dwelling elderly women who do and do not report falls. The secondary objective was to determine if lower leg muscle cross sectional area (MCSA), timed up & go (TUG) test, and relative grip strength (RGS; as a ratio to body mass) differed between fallers and non-fallers. Women (N = 135), 60 years or older (mean age 74.1, SD 7.6) were recruited from a random sample of Saskatoon residents. Fallers (n = 36) and Non-fallers (n = 99) were grouped based on 12-month retrospective falls survey response. A peripheral quantitative computed tomography (pQCT) scan of the non-dominant lower leg was acquired to determine MD and MCSA. Participant age, height, weight, TUG test result and RGS were recorded. Between-group differences in mean age, body mass index (BMI), MD, MCSA, TUG and RGS were compared using independent t-tests (P < 0.05). MD and TUG results were transformed to meet the assumption of normality for parametric analysis. Age, BMI, MCSA and RGS did not differ (P > 0.5). Fallers had 3.2% lower MD (P = 0.01) and 15.1% slower TUG scores (P = 0.02), than non-fallers. Muscle density may serve as a physiological marker for the assessment of muscular health and fall risk in community dwelling elderly women.

<p>Optical-CT has been shown to be a potentially useful imaging tool for for the two very different spheres of biologists and radiation therapy physicists, but it has yet to live up to that potential. In radiation therapy, researchers have used optical-CT for the readout of 3D dosimeters, but it is yet to be a clinically relevant tool as the technology is too slow to be considered practical. Biologists have used the technique for structural imaging, but have struggled with emission tomography as the reality of photon attenuation for both excitation and emission have made the images quantitatively irrelevant. </p><p><bold>Dosimetry.</bold> The DLOS (Duke Large field of view Optical-CT Scanner) was designed and constructed to make 3D dosimetry utilizing optical-CT a fast and practical tool while maintaining the accuracy of readout of the previous, slower readout technologies. Upon construction/optimization/implementation of several components including a diffuser, band pass filter, registration mount & fluid filtration system the dosimetry system provides high quality data comparable to or exceeding that of commercial products. In addition, a stray light correction algorithm was tested and implemented. The DLOS in combination with the 3D dosimeter it was designed for, PREAGETM, then underwent rigorous commissioning and benchmarking tests validating its performance against gold standard data including a set of 6 irradiations. </p><p>DLOS commissioning tests resulted in sub-mm isotropic spatial resolution (MTF >0.5 for frequencies of 1.5lp/mm) and a dynamic range of ~60dB . Flood field uniformity was 10% and stable after 45minutes. Stray light proved to be small, due to telecentricity, but even the residual can be removed through deconvolution. Benchmarking tests showed the mean 3D passing gamma rate (3%, 3mm, 5% dose threshold) over the 6 benchmark data sets was 97.3% ± 0.6% (range 96%-98%) scans totaling ~10 minutes, indicating excellent ability to perform 3D dosimetry while improving the speed of readout. Noise was low at ~2% for 2mm reconstructions. The DLOS/PRESAGE® benchmark tests show consistently excellent performance, with very good agreement to simple known distributions. The telecentric design was critical to enabling fast (~15mins) imaging with minimal stray light artifacts. The system produces accurate isotropic 2mm3 dose data over clinical volumes (e.g. 16cm diameter phantoms, 12 cm height), and represents a uniquely useful and versatile new tool for commissioning complex radiotherapy techniques. The system also has wide versatility, and has successfully been used in preliminary tests with protons and with kV irradiations.</p><p><bold>Biology.</bold> Attenuation corrections for optical-emission-CT were done by modeling physical parameters in the imaging setup within the framework of an ordered subset expectation maximum (OSEM) iterative reconstruction algorithm. This process has a well documented history in single photon emission computed tomography (SPECT), but is inherently simpler due to the lack of excitation photons to account for. Excitation source strength distribution, excitation and emission attenuation were modeled. The accuracy of the correction was investigated by imaging phantoms containing known distributions of attenuation and fluorophores. The correction was validated on a manufactured phantom designed to give uniform emission in a central cuboidal region and later applied to a cleared mouse brain with GFP (green-fluorescent-protein) labeled vasculature and a cleared 4T1 xenograft flank tumor with constitutive RFP (red-fluorescent-protein). Reconstructions were compared to corresponding slices imaged with a fluorescent dissection microscope. </p><p>Significant optical-ECT attenuation artifacts were observed in the uncorrected phantom images and appeared up to 80% less intense than the verification image in the central region. The corrected phantom images showed excellent agreement with the verification image with only slight variations. The corrected tissue sample reconstructions showed general agreement between the verification images. Comprehensive modeling in optical-ECT imaging was successfully implemented, creating quantitatively accurate 3D fluorophore distributions. This work represents the 1st successful attempt encompassing such a complete set of corrections. This method provides a means to accurately obtain 3D fluorophore distributions with the potential to better understand tumor biology and treatment responses.</p> / Dissertation

Accidental spills of hydrocarbons from underground storage tanks or pipelines are a common cause of subsurface contamination. Anthropogenic hydrocarbon contamination of soil is a global issue throughout the industrialised world. In England and Wales alone, 12% of all serious contamination incidents in 2007 were hydrocarbon related. Biodegradation could be in situ process leading to a decrease of benzene concentrations in groundwater. Recently, monitored natural attenuation has become an effective alternative to the more active remediation methods for the in situ treatment of contaminated subsurface environments. The main objective of this study was to examine the possibility of adopting monitored natural attenuation as a remediation technique for the contaminated groundwater aquifer. In this natural attenuation study, the following tasks were conducted bioremediation investigation, biological first-order decay rates, Mann-Kendall Test model and BIOSCREEN model for the contaminated groundwater aquifer. In this study, a full-scale natural bioremediation investigation was conducted at a petroleum hydrocarbon spill site. In this study, The calculated biodegradation capacity (8.261 mg/L) at this site is much higher than the detected concentrations of petroleum-hydrocarbons (3-4 mg/L) within the most contaminated area inside the plume. Thus, natural biodegradation should be able to remove the contaminants effectively. The calculated biological first-order decay rates for benzene were between 1.7¡Ñ10-3-9.0¡Ñ10-4 day-1 respectively. Mann-Kendall test was applied to analyze the trend of contaminant variations. Results show that the S-value of monitor wells SW-1W, SW-4W, SW-42W, SW-23W, SW-30W, SW-67W and SW-70W were -2.23607, -1.16276, -1.52053, -1.34164, -1.26323, 0 and -1.34164, respectively. The negative S values reveal that the all contaminants tended to decrease. This indicates that the hydrocarbon plume at this site is not expanding, and has been contained effectively by the natural attenuation mechanisms. BIOSCREEN model from the groundwater analyses indicate, a first-order decay model reached the downgradient monitor well located 220 m from the spill location. that approximately 89% of the contaminate removal was due to biodegradation processes. The study of petroleum-hydrocarbons bacterial consortium were include Aquincola tertiaricarbonis L10¡BBosea sp. GR060219¡BBrachymonas petroleovorans strain CHX¡BHydrogenophaga sp. p3(2011)¡BHydrogenophaga sp.¡BMethylibium sp. YIM 61602¡BMycobacterium sp.¡BRhodoferax sp. IMCC1723¡BRhodoferax sp.¡BUncultured Rhodocyclaceae bacterium clone Elev_16S_975¡BUncultured Rhodocyclaceae bacterium clone eub62B1¤ÎUncultured Beggiatoa sp. clone GE7GXPU01BJTWR. Thus, the in situ bioremediation technology has the potential to be developed into an environmentally, economically and naturally acceptable remediation technology. Evidences for the occurrence of natural attenuation include the following: (1) depletion of dissolved oxygen, nitrate, and sulfate; (2) production of dissolved ferrous iron, sulfide, and CO2; (3) decreased BTEX concentrations and BTEX as carbon to TOC ratio along the transport path; (4) increased alkalinity and microbial species; (5) limited spreading of the BTEX plume; and (6) preferential removal of certain BTEX components along the transport path. Results indicate that natural attenuation can effectively contain the plume, and biodegradation processes played an important role on contaminant removal.

To better study frequency related effects such as attenuation and tuning, we developed a frequency dependent seismic reflection analysis. Comprehensive tests on full waveform synthetics and observations from the Teal South ocean bottom seismic (OBS) data set confirmed that normal moveout (NMO) stretch could distort both frequency and amplitude information severely in shallow events and far offset traces. In synthetic tests, our algorithm recovered amplitude and frequency information ac-curately. This simple but robust target oriented NMO stretch correction scheme can be used on top of an existing seismic processing flow for further analyses. By combining the NMO stretch correction, spectral decomposition, and crossplots of am-plitude versus offset (AVO) attributes, we tested the frequency dependent workflow over Teal south and Ursa field data sets for improved reservoir characterization. As expected from NMO stretch characteristics, low frequencies have been less affected while mid and high frequency ranges were affected considerably. In seismic attribute analysis, the AVO crossplots from spectrally decomposed prestack data confirmed the improved accuracy and effectiveness of our workflow in mid and high frequency regions. To overcome poor spectral decomposition results due to low signal to noise ratio (S/N) in the Teal South application, we also implemented a substack scheme that stacks adjacent traces to increase S/N ratio while reducing the amount of data to process and increasing the accuracy of the spectral decomposition step. Synthetic tests verified the effectiveness of this additional step. An application to the Ursa, Gulf of Mexico, deep water data set showed significant improvement in high frequency data while correcting biased low frequency information.

Wave attenuation by vegetation is a highly dynamic process and its quantification is important for accurately understanding and predicting coastal hydrodynamics. However, the influence of vegetation on wave dissipation is not yet fully established nor implemented in current hydrodynamic models. A series of laboratory experiments were conducted at the Haynes Coastal Engineering Laboratory and in a two-dimensional flume at Texas A and M University to investigate the influence of relative vegetation height, stem density, and stem spacing uniformity on wave attenuation. Vegetation fields were represented as random cylinder arrays where the stem density and spatial variation were based on collected field specimens. Experimental results indicate wave attenuation is dependent on relative vegetation height, stem density, and stem spacing standard deviation. As stems occupy more of the water column, an increase in attenuation occurred given that the highest wave particle velocities are being impeded. Sparse vegetation fields dissipated less wave energy than the intermediate density; however, the extremely dense fields dissipated very little, if any, wave energy and sometimes wave growth was observed. This is possibly due to the highest density exceeding some threshold where maximum wave attenuation capabilities are exceeded and lowering of damping ensues. Additionally, wave attenuation increased with higher stem spatial variation due to less wake sheltering. A one-dimensional model with an analytical vegetation dissipation term was developed and calibrated to these experimental results to capture the wave transformation over the vegetation beds and to investigate the behavior of the vegetation field bulk drag coefficient. The best fit between predicted and measured wave heights was obtained using the least squares method considering the bulk drag coefficient as the single calibration parameter. The model was able to realistically capture the wave transformations over vegetation. Upon inspection, the bulk drag coefficient shared many of the dependencies of the total wave dissipation. The bulk drag coefficient increased with larger relative vegetation heights as well as with higher stem spacing standard deviation. Higher densities resulted in a lowering of the bulk drag coefficient but generally an increase in wave attenuation. These parameters and their influences help in identifying the important parameters for numerical studies to further our understanding of wave attenuation by wetlands.