Bayesian Markov chain Monte Carlo inversion of geophysical data for the purpose of estimating the hydraulic properties of the unsaturated zone

Ground-penetrating radar (GPR) has the potential to provide valuable information on hydrological properties of the vadose zone because of their strong sensitivity to soil water content. In particular, recent evidence has suggested that the stochastic inversion of crosshole GPR data within a coupled geophysical-hydrological framework may allow for effective estimation of subsurface van-Genuchten-Mualem (VGM) parameters and their corresponding uncertainties. An important and still unresolved issue, however, is how to best integrate GPR data into a stochastic inversion in order to estimate the VGM parameters and their uncertainties, thus improving hydrological predictions. Recognizing the importance of this issue, the aim of the research presented in this thesis was to first introduce a fully Bayesian inversion called Markov-chain-Monte-carlo (MCMC) strategy to perform the stochastic inversion of steady-state GPR data to estimate the VGM parameters and their uncertainties. Within this study, the choice of the prior parameter probability distributions from which potential model configurations are drawn and tested against observed data was also investigated. Analysis of both synthetic and field data collected at the Eggborough (UK) site indicates that the geophysical data alone contain valuable information regarding the VGM parameters. However, significantly better results are obtained when these data are combined with a realistic, informative prior. A subsequent study explore in detail the dynamic infiltration case, specifically to what extent time-lapse ZOP GPR data, collected during a forced infiltration experiment at the Arrenaes field site (Denmark), can help to quantify VGM parameters and their uncertainties using the MCMC inversion strategy. The findings indicate that the stochastic inversion of time-lapse GPR data does indeed allow for a substantial refinement in the inferred posterior VGM parameter distributions. In turn, this significantly improves knowledge of the hydraulic properties, which are required to predict hydraulic behaviour. Finally, another aspect that needed to be addressed involved the comparison of time-lapse GPR data collected under different infiltration conditions (i.e., natural loading and forced infiltration conditions) to estimate the VGM parameters using the MCMC inversion strategy. The results show that for the synthetic example, considering data collected during a forced infiltration test helps to better refine soil hydraulic properties compared to data collected under natural infiltration conditions. When investigating data collected at the Arrenaes field site, further complications arised due to model error and showed the importance of also including a rigorous analysis of the propagation of model error with time and depth when considering time-lapse data. Although the efforts in this thesis were focused on GPR data, the corresponding findings are likely to have general applicability to other types of geophysical data and field environments. Moreover, the obtained results allow to have confidence for future developments in integration of geophysical data with stochastic inversions to improve the characterization of the unsaturated zone but also reveal important issues linked with stochastic inversions, namely model errors, that should definitely be addressed in future research.

Determination of hydraulic properties of a tropical soil of Hawaii using column experiments and inverse modeling

A method for determining soil hydraulic properties of a weathered tropical soil (Oxisol) using a medium-sized column with undisturbed soil is presented. The method was used to determine fitting parameters of the water retention curve and hydraulic conductivity functions of a soil column in support of a pesticide leaching study. The soil column was extracted from a continuously-used research plot in Central Oahu (Hawaii, USA) and its internal structure was examined by computed tomography. The experiment was based on tension infiltration into the soil column with free outflow at the lower end. Water flow through the soil core was mathematically modeled using a computer code that numerically solves the one-dimensional Richards equation. Measured soil hydraulic parameters were used for direct simulation, and the retention and soil hydraulic parameters were estimated by inverse modeling. The inverse modeling produced very good agreement between model outputs and measured flux and pressure head data for the relatively homogeneous column. The moisture content at a given pressure from the retention curve measured directly in small soil samples was lower than that obtained through parameter optimization based on experiments using a medium-sized undisturbed soil column.

Bayesian-MCMC inversion of time-lapse geophysical data to characterize vadose zone hydraulic behaviour

Geophysical methods have the potential to provide valuable information on hydrological properties in the unsaturated zone. In particular, time-lapse geophysical data, when coupled with a hydrological model and inverted stochastically, may allow for the effective estimation of subsurface hydraulic parameters and their corresponding uncertainties. In this study, we use a Bayesian Markov-chain-Monte-Carlo (MCMC) inversion approach to investigate how much information regarding vadose zone hydraulic properties can be retrieved from time-lapse crosshole GPR data collected at the Arrenaes field site in Denmark during a forced infiltration experiment.

Bayesian Markov-chain-Monte-Carlo inversion of time-lapse cross hole ground-penetrating radar data to characterize the vadose zone at the Arrenaes field site, Denmark

The ground-penetrating radar (GPR) geophysical method has the potential to provide valuable information on the hydraulic properties of the vadose zone because of its strong sensitivity to soil water content. In particular, recent evidence has suggested that the stochastic inversion of crosshole GPR traveltime data can allow for a significant reduction in uncertainty regarding subsurface van Genuchten-Mualem (VGM) parameters. Much of the previous work on the stochastic estimation of VGM parameters from crosshole GPR data has considered the case of steady-state infiltration conditions, which represent only a small fraction of practically relevant scenarios. We explored in detail the dynamic infiltration case, specifically examining to what extent time-lapse crosshole GPR traveltimes, measured during a forced infiltration experiment at the Arreneas field site in Denmark, could help to quantify VGM parameters and their uncertainties in a layered medium, as well as the corresponding soil hydraulic properties. We used a Bayesian Markov-chain-Monte-Carlo inversion approach. We first explored the advantages and limitations of this approach with regard to a realistic synthetic example before applying it to field measurements. In our analysis, we also considered different degrees of prior information. Our findings indicate that the stochastic inversion of the time-lapse GPR data does indeed allow for a substantial refinement in the inferred posterior VGM parameter distributions compared with the corresponding priors, which in turn significantly improves knowledge of soil hydraulic properties. Overall, the results obtained clearly demonstrate the value of the information contained in time-lapse GPR data for characterizing vadose zone dynamics.

ROCK OUTCROPS IN THE CANADIAN SHIELD: AN INVESTIGATION OF CONTAMINANT TRANSPORT FROM SURFACE SOURCES IN FRACTURED ROCK AQUIFERS

Flow, recharge and transport dynamics in fractured rock aquifers with low lying rock outcrops is a largely unexplored area of study in hydrogeology. The purpose of this thesis is to examine these topics in an agricultural area in Eastern Ontario. The study consists of a regional scale groundwater quality study, an infiltration experiment that considers bacteria transport from the ground surface to a well, and a numerical modelling study that tests the parameters that affect surface infiltration of a tracer from a rock outcrop to a deeper horizontal fracture. In the water quality study, approximately 65% of the samples contained total coliform, 16% contained E. coli, and 1% contained nitrate-N at greater than 5 mg/L. Occurrence of E. coli increased when considering seasonality, where wells were drilled on rock outcrops, and for shallow well intervals. Nitrate-N did not occur above the Guidelines for Canadian Drinking Water Quality (Health Canada, 2012) of 10 mg/L. Rapid arrival times were observed in the infiltration study for both the microspheres (30 minutes) and a dye tracer (45 minutes) in a well approximately 6.0 m in horizontal and 2.8 m in vertical distance from the tracer source. Transport velocities were approximately 38.9 m/day for the dye tracer and 115.2 m/day for the colloidal tracer. Results of the model runs indicate that overburden can provide an effective protective layer to transport in fractures, that high groundwater velocities occur in larger fracture apertures and higher gradients dilute tracer concentrations, and that lower groundwater velocities occur with smaller fracture apertures and lower gradients result in elevated tracer concentrations. Lower rainfall rates, larger fracture apertures, early tracer time, larger gradients, and lower water levels maintained unsaturated conditions for longer time periods such that tracer transport was delayed until saturated conditions were attained. The overall heterogeneity of this aquifer environment creates a source water protection conundrum where the water quality is generally good, while transport can occur very quickly in proximity to rock outcrops and in areas with limited overburden.

ROCK OUTCROPS IN THE CANADIAN SHIELD: AN INVESTIGATION OF CONTAMINANT TRANSPORT FROM SURFACE SOURCES IN FRACTURED ROCK AQUIFERS

Flow, recharge and transport dynamics in fractured rock aquifers with low lying rock outcrops is a largely unexplored area of study in hydrogeology. The purpose of this thesis is to examine these topics in an agricultural area in Eastern Ontario. The study consists of a regional scale groundwater quality study, an infiltration experiment that considers bacteria transport from the ground surface to a well, and a numerical modelling study that tests the parameters that affect surface infiltration of a tracer from a rock outcrop to a deeper horizontal fracture. In the water quality study, approximately 65% of the samples contained total coliform, 16% contained E. coli, and 1% contained nitrate-N at greater than 5 mg/L. Occurrence of E. coli increased when considering seasonality, where wells were drilled on rock outcrops, and for shallow well intervals. Nitrate-N did not occur above the Guidelines for Canadian Drinking Water Quality (Health Canada, 2012) of 10 mg/L. Rapid arrival times were observed in the infiltration study for both the microspheres (30 minutes) and a dye tracer (45 minutes) in a well approximately 6.0 m in horizontal and 2.8 m in vertical distance from the tracer source. Transport velocities were approximately 38.9 m/day for the dye tracer and 115.2 m/day for the colloidal tracer. Results of the model runs indicate that overburden can provide an effective protective layer to transport in fractures, that high groundwater velocities occur in larger fracture apertures and higher gradients dilute tracer concentrations, and that lower groundwater velocities occur with smaller fracture apertures and lower gradients result in elevated tracer concentrations. Lower rainfall rates, larger fracture apertures, early tracer time, larger gradients, and lower water levels maintained unsaturated conditions for longer time periods such that tracer transport was delayed until saturated conditions were attained. The overall heterogeneity of this aquifer environment creates a source water protection conundrum where the water quality is generally good, while transport can occur very quickly in proximity to rock outcrops and in areas with limited overburden.

Topical interleukin-1 receptor antagonist inhibits inflammatory cell infiltration into the cornea

Interleukin (IL)-1 alpha and beta are important modulators of many functions of corneal epithelial and stromal cells that occur following injury to the cornea, including the influx of bone marrow-derived inflammatory cells into the stroma attracted by chemokines released from the stroma and epithelium. In this study, we examined the effect of topical soluble IL-1 receptor antagonist on bone marrow-derived cell influx following corneal epithelial scrape injury in a mouse model. C57BL/6 mice underwent corneal epithelial scrape followed by application of IL-1 receptor antagonist (Amgen, Thousand Oaks, CA) at a concentration of 20 mg/ml or vehicle for 24 h prior to immunocytochemical detection of marker CD11b-positive cells into the stroma. In two experiments, topical IL-1 receptor antagonist had a marked effect in blocking cell influx. For example, in experiment 1, topical IL-1 receptor antagonist markedly reduced detectible CD11b-positive cells into the corneal stroma at 24 It after epithelial injury compared with the vehicle control (3.5 +/- 0.5 (standard error of the mean) cells/400x field and 13.9 +/- 1.2 cells/400x field, respectively, p < 0.01). A second experiment with a different observer performing cell counting had the same result. Thus, the data demonstrate conclusively that topical IL-1 receptor antagonist markedly down-regulates CD-11b-positive monocytic cell appearance in the corneal stroma. Topical IL-1 receptor antagonist could be an effective adjuvant for clinical treatment of corneal conditions in which unwanted inflammation has a role in the pathophysiology of the disorder. (c) 2008 Elsevier Ltd. All rights reserved.

Short-term evaluation of non-absorbable microgranular hydroxyapatite infiltration in the guinea pig subepidermal abdominal region

Non-absorbable microgranular hydroxyapatite was infiltrated into the subepidermal abdominal region of guinea pigs in order to assess the possibility of using this material to correct deficiencies in orbital volume. Microgranular hydroxyapatite (2.0 ml) was subepidermally infiltrated into the abdominal region of 20 guinea pigs. The animals were divided into four experimental groups of 5 animals each, which were killed 7 (G1), 15 (G2), 30 (G3) and 60 (G4) days after infiltration. The area and the largest and smallest diameters of the nodules formed by infiltration were evaluated at the site of infiltration and histological examination was performed. The mean granuloma area was similar in all groups. Histopathological examination showed that the material remained isolated from surrounding tissues by a pseudocapsule that became denser throughout the experiment. A host reaction started with young fibroblastic tissue that evolved to dense tissue until cartilaginous tissue was formed in G4, progressively advancing towards the center of the granuloma from G1 to G4. Non-absorbable microgranular hydroxyapatite is an inert material that was well tolerated by the animals studied, with maintenance of the infiltrated volume, and may perhaps be useful to fill anophthalmic cavities.

Short-term evaluation of non-absorbable microgranular hydroxyapatite infiltration in the guinea pig subepidermal abdominal region

Non-absorbable microgranular hydroxyapatite was infiltrated into the subepidermal abdominal region of guinea pigs in order to assess the possibility of using this material to correct deficiencies in orbital volume. Microgranular hydroxyapatite (2.0 ml) was subepidermally infiltrated into the abdominal region of 20 guinea pigs. The animals were divided into four experimental groups of 5 animals each, which were killed 7 (G1), 15 (G2), 30 (G3) and 60 (G4) days after infiltration. The area and the largest and smallest diameters of the nodules formed by infiltration were evaluated at the site of infiltration and histological examination was performed. The mean granuloma area was similar in all groups. Histopathological examination showed that the material remained isolated from surrounding tissues by a pseudocapsule that became denser throughout the experiment. A host reaction started with young fibroblastic tissue that evolved to dense tissue until cartilaginous tissue was formed in G4, progressively advancing towards the center of the granuloma from G1 to G4. Non-absorbable microgranular hydroxyapatite is an inert material that was well tolerated by the animals studied, with maintenance of the infiltrated volume, and may perhaps be useful to fill anophthalmic cavities.

Experimental characterization of cement–bentonite interaction using core infiltration techniques and 4D computed tomography

Deep geological storage of radioactive waste foresees cementitious materials as reinforcement of tunnels and as backfill. Bentonite is proposed to enclose spent fuel drums, and as drift seals. The emplacement of cementitious material next to clay material generates an enormous chemical gradient in pore water composition that drives diffusive solute transport. Laboratory studies and reactive transport modeling predict significant mineral alteration at and near interfaces, mainly resulting in a decrease of porosity in bentonite. The goal of this project is to characterize and quantify the cement/bentonite skin effects spatially and temporally in laboratory experiments. A newly developed mobile X-ray transparent core infiltration device was used, which allows performing X-ray computed tomography (CT) periodically without interrupting a running experiment. A pre-saturated cylindrical MX-80 bentonite sample (1920 kg/m3 average wet density) is subjected to a confining pressure as a constant total pressure boundary condition. The infiltration of a hyperalkaline (pH 13.4), artificial OPC (ordinary Portland cement) pore water into the bentonite plug alters the mineral assemblage over time as an advancing reaction front. The related changes in X-ray attenuation values are related to changes in phase densities, porosity and local bulk density and are tracked over time periodically by non-destructive CT scans.

Experimental Characterization and Quantification of Cement-Bentonite Interaction using Core Infiltration Techniques Coupled with X-ray Tomography

Deep geological storage of radioactive waste foresees cementitious materials as reinforcement of tunnels and as backfill. Bentonite is proposed to enclose spent fuel canisters and as drift seals. Sand/bentonite (s/b) is foreseen as backfill material of access galleries or as drift seals. The emplacement of cementitious material next to clay material generates an enormous chemical gradient in pore-water composition that drives diffusive solute transport. Laboratory studies and reactive transport modeling predicted significant mineral alteration at and near interfaces, mainly resulting in a decrease of porosity in bentonite. The goal of this thesis was to characterize and quantify the cement/bentonite interactions both spatially and temporally in laboratory experiments. A newly developed mobile X-ray transparent core infiltration device was used to perform X-ray computed tomography (CT) scans without interruption of running experiments. CT scans allowed tracking the evolution of the reaction plume and changes in core volume/diameter/density during the experiments. In total 4 core infiltration experiments were carried out for this study with the compacted and saturated cores consisting of MX-80 bentonite and sand/MX-80 bentonite mixture (s/b; 65/35%). Two different high-pH cementitious pore-fluids were infiltrated: a young (early) ordinary Portland cement pore-fluid (APWOPC; K+–Na+–OH-; pH 13.4; ionic strength 0.28 mol/kg) and a young ‘low-pH’ ESDRED shotcrete pore-fluid (APWESDRED; Ca2+–Na+–K+–formate; pH 11.4; ionic strength 0.11 mol/kg). The experiments lasted between 1 and 2 years. In both bentonite experiments, the hydraulic conductivity was strongly reduced after switching to high-pH fluids, changing eventually from an advective to a diffusion-dominated transport regime. The reduction was mainly induced by mineral precipitation and possibly partly also by high ionic strength pore-fluids. Both bentonite cores showed a volume reduction and a resulting transient flow in which pore-water was squeezed out during high-pH infiltration. The outflow chemistry was characterized by a high ionic strength, while chloride in the initial pore water got replaced as main anionic charge carrier by sulfate, originating from gypsum dissolution. The chemistry of the high-pH fluids got strongly buffered by the bentonite, consuming hydroxide and in case of APWESDRED also formate. Hydroxide got consumed by mineral reactions (saponite and possibly talc and brucite precipitation), while formate being affected by bacterial degradation. Post-mortem analysis showed reaction zones near the inlet of the bentonite core, characterized by calcium and magnesium enrichment, consisting predominately of calcite and saponite, respectively. Silica got enriched in the outflow, indicating dissolution of silicate-minerals, identified as preferentially cristobalite. In s/b, infiltration of APWOPC reduced the hydraulic conductivity strongly, while APWESDRED infiltration had no effect. The reduction was mainly induced by mineral precipitation and probably partly also by high ionic strength pore-fluids. Not clear is why the observed mineral precipitates in the APWESDRED experiment had no effect on the fluid flow. Both s/b cores showed a volume expansion along with decreasing ionic strengths of the outflow, due to mineral reactions or in case of APWESDRED infiltration also mediated by microbiological activity, consuming hydroxide and formate, respectively. The chemistry of the high-pH fluids got strongly buffered by the s/b. In the case of APWESDRED infiltration, formate reached the outflow only for a short time, followed by enrichment in acetate, indicating most likely biological activity. This was in agreement to post-mortem analysis of the core, observing black spots on the inflow surface, while the sample had a rotten-egg smell indicative of some sulfate reduction. Post-mortem analysis showed further in both cores a Ca-enrichment in the first 10 mm of the core due to calcite precipitation. Mg-enrichment was only observed in the APWOPC experiment, originating from newly formed saponite. Silica got enriched in the outflow of both experiments, indicating dissolution of silicate-minerals, identified in the OPC experiment as cristobalite. The experiments attested an effective buffering capacity for bentonite and s/b, a progressing coupled hydraulic-chemical sealing process and also the preservation of the physical integrity of the interface region in this setup with a total pressure boundary condition on the core sample. No complete pore-clogging was observed but the hydraulic conductivity got rather strongly reduced in 3 experiments, explained by clogging of the intergranular porosity (macroporosity). Such a drop in hydraulic conductivity may impact the saturation time of the buffer in a nuclear waste repository, although the processes and geometry will be more complex in repository situation.

Collection of measurements on physical soil properties in plots of the Jena Experiment (time series since 2002)

This collection contains measurements on physical soil properties of the plots of the different sub-experiments at the field site of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing

Soil porosity along a plant diversity gradient in the Jena Experiment (Main Experiment, 2013)

Soil porosity is the fraction of total volume occupied by pores or voids measured at matric potential 0. To measure soil porosity, soil samples were taken from each plot using sample rings with an internal diameter of 57 mm and height of 40.5 mm (inner volume of Vs=100 cm3). The samples were placed on a sand bed box with water level set to allow saturation of the samples with water. After 48 h the samples were weighed (ms), oven dried at 105 °C and weighed again to determine the dry weight (md). We calculated soil porosity (n [%]) using the density of water (?w=1 g cm?3), n=100 ? (mw-md) / (?w?Vs). To account for the spatial variation of soil properties, three replicates were taken per plot, approximately 2, 3 and 4 weeks after the flood that occurred at the field site during June 2013. Data are the average soil porosity values per plot. All data where measured in the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown in the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, or 4 functional groups). Plots were maintained by bi-annual weeding and mowing.

Bilateral Peripheral Facial Palsy And Mastoid Infiltration As Symptoms Of Relapsed Acute Myeloid Leukemia.

Although Bell's palsy (BP) is the most common cause of peripheral facial palsy (PFP), other etiologies merit investigation. A 60-year-old female patient presented with recurrent bilateral PFP. Although the patient had a history of acute myeloid leukemia (AML), she had initially been diagnosed with BP-related PFP and had been treated accordingly. When the PFP recurred, additional diagnostic tests were performed. The resulting immunohistochemical profile included CD3 positivity in a few reactive T lymphocytes; positivity for myeloperoxidase in atypical cells; and focal positivity for CD34 and proto-oncogene c-kit proteins in neoplastic cells, thus confirming the suspicion of mastoid infiltration caused by relapsed AML. In patients with neoplastic disease, a finding of PFP calls for extensive investigation in order to rule out the involvement of the temporal bone.

Are Human Peripheral Nerves Sensitive To X-ray Imaging?

Diagnostic imaging techniques play an important role in assessing the exact location, cause, and extent of a nerve lesion, thus allowing clinicians to diagnose and manage more effectively a variety of pathological conditions, such as entrapment syndromes, traumatic injuries, and space-occupying lesions. Ultrasound and nuclear magnetic resonance imaging are becoming useful methods for this purpose, but they still lack spatial resolution. In this regard, recent phase contrast x-ray imaging experiments of peripheral nerve allowed the visualization of each nerve fiber surrounded by its myelin sheath as clearly as optical microscopy. In the present study, we attempted to produce high-resolution x-ray phase contrast images of a human sciatic nerve by using synchrotron radiation propagation-based imaging. The images showed high contrast and high spatial resolution, allowing clear identification of each fascicle structure and surrounding connective tissue. The outstanding result is the detection of such structures by phase contrast x-ray tomography of a thick human sciatic nerve section. This may further enable the identification of diverse pathological patterns, such as Wallerian degeneration, hypertrophic neuropathy, inflammatory infiltration, leprosy neuropathy and amyloid deposits. To the best of our knowledge, this is the first successful phase contrast x-ray imaging experiment of a human peripheral nerve sample. Our long-term goal is to develop peripheral nerve imaging methods that could supersede biopsy procedures.