Understanding soil structure, in particular the void spaces through which water, gases and solutes flow and in which organisms exist, is vital to a sustainable future on earth. The investigation of the structural behaviour of soil under different influences is fundamental to understanding and protecting the soil. This study has investigated the impact of bacteria on the biophysics of water retention and flow, aiming to elucidate the effect of three key components produced by the model organism, Pseudomonas fluorescens SBW25. Cellulose is an extracellular polysaccharide involved in the formation of the matrix of the bacterial biofilm, lipopolysaccharide is a cell membrane component required for bacterial attachment, and viscosin is a biosurfactant released from the bacteria. Four isogenic strains mutated so as to heighten or suppress production of one of these key components were used in addition to the wild-type strain. Labfield sandy loam soil was sieved and packed into replicate experimental cores which were incubated with different bacterial treatments. Following sterilisation, the gravimetric water content (u g g-1) of the soil was determined at equilibrated matric potentials from -1 cm to -100 cm during two wet-dry cycles. Sorptivity (S, mm s-1/2) of the soil, indicative of water repellency, was determined using a mini-infiltrometer setup and has been reported as the rate of infiltration of water into the soil. Bacteria have been shown to increase water repellency of soil, decrease the total water content at saturation and increase the water retaining ability of the soil as it drains (p < 0.05). Three-dimensional analysis of core scale structure was carried out using micro X-ray computed tomography (µXCT) and of aggregate scale structure using synchrotron-µXCT. Volumetric analyses of the 3D structures has shown decreased pore connectivity and destabilisation of aggregates in soil systems treated with bacteria deficient in the production of a key extracellular component, cellulose, LPS or viscosin (p < 0.05). Analyses of cracking patterns in two types of sandy loam soil, Labfield and Bullionfield has highlighted the importance of taking into account the soil type and its composition when studying soils, as even within soil classification groups different behaviours are observed. This study has provided clear evidence of the ability of bacteria and their extracellular components to impact upon (i) the hydrodynamics of water retention and flow in soil and (ii) the structural organisation, aggregation and stabilisation of soil.

No description available.

No description available.

High-resolution micro computed tomography (micro-CT) offers 3D image resolution of 1 um for non-destructive evaluation of various samples. However, the micro-CT performance is limited by several factors. Primarily, scan time is extremely long, and sample dimension is restricted by the x-ray beam and the detector size. The latter is the cause for the well-known interior problem. Recent advancement in image reconstruction, spurred by the advent of compressed sensing (CS) theory in 2006 and interior tomography theory since 2007, offers great reduction in the number of views and an increment in the volume of samples, while maintaining reconstruction accuracy. Yet, for a number of reasons, traditional filtered back-projection based reconstruction methods remain the de facto standard on all manufactured scanners. This work demonstrates that CS based global and interior reconstruction methods can enhance the imaging capability of micro-CT scanners. First, CS based few-view reconstruction methods have been developed for use with data from a real micro-CT scanner. By achieving high quality few-view reconstruction, the new approach is able to reduce micro-CT scan time to up to 1/8th of the time required by the conventional protocol. Next, two new reconstruction techniques have been developed that allow accurate interior reconstruction using just a limited number of global scout views as additional information. The techniques represent a significant progress relative to the previous methods that assume a fully sampled global scan. Of the two methods, the second method uses CS techniques and does not place any restrictions on scanning geometry. Finally, analytic and iterative reconstruction methods have been developed for enlargement of the field of view for the interior scan with a small detector. The idea is that truncated projections are acquired in an offset detector geometry, and the reconstruction procedure is performed through the use of a weighting function / weighted iteration updates, and projection completion. The CS based reconstruction yields the highest image quality in the numerical simulation. Yet, some limitations of the CS based techniques are observed in case of real data with various imperfect properties. In all the studies, physical micro-CT phantoms have been designed and utilized for performance analysis. Also, important guidelines are suggested for future improvements. / Ph. D.

Fossils recovered from limestones of the lower Cambrian (Stage 2-3) Yanjiahe Formation in Hubei Province, South China, recovered using acetic acid maceration, fracturing, and thin sectioning techniques were examined using a combination of analytical techniques, including energy dispersive spectroscopic (EDS) elemental mapping and micro-focus X-ray computed tomography (micro-CT). One important fossil recovered and analyzed with these techniques is a fossilized embryo. Fossilized animal embryos from lower Cambrian rocks provide a rare opportunity to study the ontogeny and developmental biology of early animals during the Cambrian explosion. The fossil embryos in this study exhibit a phosphatized outer envelope (interpreted as the chorion) that encloses a multicelled blastula-like embryo or a calcitized embryo marked by sets of grooves on its surface. The arrangement of these grooves resembles annulations found on the surface of the Cambrian-Ordovician fossil embryo Markuelia. Previously described late-stage Markuelia embryos exhibit annulations and an introvert ornamented by scalids, suggesting a scalidophoran affinity. In the Yanjiahe fossils illustrated herein, however, the phosphatized chorions and blastulas are not taxonomically or phylogenetically diagnostic, and the late-stage embryo is secondarily calcitized and thus poorly preserved, with only vague grooves indicative of Markuelia-type annulations. Consequently, their taxonomic assignment to the genus Markuelia is uncertain. If they indeed belong to the genus Markuelia, they are the oldest known Markuelia fossils from China, and represent both a new occurrence and possibly a new species. / Master of Science

No / Rationale and Objectives: To determine whether a single source computed tomography (CT) system utilizing fast kV switching and low dose settings can characterize (diameter and chemical composition) renal stones accurately when compared infrared spectroscopy. Materials and Methods: The chemical composition of 15 renal stones was determined using Fourier transform infrared spectroscopy. The stones were inserted into a porcine kidney and placed within a water tank for CT scanning using both fast kV switching dual energy and standard protocols. Effective atomic number of each stone was measured using scanner software. Stone diameter measurements were repeated twice to determine intra-rater variation and compared to actual stone diameter as measured by micro CT. Results: The chemical composition of three stones (one calcium phosphate and two carbonite apatite) could not be determined using the scanner software. The composition of 10/12 remaining stones was correctly identified using dual energy computed tomography (83% absolute agreement; k = 0.69). No statistical difference (p = 0.051) was noted in the mean stone diameter as measured by clinical CT and micro CT. Conclusion: Dual energy computed tomography using fast kV switching may potentially be developed as a low dose clinical tool for identifying and classifying renal stones in vivo supporting clinical decision-making.

Ziel der Studie: Vergleich zweier Methoden zur Entfernung der medikamentösen Einlage Kalziumhydroxid aus runden und ovalen Wurzelkanälen mithilfe eines Micro-CTs. Material und Methode: Es wurden 80 extrahierte menschliche Prämolaren und Inzisivi verwendet. Die Wurzelkanäle wurden von koronal auf eine einheitliche Länge von 18 mm gekürzt und mit dem FlexMaster-System (VDW, München) bis zu Größe 40/.04 präpariert. Nach jeder Instrumentengröße wurden die Kanäle mit 2 ml 3%igem Natriumhypochlorit gespült. Die Spülung erfolgte mit einer 2 ml Spritze und einer Nadel der Größe 30 (NaviTip 30 Gauge, Ultradent, München). Die Applikation des Kalziumhydroxidpräparates (UltraCal XS. Ultradent Products Inc., Utah, USA) wurde mit einer Injektionsnadel der Größe 30 durchgeführt. Eine anschließende röntgenologische Kontrolle sicherte die vollständige und homogene Verteilung des Präparates im Wurzelkanal. Alle Probenzähne wurden für sieben Tage bei 37°C Lufttemperatur und 100% Luftfeuchtigkeit gelagert. Nach Anfertigung präoperativer Micro-CT-Scans von jedem Wurzelkanal erfolgte eine Volumenbestimmung der applizierten Kalziumhydroxideinlage. Außerdem konnten die Proben anhand der Bilddaten einer runden oder ovalen Querschnittsform zugeteilt werden. Anschließend erfolgte die Einteilung der Probenzähne in vier Gruppen; Gruppe 1 (n = 10, ovale Querschnittsform), Gruppe 2 (n = 10, ovale Querschnittsform), Gruppe 3 (n = 30, runde Querschnittsform), Gruppe 4 (n = 30, runde Querschnittsform). Die Gruppen 1 und 3 wurden dem Spülprotokoll der Self-Adjusting File (SAF) zugeteilt, die Gruppen 2 und 4 dem der passiven Ultraschallspülung (PUI). Das Spülprotokoll beider Entfernungsmethoden sah eine 4-minütige Anwendung, aufgeteilt in 8 jeweils 30 Sekunden lange Zyklen und eine Gesamtspülmenge von 20 ml 3%igem Natriumhypochlorit vor. Die Auswertung erfolgte durch Anfertigung postoperativer Micro-CT-Scans und erneute Bestimmung des verbliebenen Volumens an medikamentöser Einlage. Zur statistischen Auswertung wurde der Quotient aus Volumen nach der Entfernung zu dem Volumen vor der Entfernung berechnet und eine zweifaktorielle Varianzanalyse (ANOVA) durchgeführt.   Ergebnisse: Keine der verwendeten Methoden konnte eine vollständige Entfernung der medikamentösen Einlage Kalziumhydroxid erreichen. Die SAF-Spülung erreichte signifikant bessere Ergebnisse als die PUI. Es konnte kein signifikanter Einfluss der Kanalform (rund/oval) auf die Reinigungswirkung beider Systeme festgestellt werden. Schlussfolgerung: Das SAF-System entfernt Kalziumhydroxid effektiver aus runden und ovalen Wurzelkanälen als die passive Ultraschallspülung. Mit beiden Systemen konnten relativ saubere, aber keine vollständig von Kalziumhydroxid gereinigten Kanalwände erzielt werden.

Os bisfosfonatos são medicamentos amplamente e efetivamente utilizados para o tratamento de doenças osteolíticas. Entretanto, na cavidade oral, é de particular relevância, pois possuem como efeito adverso a osteonecrose dos maxilares induzida pelo uso de bisfosfonatos. Sua etiopatogenia ainda não é bem estabelecida, os métodos de detecção são insatisfatórios e as terapias recomendadas são por vezes, medidas paliativas e ineficazes. Pouco ainda é sabido sobre o efeito do Ácido Zoledrônico na microestrutura óssea, portanto, propusemo-nos a realizar um estudo em modelo animal que analisasse o trabeculado ósseo da mandíbula através da Micro-CT. Foram utilizados 24 ratos machos (Rattus novergicus, albinus, Wistar), com 12 semanas de vida, divididos em 2 grupos: grupo controle (cloreto de sódio 0,9%) e grupo ácido zoledrônico (ácido zoledrônico 0,6mg/kg). As substâncias foram administradas via intraperitoneal a cada 28 dias em um total de 5 doses. Após 150 dias do início do experimento, foi realizada a eutanásia dos animais e então as amostras foram preparadas e escaneadas (Skyscan 1174) para análise da microestrutura óssea através da Micro- CT. O teste t-student demonstrou diferença estatisticamente significativa (p<0,05) em todos os fatores: volume ósseo, densidade óssea, fator de padrão trabecular, índice de modelo estrutural, espessura trabecular, separação trabecular, porosidade total exceção de número de trabéculas e volume tecidual, demonstrando que há alterações significativas na estrutura trabecular pelo uso de bisfosfonatos. O grupo medicado com ácido zoledrônico comparado ao grupo controle demonstrou trabéculas mais espessas, menos separadas e com menores ligações. / Bisphosphonates are widely and effectively drugs used for the treatment of osteolytic disorders. However, in the oral cavity, this situation is of particular relevance as it can lead to bisphosphonate related osteonecrosis of the jaws. Its etiopathogenesis is still not established, detection methods are unsatisfactory and recommended therapies are sometimes palliative and often ineffective. Little is known about the effect of zoledronic acid on the quality of trabecular bone, therefore, we proposed to conduct a study in an animal model to examine the trabecular bone of the jaw through the Micro-CT. 24 male rats were used (Rattus norvegicus, Albinus, Wistar), with 12 weeks old, divided into 2 groups: control group (sodium chloride 0.9%) and group with zoledronic acid (zoledronic acid 0.6 mg / kg). The substances were administered intraperitoneally every 28 days for a total of 5 doses. After 150 days from the beginning of the experiment, the animals were sacrificed and then the samples were prepared and scanned (Skyscan 1174) for analysis of the bone microstructure through Micro-CT. The \"t-student\" test demonstrated statistically significant differences (p<0.05) in all factors: bone volume, osseous density, trabecular pattern, structure model index, trabecular thickness, trabecular separation, total porosity except trabecular number and tissue volume, demonstrating that there are significant changes in the trabecular structure of the bisphosphonates. Zoledronic Acid compared to control group shows thicker, less separate and lower connected trabeculae.

Os bisfosfonatos são medicamentos amplamente e efetivamente utilizados para o tratamento de doenças osteolíticas. Entretanto, na cavidade oral, é de particular relevância, pois possuem como efeito adverso a osteonecrose dos maxilares induzida pelo uso de bisfosfonatos. Sua etiopatogenia ainda não é bem estabelecida, os métodos de detecção são insatisfatórios e as terapias recomendadas são por vezes, medidas paliativas e ineficazes. Pouco ainda é sabido sobre o efeito do Ácido Zoledrônico na microestrutura óssea, portanto, propusemo-nos a realizar um estudo em modelo animal que analisasse o trabeculado ósseo da mandíbula através da Micro-CT. Foram utilizados 24 ratos machos (Rattus novergicus, albinus, Wistar), com 12 semanas de vida, divididos em 2 grupos: grupo controle (cloreto de sódio 0,9%) e grupo ácido zoledrônico (ácido zoledrônico 0,6mg/kg). As substâncias foram administradas via intraperitoneal a cada 28 dias em um total de 5 doses. Após 150 dias do início do experimento, foi realizada a eutanásia dos animais e então as amostras foram preparadas e escaneadas (Skyscan 1174) para análise da microestrutura óssea através da Micro- CT. O teste t-student demonstrou diferença estatisticamente significativa (p<0,05) em todos os fatores: volume ósseo, densidade óssea, fator de padrão trabecular, índice de modelo estrutural, espessura trabecular, separação trabecular, porosidade total exceção de número de trabéculas e volume tecidual, demonstrando que há alterações significativas na estrutura trabecular pelo uso de bisfosfonatos. O grupo medicado com ácido zoledrônico comparado ao grupo controle demonstrou trabéculas mais espessas, menos separadas e com menores ligações. / Bisphosphonates are widely and effectively drugs used for the treatment of osteolytic disorders. However, in the oral cavity, this situation is of particular relevance as it can lead to bisphosphonate related osteonecrosis of the jaws. Its etiopathogenesis is still not established, detection methods are unsatisfactory and recommended therapies are sometimes palliative and often ineffective. Little is known about the effect of zoledronic acid on the quality of trabecular bone, therefore, we proposed to conduct a study in an animal model to examine the trabecular bone of the jaw through the Micro-CT. 24 male rats were used (Rattus norvegicus, Albinus, Wistar), with 12 weeks old, divided into 2 groups: control group (sodium chloride 0.9%) and group with zoledronic acid (zoledronic acid 0.6 mg / kg). The substances were administered intraperitoneally every 28 days for a total of 5 doses. After 150 days from the beginning of the experiment, the animals were sacrificed and then the samples were prepared and scanned (Skyscan 1174) for analysis of the bone microstructure through Micro-CT. The \"t-student\" test demonstrated statistically significant differences (p<0.05) in all factors: bone volume, osseous density, trabecular pattern, structure model index, trabecular thickness, trabecular separation, total porosity except trabecular number and tissue volume, demonstrating that there are significant changes in the trabecular structure of the bisphosphonates. Zoledronic Acid compared to control group shows thicker, less separate and lower connected trabeculae.

Le but de cette étude est de comparer le respect de la morphologie canalaire après instrumentation à l’aide de trois systèmes de mise en forme canalaire différents : le One Shape NEW Generation®, le Wave One® et le Revo-S® grâce à une étude en Micro-tomographie assistée par ordinateur ou micro-CT (Computed Tomography). La mise en place d’une chaîne méthodologique totalement tridimensionnelle (3D) comprenant la reconstruction, le recalage et la segmentation a permis de traiter les images acquises et d’extraire les images recalées des canaux dentaires avant et après instrumentation. Les artéfacts de segmentation dus aux calcifications et aux débris dentinaires ont été traités. Une méthode d’estimation des zones non instrumentées a également été décrite.Le transport canalaire a été calculé pour chaque coupe de chaque tiers radiculaire, en comparant la position du centroïde avant et après instrumentation. La comparaison des moyennes de transport canalaire ne montre pas de différence significative entre les 3 systèmes d’instrumentation.Cette approche méthodologique en 4 parties a permis de valider un protocole d’imagerie 3D reproductible, qui pourra être appliqué in vitro en recherche endodontique dans l’analyse des effets instrumentaux. / The aim of this study is to compare the respect of the root canal morphology after instrumentation with different shaping systems (One Shape NEW Generation®, Wave One® and Revo-S®), by using Micro-Computed Tomography.We used a fully three-dimensional (3D) methodological process which involved the reconstruction, registration and segmentation. By this methodological process, images have been acquired and processed in order to extract registered canals images before and after the instrumentation. The segmentation artifacts like calcifications and debris have been taken into account. A method to estimate the non-instrumented zones is also described.The canal transportation was calculated for each slice of each root-third by comparing the position of the centroids before and after instrumentation. No significant difference was found between the three instrumentation systems when canal transport means were done.This 4-part methodological approach has enabled the validation of a reproducible 3D imaging protocol. This can be applied in vitro in endodontic research for analysis of the instrumental effects.