An estimated 45% of all deaths can be attributed to various chronic fibroproliferative diseases. Idiopathic pulmonary fibrosis (IPF) is the most common form of interstitial lung disease which is characterized by progressive decline in lung function. While the pathogenesis of IPF is not fully understood, alternatively activated macrophages (M2) have been implicated as a key contributor to the fibrotic process. The plasticity of macrophages in vivo challenges the ability to specifically target the M2 macrophage phenotype across species. Previous bioinformatic analysis from our lab identified Dectin-1/Clec7a as a unique marker of M2 macrophages in both human and murine model systems. The expression of the transmembrane receptor Dectin-1 has not been elucidated in the context of pulmonary fibrosis. To prevent the progression of fibrosis by targeting alternatively activated macrophages, we investigated the expression of Dectin-1 in IPF and an experimental model of fibrotic lung disease. Our data demonstrated that while protein expression of Dectin-1 was increased in archived lung tissues of patients with IPF, mRNA expression of this receptor was downregulated in the tissues of these IPF patients. Gene expression of Dectin-1 was shown to be increased in monocyte-derived macrophages, further suggesting a circulatory component contributing to lung fibrosis. As expected, we confirmed that Dectin-1 was highly expressed past the injury phase of the bleomycin-model of induced pulmonary fibrosis which aligns with the increased immune infiltrates at this time point. Preliminary work into the time dependency of the resolution phase of the bleomycin-induced model of lung fibrosis was shown. All in all, our data suggests that Dectin-1 may be a useful marker in characterizing and differentiating phenotypes of macrophages implicated in the fibrotic process. Future efforts aim to gain insight into the functional requirement of Dectin-1 in the alternative activation of profibrotic macrophages to identify novel therapeutic targets for fibrotic lung disease. / Thesis / Master of Science (MSc)

An investigation of the temperature response and corresponding lesion growth resulting from in vivo interstitial laser photocoagulation was performed in order to test the applicability of Arrhenius theory. The irradiations were performed in vivo in rabbit muscle for various exposures at 1.0W using an 805 nm diode laser source coupled to an optical fibre with a pre-charred tip, thereby forcing it to function as a point heat source. Temperature responses were measured using a five-microthermocouple array along a range of radial distances from the point heat source. Each temperature profile was fitted with a curve predicted by the Weinbaum-Jiji bioheat transfer equation. The lesions were resected 48 hours after irradiation and the boundary of thermal damage resulting in necrosis was determined histologically. Numerical integration of the Arrhenius integral using temperature-time data at the lesion boundary produced corresponding activation energy and pre-exponential factor pairs (Ea , a) consistent with reported values for various other endpoints and tissue types. As well, theoretical predictions of the lesion growth from Arrhenius theory agreed well with experimental results. However, the thermal parameters, which are generally assumed to be constant when solving the bioheat transfer equation, were found to vary with radial distance from the source, presumably due to a dependence on temperature. / Thesis / Master of Science (MS)

Idiopathic pulmonary fibrosis (IPF) is a disease of unknown pathogenesis characterized by scarring of the lung and declining respiratory function. Originating from bone marrow, circulating monocytes can be recruited into the lung tissue and polarized toward the alternatively activated (M2) profibrotic macrophage phenotype. Recent literature has shown that cluster of differentiation 14 positive (CD14+) monocytes are more abundant in IPF patient blood and are associated with disease outcome and acute exacerbation. Additionally, a 52-gene risk profile from peripheral blood mononuclear cells for outcome prediction in IPF was recently published. Here, we began by characterizing macrophages in human IPF lung tissue. We then assembled a biobank and examined transcriptomic characteristics of blood-derived circulating monocytes from IPF patients. Various histological assessments were completed on a tissue microarray including lung biopsies from 24 IPF patients and 17 controls, to characterize M2 macrophage expression in human tissue. Whole blood samples were collected from 50 IPF patients and 12 control subjects. CD14+ monocytes were isolated and mRNA was extracted for bulk RNA sequencing. Data were analyzed for differential expression (DE), and Gene Set Enrichment Analysis (GSEA) was performed to examine enrichment of the previously published 52-gene risk profile in our dataset. We found that M2 macrophage expression was increased in IPF lung tissue compared to controls. CD14+ monocyte levels were significantly elevated in IPF patients in our cohort compared to control participants, and was negatively correlated with forced vital capacity (FVC). DE analysis comparing IPF and control monocytes yielded a 35-gene signature, with 16 up-regulated genes and 19 down-regulated genes. When comparing the signature related to long transplant-free survival from the published dataset to our data, GSEA demonstrated that this signature is enriched in donors from our dataset, supporting concurrence between the meanings of the two datasets. Overall, these results provide insight to identify targets to modulate monocyte/macrophage function in IPF and potentially affect progressive disease. / Thesis / Master of Science (MSc) / Idiopathic pulmonary fibrosis (IPF) is a disease of unknown cause that results in excessive scarring of the lungs and progressive impairment in lung function. We believe that white blood cells called monocytes and macrophages play a key role in the development and progression of this disease. Overall, it is thought that monocytes, which circulate in the blood, enter the lung tissue and become macrophages. These macrophages then lead to the formation of scar tissue, which is characteristic to IPF. In order to better understand how these cells contribute to IPF, we studied their properties in blood and lung biopsies from IPF patients. We found significant differences between monocytes/macrophages in IPF than those in healthy controls, that may help explain disease progression. We hope that these findings will provide insight into causes of the IPF, and potential avenues for therapeutic intervention.

yes / This paper presents field measurements in which dye solute was injected into coastal sand to investigate contaminant advection in intertidal beach sand. The measurements show the pathways of a contaminated plume in the unsaturated zone during both the flood and ebb tides. A prescribed amount of dye tracer solution was directly injected through the topsoil, with average porosity 0.3521±0.01, at predetermined locations of the River Mersey’s outer estuarial beach during ebb-tide. The injected dye was monitored, sampled and photographed over several tidal cycles. The distinctive features of the plume (full two dimensional cross-sections), sediments and water-table depth were sampled in-situ, close to the injection point (differing from previous contaminant monitoring tests in aquifers). The advective movement is attributed to tidal impact which is different from contaminant transport in aquifers. The experimental results show that plumes have significantly large spatial variability, diverging upwards and converging downwards, with a conical geometric shape which is different from the usual spherical/elliptical shape reported in literature. The mean vertical motion of the plume reaches three times the top-width within ten tidal cycles, exceeding the narrow bottom-width by a factor of order 2. The observed transport features of the plume within the beach sand have significant relevance to saltwater intrusion, surface water and groundwater quality. The field observations are unique and can serve as a valuable benchmark database for relevant numerical studies. / China Ministry of Science and Technology 973 program (2014CB745001), Special Program of future development in Shenzhen (201411201645511650) and Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment（ZDSY20130402163735964).

The human brain is a complex organ that is responsible for regulating all the physiological processes in the body, ranging from memory to movement. As humans age, the brain goes through a variety of changes including a reduction in glymphatic waste clearance and increase in glial reactivity. Two neurological conditions that affect individuals over the age of 65 include glioblastoma (GBM) and Alzheimer's disease (AD). Interestingly, patients with GBM do not present with AD and vice versa. Both conditions are characterized by a disruption in interstitial fluid flow (IFF) and an increase in neuroinflammation. Throughout the following dissertation, we examined the role of IFF in AD and GBM progression using a three-sided approach (in vivo, in vitro, and in silico). Increased IFF underlies glioma invasion into the surrounding tumor microenvironment (TME) in GBM. We used a 3D hydrogel model of the GBM TME to examine potential pathways by which astrocytes and microglia contribute to glioma invasion. A reduction in IFF contributes to accumulation of the toxic protein amyloid beta (Aβ) in AD. We sought to create a novel, patient-inspired model of the AD hippocampus for examination of the relationship between IFF and Aβ clearance. Human AD and unaffected control hippocampal brain samples were stained for markers of neurons, astrocytes, microglia and Aβ. The percentage of each cell population in the CA1 region of the hippocampus was calculated. We also analyzed the amount and characteristics of the Aβ aggregates present in this hippocampal region. Pearson correlation analysis was completed to assess the relationships between the various cell populations, Aβ load, and patient descriptors. The cell ratios gleaned from the patient samples were incorporated into a novel, 3D hydrogel model of the AD hippocampus. This model features a hydrogel mixture like the native brain extracellular matrix (ECM) and allows for the application of IFF and Aβ. To our knowledge, we are the first group to create a patient-specific triculture model of the AD hippocampus, which is the main site of Aβ aggregation in the AD brain. We used this model to examine the relationship between IFF-mediated Aβ clearance and glial reactivity. The last aim of this dissertation was to create a computational model for examining Aβ binding within the ECM and the effects of IFF on Aβ clearance. In vitro experiments were conducted to generate 3D renderings of glial cells and to determine relevant parameters for our model. Throughout this work, we discuss the relationship between disruption in IFF and glial reactivity in the context of GBM and AD. / Doctor of Philosophy / The human brain is a complex organ that is responsible for regulating all the physiological processes in the body, ranging from memory to movement. As humans age, the brain goes through a variety of changes including a reduction in brain waste removal and an increase in inflammation. Two neurological conditions that affect individuals over the age of 65 include glioblastoma (GBM) and Alzheimer's disease (AD). Interestingly, patients with GBM do not present with AD and vice versa. Both conditions are characterized by a disruption in brain interstitial fluid flow (IFF) and an increase in neuroinflammation. Throughout the following dissertation, we examined the role of IFF in AD and GBM progression using a three-sided approach including analysis of mouse and human tissues, engineered cell models, and computational methods. Specific interactions between brain cell types and their relationships with glioma invasion were examined using a 3D cell model that mimics the brain. Through the work presented here, we also sought to create a novel cell model of the hippocampus region located in the AD brain. We quantified the various cell types in the hippocampus of AD patient samples and incorporated this information into our hydrogel model. The resulting model features three brain cell types (astrocytes, microglia, and neurons) that are added at patient relevant ratios, a matrix that mimics the native brain scaffold, and allows for the application of IFF. In the AD brain there is a reduction in brain waste removal that leads to accumulation of the toxic protein amyloid beta (Aβ). We were successfully able to incorporate this protein within our model so we could assess the relationship between IFF and Aβ removal from the brain. We further studied this relationship using a new computational model of Aβ accumulation in the brain. Throughout this work, we discuss the connection between disrupted IFF and neuroinflammation in the context of GBM and AD.

The river drainages originating in the Cumberland region of Virginia, Tennessee and Kentucky are home to some of the last surviving and most diverse assemblages of native freshwater mussels. This region of the country also has historically and continues to be a major source of coal for the United States. Numerous experiments were carried out in an attempt to determine what ecotoxicological effects these activities have had on mussels as well as what has been done to correct some of the most severe cases of environmental pollution due to historical coal mining operations. Analysis of interstitial water (IW), sediment and in situ toxicity testing and chemical analyses showed that the most likely cause for mussel declines was elevated metal concentrations (Al, Cu, Fe, Pb) found in IW. Ecotoxicological assessments of the two streams (Black and Ely Creeks) most impacted by acid mine drainage (AMD) in the state of Virginia were carried out to determine their potential for future degradation of the Powell River watershed into which they drain. The Powell River is a major system still inhabited by native mussels. Sophisticated wetland systems built at Ely Creek have significantly improved the ecological health of Ely Creek, decreasing the pollution into the Powell River. Reclamation and wetland construction at Black Creek have had a positive impact but active coal mining and un-remediated AMD are still negatively affecting this system. After the watershed has been fully reclaimed the discharge from Black Creek will likely be improved. / Master of Science

Glioblastoma (GBM) is the most aggressive and malignant glioma. It accounts for 48.6% of all primary, malignant gliomas with a median survival of 15 months. Infiltration into the surrounding parenchyma is a hallmark of GBM. Radiotherapy is used to address the invasion; however, recent studies have implicated that radiation contributes to increased invasiveness of glioma. Although the effect of radiation on cells has been studied extensively, its effect on the transport of fluid is not well characterized. Transport in the brain which has significant roles in physiology, GBM pathophysiology, and GBM treatment. Thus, understanding the effect of radiation on transport within the lesion and surrounding interstitium will be beneficial in characterizing the effects of radiotherapy in GBM patients. This dissertation seeks to explore the relationship between radiation, transport, and movement of glioma cells and includes the following: 1) Characterizing in vitro motility metrics of glioma stem cell lines in and relating them to in vivo invasion. 2) Studying the effect of radiation on motility, flow-mediated invasion, extracellular matrix components, and transport within the lesion and interstitium. 3) Assessing transport in clinical images and relating transport parameters to progression of GBM. 4) Developing a novel pipeline for applying vector field topology to the study of interstitial fluid flow in glioma. Surprisingly, we found that motility metrics in vitro have a negative correlation trend with in vivo invasion. Next, we found that radiation causes a transient increase in advective flow, and a more sustained decrease in diffusivity in a murine glioma model. Tenascin C was found to correlate significantly with invasion and diffusivity, indicating that it might be a link between radiation, transport, and invasion. Furthermore, interstitial fluid flow was calculated and assessed in clinical images. This showed that interstitial fluid flow velocity magnitude in the tumor correlates with overall survival in GBM patients. Lastly, vector field topology was introduced as a novel method of studying transport that provides more detailed information to identify potential drivers of transport within a flow field. Altogether, this work presents novel insight into the effects of radiation on invasion and transport in GBM. Hopefully, this work can provide a foundation to build upon in efforts of improving treatment planning and clinical outcomes for GBM patients. / Doctor of Philosophy / Glioblastoma (GBM) is the most aggressive glioma. It accounts for 48.6% of all primary, malignant gliomas with a median survival of 15 months. The movement of cancer cells into the surrounding tissue is a defining factor of GBM. Radiotherapy is used after surgery to treat the remaining cancer cells in tissue surrounding the tumor; however, recent studies have implicated that radiation contributes to increased movement of glioma into surrounding tissue. Although the effect of radiation on cells has been studied extensively, its effect on transport of fluid is not well characterized. Interstitial fluid flow in the brain has significant roles in healthy bodily functions, GBM disease state, and GBM treatment. Thus, understanding the effect of radiation on transport within the tumor and surrounding tissue is beneficial in better characterizing the effects of radiotherapy. This dissertation seeks to explore the relationship between radiation, transport, and movement of glioma cells and includes the following: 1) Characterizing in vitro motility metrics of glioma cells in and relating them to in vivo movement into healthy tissue. 2) Studying the effect of radiation on motility, flow-mediated infiltration into healthy tissue, tissue matrix components, and fluid flow within the tumor and surrounding tissue. 3) Assessing transport in clinical images and relating transport parameters to progression of GBM. 4) Developing a novel pipeline for applying vector field topology to the study of interstitial fluid flow in glioma. Surprisingly, we found that motility metrics in vitro have a negative correlation trend with in vivo invasion. Next, we found that radiation causes a transient increase in flow velocity magnitude, and a more sustained decrease in diffusivity in a murine glioma model. Tenascin C, a component of the tissue matrix, was found to correlate significantly with invasion and diffusivity. This indicates that Tenascin C might be a link between radiation, transport, and invasion. Furthermore, interstitial fluid flow was calculated and assessed in clinical images which showed that interstitial fluid flow velocity magnitude in the tumor correlates with survival. Lastly, vector field topology was introduced as a novel method of studying fluid flow in glioma that provides more detailed information regarding the flow field. Altogether, this work presents novel insight into the effects of radiation on fluid flow and cellular movement in GBM. Hopefully, this work can provide a foundation to build upon in efforts of improving treatment planning and clinical outcomes for GBM patients.

In der vorliegenden Arbeit wurde die Beeinflussung der Wechselwirkungen zwischen Oberflächenwasser, Interstitial und Grundwasser durch eutrophierungsbedingte Kolmationszyklen in einem anthropogen belasteten Fließgewässer (Lahn, Hessen) untersucht. Dabei wurden Mesokosmosexperimente und Freilanduntersuchungen an einer hyporhithralen Pool-Riffle-Sequenz miteinander kombiniert und die Ergebnisse vergleichend interpretiert. Im Rahmen der Arbeit wurde ein experimenteller Versuchsstand aufgebaut, der aus einer kontinuierlich durchströmten Sedimentsäule bestand und in einem mobilen Laborcontainer an der Lahn installiert war. Mit Hilfe dieses mesoskaliges Sedimentkörperexperimentes wurden jahreszeitliche Verlaufsmuster der inneren Kolmation analysiert, parametrisiert und mit physikalischen (Schwebstoffdynamik) und biologischen Kolmationskomponenten in Beziehung gesetzt. Besonderer Fokus lag dabei auf der Entwicklung des Periphytons, das in eutrophierten Fliessgewässern verstärkender Faktor der Kolmation werden kann. Ferner ließ sich mit dem aufgebauten Sedimentkörperexperiment der Einfluss von Kolmation auf Stoffumsetzungsprozesse (O2) im Interstitial modellhaft erfassen. In einem zweiten mesoskaligen Versuchsstand wurde die Bedeutung der hyporheischen Meiofauna für biogene Dekolmationsvorgänge (Fraß und Bioturbation) untersucht.

In der vorliegenden Arbeit wurde die Beeinflussung der Wechselwirkungen zwischen Oberflächenwasser, Interstitial und Grundwasser durch eutrophierungsbedingte Kolmationszyklen in einem anthropogen belasteten Fließgewässer (Lahn, Hessen) untersucht. Dabei wurden Mesokosmosexperimente und Freilanduntersuchungen an einer hyporhithralen Pool-Riffle-Sequenz miteinander kombiniert und die Ergebnisse vergleichend interpretiert. Im Rahmen der Arbeit wurde ein experimenteller Versuchsstand aufgebaut, der aus einer kontinuierlich durchströmten Sedimentsäule bestand und in einem mobilen Laborcontainer an der Lahn installiert war. Mit Hilfe dieses mesoskaliges Sedimentkörperexperimentes wurden jahreszeitliche Verlaufsmuster der inneren Kolmation analysiert, parametrisiert und mit physikalischen (Schwebstoffdynamik) und biologischen Kolmationskomponenten in Beziehung gesetzt. Besonderer Fokus lag dabei auf der Entwicklung des Periphytons, das in eutrophierten Fliessgewässern verstärkender Faktor der Kolmation werden kann. Ferner ließ sich mit dem aufgebauten Sedimentkörperexperiment der Einfluss von Kolmation auf Stoffumsetzungsprozesse (O2) im Interstitial modellhaft erfassen. In einem zweiten mesoskaligen Versuchsstand wurde die Bedeutung der hyporheischen Meiofauna für biogene Dekolmationsvorgänge (Fraß und Bioturbation) untersucht.

Cette recherche vise à développer un système de diagnostic assisté par ordinateur pour la détection automatique et la classification des pathologies du parenchyme pulmonaire telles que les pneumonies interstitielles idiopathiques et l'emphysème, en tomodensitométrie multicoupe. L’approche proposée repose sur morphologie mathématique 3-D, analyse de texture et logique floue, et peut être divisée en quatre étapes : (1) un schéma de décomposition multi-résolution basé sur un filtre 3-D morphologique exploitée pour discriminer les régions pulmonaires selon différentes échelles d’analyse. (2) Un partitionnement spatial supplémentaire du poumon basé sur la texture du tissu pulmonaire a été introduit afin de renforcer la séparation spatiale entre les motifs extraits au même niveau résolution dans la pyramide de décomposition. Puis, (3) une structure d'arbre hiérarchique a été construite pour décrire la relation d’adjacence entre les motifs à différents niveaux de résolution, et pour chaque motif, six fonctions d'appartenance floue ont été établies pour attribuer une probabilité d'association avec un tissu normal ou une cible pathologique. Enfin, (4) une étape de décision exploite les classifications par la logique floue afin de sélectionner la classe cible de chaque motif du poumon parmi les catégories suivantes : normal, emphysème, fibrose/rayon de miel, et verre dépoli. La validation expérimentale du système développé a permis de définir des spécifications relatives aux valeurs recommandées pour le nombre de niveaux de résolution NRL = 12, et le protocole d'acquisition comportant le noyau de reconstruction “LUNG” / ”BONPLUS” et des collimations fines (1.25 mm ou moins). Elle souligne aussi la difficulté d'évaluer quantitativement la performance de l'approche proposée en l'absence d'une vérité terrain, notamment une évaluation volumétrique, la sélection large des bords de la pathologie, et la distinction entre la fibrose et les structures (vasculaires) de haute densité / This research aims at developing a computer-aided diagnosis (CAD) system for fully automatic detection and classification of pathological lung parenchyma patterns in idiopathic interstitial pneumonias (IIP) and emphysema using multi-detector computed tomography (MDCT). The proposed CAD system is based on 3-D mathematical morphology, texture and fuzzy logic analysis, and can be divided into four stages: (1) a multi-resolution decomposition scheme based on a 3-D morphological filter was exploited to discriminate the lung region patterns at different analysis scales. (2) An additional spatial lung partitioning based on the lung tissue texture was introduced to reinforce the spatial separation between patterns extracted at the same resolution level in the decomposition pyramid. Then, (3) a hierarchic tree structure was exploited to describe the relationship between patterns at different resolution levels, and for each pattern, six fuzzy membership functions were established for assigning a probability of association with a normal tissue or a pathological target. Finally, (4) a decision step exploiting the fuzzy-logic assignments selects the target class of each lung pattern among the following categories: normal (N), emphysema (EM), fibrosis/honeycombing (FHC), and ground glass (GDG). The experimental validation of the developed CAD system allowed defining some specifications related with the recommendation values for the number of the resolution levels NRL = 12, and the CT acquisition protocol including the “LUNG” / ”BONPLUS” reconstruction kernel and thin collimations (1.25 mm or less). It also stresses out the difficulty to quantitatively assess the performance of the proposed approach in the absence of a ground truth, such as a volumetric assessment, large margin selection, and distinguishability between fibrosis and high-density (vascular) regions