Outlier Detection for Shape Model Fitting

Medical image analysis applications often benefit from having a statistical shape model in the background. Statistical shape models are generative models which can generate shapes from the same family and assign a likelihood to the generated shape. In an Analysis-by-synthesis approach to medical image analysis, the target shape to be segmented, registered or completed must first be reconstructed by the statistical shape model. Shape models accomplish this by either acting as regression models, used to obtain the reconstruction, or as regularizers, used to limit the space of possible reconstructions. However, the accuracy of these models is not guaranteed for targets that lie out of the modeled distribution of the statistical shape model. Targets with pathologies are an example of out-of-distribution data. The target shape to be reconstructed has deformations caused by pathologies that do not exist on the healthy data used to build the model. Added and missing regions may lead to false correspondences, which act as outliers and influence the reconstruction result. Robust fitting is necessary to decrease the influence of outliers on the fitting solution, but often comes at the cost of decreased accuracy in the inlier region. Robust techniques often presuppose knowledge of outlier characteristics to build a robust cost function or knowledge of the correct regressed function to filter the outliers. This thesis proposes strategies to obtain the outliers and reconstruction simultaneously without previous knowledge about either. The assumptions are that a statistical shape model that represents the healthy variations of the target organ is available, and that some landmarks on the model reference that annotate locations with correspondence to the target exist. The first strategy uses an EM-like algorithm to obtain the sampling posterior. This is a global reconstruction approach that requires classical noise assumptions on the outlier distribution. The second strategy uses Bayesian optimization to infer the closed-form predictive posterior distribution and estimate a label map of the outliers. The underlying regression model is a Gaussian Process Morphable Model (GPMM). To make the reconstruction obtained through Bayesian optimization robust, a novel acquisition function is proposed. The acquisition function uses the posterior and predictive posterior distributions to avoid choosing outliers as next query points. The algorithms give as outputs a label map and a a posterior distribution that can be used to choose the most likely reconstruction. To obtain the label map, the first strategy uses Bayesian classification to separate inliers and outliers, while the second strategy annotates all query points as inliers and unused model vertices as outliers. The proposed solutions are compared to the literature, evaluated through their sensitivity and breakdown points, and tested on publicly available datasets and in-house clinical examples. The thesis contributes to shape model fitting to pathological targets by showing that: - performing accurate inlier reconstruction and outlier detection is possible without case-specific manual thresholds or input label maps, through the use of outlier detection. - outlier detection makes the algorithms agnostic to pathology type i.e. the algorithms are suitable for both sparse and grouped outliers which appear as holes and bumps, the severity of which influences the results. - using the GPMM-based sequential Bayesian optimization approach, the closed-form predictive posterior distribution can be obtained despite the presence of outliers, because the Gaussian noise assumption is valid for the query points. - using sequential Bayesian optimization instead of traditional optimization for shape model fitting brings forth several advantages that had not been previously explored. Fitting can be driven by different reconstruction goals such as speed, location-dependent accuracy, or robustness. - defining pathologies as outliers opens the door for general pathology segmentation solutions for medical data. Segmentation algorithms do not need to be dependent on imaging modality, target pathology type, or training datasets for pathology labeling. The thesis highlights the importance of outlier-based definitions of pathologies in medical data that are independent of pathology type and imaging modality. Developing such standards would not only simplify the comparison of different pathology segmentation algorithms on unlabeled datsets, but also push forward standard algorithms that are able to deal with general pathologies instead of data-driven definitions of pathologies. This comes with theoretical as well as clinical advantages. Practical applications are shown on shape reconstruction and labeling tasks. Publicly-available challenge datasets are used, one for cranium implant reconstruction, one for kidney tumor detection, and one for liver shape reconstruction. Further clinical applications are shown on in-house examples of a femur and mandible with artifacts and missing parts. The results focus on shape modeling but can be extended in future work to include intensity information and inner volume pathologies

A comparison between the suspended sediment concentrations derived from DELFT3D model and collected using transmissometer – a case study in tidally dominated area of Dithmarschen Bight

SummaryThe objective of this investigation is to verify the deficiencies that incorporate both modelled and measured suspended sediment concentrations (SSC) data in a tidal dominated area. For this purpose a tidal channel, in the North Sea, was considered as the case study.The profiles of SSC from a model were compared with those from the field, in which some dissimilarity was observed. Intensive investigations were carried out to detect that the most discrepancies occur in shallow parts of the area and also during the low velocities. The origin of the shortcomings in regard with the modelling and measuring technique are discussed

Optimisation, étude de la cinétique et dimensionnement de la production des biopesticides à base de souches de Bacillus thuringiensis isolées du sol Libanais

Parmi les méthodes alternatives respectueuses de l'environnement pour la lutte contre les ravageurs et la protection des cultures agricoles, les bioinsecticides à base de Bacillus thuringiensis sont les plus largement utilisés. L’activité insecticide de B.thuringiensis réside dans la production d’inclusions cristallines protéiques appelées δ-endotoxines qui sont formées au cours de la sporulation. En préalable à ces travaux, de nouvelles souches de B.thuringiensis ont été isolées du sol libanais et ont montré un potentiel insecticide élevé, supérieur à des souches classiquement utilisées. Dans le cadre du développement d'une production industrielle, au Liban, de biopesticides à base de ces souches de B.thuringiensis, ce travail a visé à optimiser la production des δ-endotoxines afin d'augmenter les rendements et de réduire les coûts de production. A l'échelle industrielle, le milieu de culture des bactéries représente une part importante du coût de production. Ainsi, l'effet, sur la concentration des δ-endotoxines, de substitution des sources synthétiques coûteuses d'azote, de carbone et de minéraux, par un sous-produit de la minoterie de blé (le son de blé) a été étudié. L’efficacité de ce sous-produit agro-industriel comme source complète de nutriments, disponible localement à faible prix, a été prouvée pour des fermentations submergées de deux souches différentes toxiques contre des diptères ou des lépidoptères. La comparaison du milieu son de blé à d’autres milieux (synthétiques ou non), classiquement utilisés en bibliographie, a montré que ce milieu présente de nombreux avantages en termes de productivité, de rendement relatif des δ-endotoxines et de coût. Parallèlement à ce travail, une méthode simple et rapide de purification des cristaux a été développée de façon à obtenir des cristaux protéiques purs à 99 % nécessaires comme standards pour le dosage des cristaux dans le milieu de fermentation. Un autre objectif du travail a été d’analyser l'effet de l'aération sur la cinétique de croissance et de sporulation d'une nouvelle souche de B.thuringiensis var kurstaki. Les différentes conditions d’aération testées en fermenteurs de 2 L, caractérisées par le coefficient volumétrique de transfert de dioxygène (KLa), ont permis de montrer l’importance de ce paramètre et de l’optimiser pour obtenir la meilleure productivité en biopesticides. Le meilleur rendement en protéines de toxines a été obtenu dans un milieu son de blé 6 % (masse/volume) dans des conditions d’aération correspondant à un KLa de 65,5 h-1 alors que la meilleure productivité des protéines de toxines a été atteinte dans le milieu 9 % pour un KLa de 102 h-1. Sur la base de cette étude, le dimensionnement de la production de B.thuringiensis à l’échelle 1000 L a été réalisé. L’unité de production a été construite et les premiers essais réalisés ont permis de produire de façon satisfaisante des lots de biopesticides. L’ajustement des protocoles industriels reste à faire

Strong Equality of Perfect Roman and Weak Roman Domination in Trees

Let G=(V,E) be a graph and f:V⟶{0,1,2} be a function. Given a vertex u with f(u)=0, if all neighbors of u have zero weights, then u is called undefended with respect to f. Furthermore, if every vertex u with f(u)=0 has a neighbor v with f(v)>0 and the function f′:V⟶{0,1,2} with f′(u)=1, f′(v)=f(v)−1, f′(w)=f(w) if w∈V∖{u,v} has no undefended vertex, then f is called a weak Roman dominating function. Also, the function f is a perfect Roman dominating function if every vertex u with f(u)=0 is adjacent to exactly one vertex v for which f(v)=2. Let the weight of f be w(f)=∑v∈Vf(v). The weak (resp., perfect) Roman domination number, denoted by γr(G) (resp., γpR(G)), is the minimum weight of the weak (resp., perfect) Roman dominating function in G. In this paper, we characterize those trees where the perfect Roman domination number strongly equals the weak Roman domination number, in the sense that each weak Roman dominating function of minimum weight is, at the same time, perfect Roman dominating

Numerische Modellirung der Küstenprozesse in der Dithmarscher Bucht unter Einbeziehung von Naturdaten

The main purpose of this dissertation is to investigate the applicability of numerical models in the study of the sediment transport in a tidal channel of the Dithmarschen Bight in the North Sea. The field data collected at different stages of the neap-spring tidal cycle was used for the evaluation of hydrodynamic and sediment dynamic of Delft3D package (Delft Hydraulics, The Netherlands) numerical model. The package was employed in both two and three dimensional. The investigation was conducted in two stages. At first the performance of the two dimensional model (2DH) was appraised against the field data. The model was calibrated and validated at this stage. Afterwards, the assessment and comparison of the three dimensional model results (3D) with the field data and also with the two dimensional model results was investigated. It was found that both the 2DH and 3D models are capable of predicting hydrodynamics of the area in good agreement with the field data. It was also observed that the effect of waves on water levels and current velocities was not significant under moderate conditions. The comparison of the modelled and measured suspended sediment concentration showed some disagreements especially during ebb current, due to some model shortcomings and to some measuring approximations and methods. The lack of precise techniques for deriving or calculating settling velocity and critical bed shear stresses were found to be the main sources for the model shortcoming. Two sources of error were also suggested relevant to the limitations of the measuring coverage and devices. The first was insufficient field measurements of grain size distributions, specifically on the tidal flat area; the second was the use of transmissometer device for deriving suspended sediment concentration at shallow water regions. Furthermore the difference between results, i.e. the current velocity and the suspended sediment concentration from the two and the three dimensional simulations are not significant as a result of well-mixed nature of the area. Thus, the use of the 3D model may not be justified with the currently available data for the area of investigation. However, the 3D model made it possible to find some weak points and deficiencies in the overall model. The three dimensional model has also provided very useful information about the flow and sediment dynamics of the area and the type of data required for further studies. Finally it was concluded that at this specific area of investigation to develop a model capable of predicting both hydrodynamic and sediment dynamics in agreement with those in the field, we do need to improve both measuring techniques and also model capability in the tidal flat area.Das Hauptaugenmerk dieser Arbeit liegt bei der Evaluierung der Anwendbarkeit von numerischen Modellen zur Untersuchung des Sedimenttransports im Prielsytem der Dithmarscher Bucht in der Nordsee. Naturdaten, gemessen während verschiedener Phasen im Tidenzyklus, wurden zum Aufbau und zur Auswertung der Modelle des Delft3D-Pakets (Delft Hydraulics, Niederlande) genutzt. Es wurde sowohl ein 2-, als auch ein 3-dimensionales Model erstellt. Die Untersuchung wurde in zwei Schritten ausgeführt. Zunächst wurde das 2-dimensionale Modell (2DH) anhand der Messdaten evaluiert. In diesem Schritt wurde das Modell kalibriert und validiert. Darauf aufbauend wurde das 3-dimensionale Modell (3D) erstellt und mit Hilfe der Naturmessungen und der Ergebnisse des 2DH-Modells bewertet. Die Untersuchung ergab, dass beide Modelle in der Lage sind, die Hydrodynamik des Interessengebietes in guter Übereinstimmung mit den Messwerten wiederzugeben. Weiterhin wurde festgestellt, dass der Einfluss von Wellen auf die Wasserstände und Fließgeschwindigkeiten unter moderaten Bedingungen nicht signifikant ist. Der Vergleich von modelliertem und gemessenem Sedimenttransport in der Wassersäule ergab einige Unterschiede, speziell während der Ebbphase. Dies liegt an einigen Beschränkungen des Modells, der Messgenauigkeit und den Messmethoden. Der Mangel an präzisen Techniken zur Bestimmung oder Berechnung von der Fallgeschwindigkeit und der Sohlschubspannung wurden als Hauptgründe für die Beschränkung des Modells identifiziert. Zwei Fehlerquellen lagen bei der Dichte der Feldmessungen und bei der Wahl der Messgeräte. Der erste betriff die ungenügende Messdichte bezüglich der Korngrößenverteilung der Wattenflächen, der zweite die Verwendung eines Transmissometers zur Messung der Sedimentkonzentration im Flachwasser. Beim Vergleich der Ergebnisse des 2- und 3-dimensionalen Modells, vor allem bei Fließgeschwindigkeit und Sedimenttransport, waren nur geringe Unterschiede erkennbar. Hier bringt die Verwendung eines 3D-Modells unter den gegebenen Umständen, ohne genügende Messwerte, keine signifikanten Vorteile. Gleichwohl wurden durch die Verwendung des 3D-Modells Schwachstellen und Mängel des allgemeinen Modells offengelegt. Das 3D-Modell trug ferner zum besseren Verständnis der Hydrologie und des Sedimenttransports im Untersuchungsgebiet bei. Ebenso wurde ein Überblick geschaffen über die Art von Messungen, welche für eine weitere Entwicklung des 3DModells erforderlich sind. Als abschließende Erkenntnis wurde festgestellt, dass sowohl die Messtechniken als auch die Modellkapazität verbessert werden muss, um ein gut funktionierendes Hydrodynamik- und Sedimenttransportmodell für das vorliegende Interessengebiet zu erstellen

Optimisation, étude de la cinétique et dimensionnement de la production des biopesticides à base de souches de Bacillus thuringiensis isolées du sol Libanais

Parmi les méthodes alternatives respectueuses de l'environnement pour la lutte contre les ravageurs et la protection des cultures agricoles, les bioinsecticides à base de Bacillus thuringiensis sont les plus largement utilisés. L’activité insecticide de B.thuringiensis réside dans la production d’inclusions cristallines protéiques appelées δ-endotoxines qui sont formées au cours de la sporulation. En préalable à ces travaux, de nouvelles souches de B.thuringiensis ont été isolées du sol libanais et ont montré un potentiel insecticide élevé, supérieur à des souches classiquement utilisées. Dans le cadre du développement d'une production industrielle, au Liban, de biopesticides à base de ces souches de B.thuringiensis, ce travail a visé à optimiser la production des δ-endotoxines afin d'augmenter les rendements et de réduire les coûts de production. A l'échelle industrielle, le milieu de culture des bactéries représente une part importante du coût de production. Ainsi, l'effet, sur la concentration des δ-endotoxines, de substitution des sources synthétiques coûteuses d'azote, de carbone et de minéraux, par un sous-produit de la minoterie de blé (le son de blé) a été étudié. L’efficacité de ce sous-produit agro-industriel comme source complète de nutriments, disponible localement à faible prix, a été prouvée pour des fermentations submergées de deux souches différentes toxiques contre des diptères ou des lépidoptères. La comparaison du milieu son de blé à d’autres milieux (synthétiques ou non), classiquement utilisés en bibliographie, a montré que ce milieu présente de nombreux avantages en termes de productivité, de rendement relatif des δ-endotoxines et de coût. Parallèlement à ce travail, une méthode simple et rapide de purification des cristaux a été développée de façon à obtenir des cristaux protéiques purs à 99 % nécessaires comme standards pour le dosage des cristaux dans le milieu de fermentation. Un autre objectif du travail a été d’analyser l'effet de l'aération sur la cinétique de croissance et de sporulation d'une nouvelle souche de B.thuringiensis var kurstaki. Les différentes conditions d’aération testées en fermenteurs de 2 L, caractérisées par le coefficient volumétrique de transfert de dioxygène (KLa), ont permis de montrer l’importance de ce paramètre et de l’optimiser pour obtenir la meilleure productivité en biopesticides. Le meilleur rendement en protéines de toxines a été obtenu dans un milieu son de blé 6 % (masse/volume) dans des conditions d’aération correspondant à un KLa de 65,5 h-1 alors que la meilleure productivité des protéines de toxines a été atteinte dans le milieu 9 % pour un KLa de 102 h-1. Sur la base de cette étude, le dimensionnement de la production de B.thuringiensis à l’échelle 1000 L a été réalisé. L’unité de production a été construite et les premiers essais réalisés ont permis de produire de façon satisfaisante des lots de biopesticides. L’ajustement des protocoles industriels reste à faire. ABSTRACT : Among the safe and environment friendly methods for the fight against pests and agricultural crops protection, Bacillus thuringiensis based biopesticides are the most widely used. The insecticidal activity of B. thuringiensis resides in the production of protein crystal inclusions called δ-endotoxins, which are formed during sporulation. Preliminary to this work, new B. thuringiensis strains were isolated from Lebanese soil and showed higher insecticidal potential than the conventionally used strains. As part of the development of an industrial production, in Lebanon, of biopesticides based on these strains of B.thuringiensis, this work aimed to optimize the production of δ-endotoxins to increase yields and reduce the cost of mass production. At industrial scale, the bacteria culture medium represents a significant part of the production cost. Thus, the effect on the concentration of the δ-endotoxins, of substituting expensive synthetic sources of nitrogen, carbon, and minerals, with a byproduct of wheat mill (wheat bran) was studied. The effectiveness of this agro-industrial by-product available locally at low prices, as complete source of nutrients, in submerged fermentations of two different strains of B.thuringiensis toxic against Lepidoptera and Diptera, has been proven. The comparison of the wheat bran medium to other mediums (synthetic or not), conventionally used in the bibliography, has shown that this medium this medium has many advantages in terms of productivity, relative yield of δ-endotoxins and cost. In parallel to this work, a simple and quick method of crystal purification was developed to obtain pure protein crystals to 99 % required as standards for the determination of crystals concentration in the fermentation medium. Another objective of the study was to analyze the effect of aeration on growth and sporulation kinetics of a new strain of B.thuringiensis var kurstaki. The different aeration conditions tested in fermenters of 2 L, characterized by the volumetric oxygen transfer coefficient (KLa), permitted to show the importance of this parameter and to optimize it to get the best biopesticides productivity. The best yield of toxin proteins relative to the wheat bran ratio in the culture medium was obtained in the 6 % (weight/volume) medium in aeration conditions corresponding to a KLa of 65.5 h-1, while the highest productivity of toxin proteins has been reached in the 9 % medium for KLa of 102 h-1. On this study basis, the scale up of B. thuringiensis production was performed in a bioreactor of 1000 L. The production unit was built and the first tests carried out have produced satisfactory batches of biopesticides. Industrial protocols are still to be adjusted

Detecting missing teeth on PMCT using statistical shape modeling

The identification of teeth in 3D medical images can be a first step for victim identification from scant remains, for comparison of ante- and postmortem images or for other forensic investigations. We evaluate the performance of a tooth detection approach on mandibles with missing parts or pathologies based on statistical shape models. The proposed approach relies on a shape model that has been built from the full lower jaw, including the mandible and teeth. The model is fitted to the target, resulting in a reconstruction, in addition to a label map that indicates the presence or absence of teeth. We evaluate the accuracy of the proposed solution on a dataset consisting of 76 target mandibles, all extracted from CT images and exhibiting various cases of missing teeth or other cases, such as roots, implants, first dentition, and gap closure. We show an accuracy of approximately 90% on the front teeth (including incisors and canines in our study) that decreases for the molars due to high false-positive rates at the wisdom teeth level. Despite the drop in performance, the proposed approach can be used to obtain an estimate of the tooth count without wisdom teeth, tooth identification, reconstruction of the existing teeth to automate measurements taken as part of routine forensic procedures, or prediction of the missing teeth shape. In comparison to other approaches, our solution relies solely on shape information. This means it can be applied to cases obtained from either medical images or 3D scans because it does not depend on the imaging modality intensities. Another novelty is that the proposed solution avoids heuristics for the separation of teeth or for fitting individual tooth models. The solution is therefore not target-specific and can be directly applied to detect missing parts in other target organs using a shape model of the new target

Northwest current of Gulf of Oman effects on coastal classification of east of Hormozgan Province by shepard’s method

This investigation, which involved the satellite images together with simulation model, focuses on the effect of the sea hydrodynamics on coastal area classification. The study area is the North-West coasts of Gulf of Oman. Mike 21 was employed to simulate the hydrodynamics of the Oman Gulf and Aster images were used to classify the coastal area applying Shepard’s method. Coastal classification of the area proposed the secondary coasts cover just 7% of the area including the Sirik headland and Jask regions. Intrusion of land toward the sea for Sirik headland and existence of longshore current in the area are the main reasons. The Jask area is located in transition zone between deep water of Gulf of Oman and shallow water of Hormoz Strait and was influenced by marine affects

Revascularization of an Immature Maxillary First Premolar with Necrotic Tissue: A Case Report

Objectives The purpose of this study was to present a case of regenerative endodontic procedure.Case The maxillary 1st premolar of a 9-year-old patient was diagnosed as necrotic. Since the tooth was immature, we decided to treat this tooth with regenerative endodontic procedure. After disinfection of the canal, bleeding was induced by lacerating the peri-apical tissues and a blood clot was formed. Orifice was sealed by MTA and the tooth was restored. 6-months and 1-year follow-ups showed increased root thickness and closure of the apical.Conclusion It can be concluded that the regenerative endodontic procedure used in this study was successful since there was an evident development in root width