This study developed an informative model of a nasal cavity of a Neanderthal and Anatomically Modern Human (AMH) hybrid based on the morphological measurements and nonmetric features of nonhuman primate hybrids. This study examined morphometric measurements and nonmetric traits of the interior nasal cavity of two species of baboons (olive and yellow) and their first generation hybrids to determine how hybridization affects the internal anatomy of the nasal cavity. The nasal cavity was chosen because the nasal cavities of Neanderthals and AMH are recognized as uniquely different in size and shape. This study found that functionally different regions within the baboon nasal cavity are altered in size and shape in response to hybridization. Changes in size and shape due to hybridization occurred in three regions, at the rhinion, choana, and mid-nasopharynx. In regions of more complex physiological function, the mid-bony cavity and the posterior nasopharynx, no size or shape response was observed, except a wider lateral recess. Males and females responded differently to hybridization; males showed heterosis and females showed heterosis in most areas, though dysgenesis in the inferior meatus. The opposing male and female trends may contribute to the greater sexual dimorphism observed in hybrids compared to parental taxa. This study found that frequencies of nonmetric traits in the baboon hybrid nasal cavity were no different from frequencies in parental taxa, nor were regional frequency differences observed because anterior and posterior nonmetric traits occurred at the same frequency. However, males expressed a significantly higher frequency of nonmetric traits than females. Assuming Neanderthal and AMH hybrid nasal cavities follow the trends observed in the baboon hybrid model, the Neanderthal and AMH hybrid nasal cavity would have a different shape and larger size at the rhinion, choana, and mid-nasopharynx, while the mid-bony cavity and posterior nasopharynx remained unchanged compared to parental taxa. However, because Neanderthals and AMH have been diverged for a longer time period, the traits of the nasal cavity may be very different in parental taxa due to adaptations to local conditions, which may result in hybrids with traits from one parent or the other. Further, an analysis of different hybridization scenarios between Neanderthals and AMH, based on observed hybridization in baboons and paleoanthropological evidence, suggests rapid gene swamping of the Neanderthal population by AMH during hybridization, as other authors have also concluded.

Archaeological bones are usually dated by radiocarbon measurement of extracted collagen. However, low collagen content, contamination from the burial environment or museum conservation work have previously lead to inaccurate results, especially for old bones, compromising the ability to reconstruct reliable past chronologies. It is reported, for example, that up to 70% of Palaeolithic radiocarbon dates on bones are likely to be underestimates of the real age, blurring the picture of modern human dispersals and Neanderthal extinction. In this thesis, a method for isolating and radiocarbon dating the collagen amino acid hydroxyproline is described. Hydroxyproline consists of about 10% of bone collagen but is not found in significant amounts elsewhere in nature. The hydroxyproline dating method uses a mixed-mode (i.e. ion-exchange combined with hydrophobic chemistry), semi preparative HPLC methodology. The amino acids do not require derivatisation, and no organic solvents are used, thereby avoiding addition of carbon. The hypothesis of this thesis is that the hydroxyproline can be used as a bone specific biomarker, improving dating accuracy and making it possible to obtain radiocarbon determinations where previously it has been impossible. It was calculated that on average 3.3±1.4μg of contaminant carbon are added to each sample in the process of isolating the hydroxyproline, a low level suitable for 14C dating. It was investigated whether a deliberately contaminated bone and 'naturally' contaminated archaeological bones, yielding erroneous dates when dated using the normal pretreatment method, could be dated accurately using this method. In addition, a hydroxyproline date was obtained for a bone with too little surviving collagen to be dateable by the bulk collagen method. Finally, using the hydroxyproline dating method, the earliest direct ages for the presence of anatomically modern humans on the Russian Plain were obtained. The method proved to be a powerful tool that can help resolve longstanding archaeological questions.

The purpose of the present study is to develop techniques for manufacturing anatomically-shaped substrates of implants made from calcium polyphosphate (CPP) ceramic. These substrates have tissue-engineered cartilage growing on their top surfaces and can be used as implants for osteochondral focal defect repair. While many research groups have been fabricating such substrates using standard material shapes, e.g., rectangles and circular discs, it is considered beneficial to develop methods that can be integrated in the substrate fabrication process to produce an implant that is specific to a patient’s own anatomy (as obtained from computer tomography data) to avoid uneven and/or elevated stress distribution that can affect the survival of cartilage. The custom-made, porous CPP substrates were fabricated with three-dimensional printing (3DP) and computer numerically controlled (CNC) machining for the first time to the best of the author’s knowledge. The 3DP technique was employed in two routines: indirect- and direct-3DP. In the former, 3DP was used to fabricate molds for pre-shaping of the CPP substrates from two different powder size ranges (<75 μm and 106-150 μm). In the latter, CPP substrates were produced directly from the retrofitted 3DP apparatus in a layer-by-layer fashion from 45-75 μm CPP powder with a polymeric binder. The prototyped samples were then sintered to obtain the required porosity and mechanical properties. These substrates were characterized in terms of their dimensional shrinkage and density. Also, SEM images were used to assess the particle distribution and neck and bond formations. The substrates produced using the indirect-3DP method yielded densities (<75 μm: 66.28 ± 11.62% and 106-150 μm: 65.87 ± 6.12%), which were comparable to the substrates used currently and with some success in animal studies. Geometric adjustment factors were devised to compensate for the slight expansion inherent in the 3DP mold fabricating process. These equations were used to bring the plaster molds into true dimension. The direct-3DP method has proven to be the ultimate choice due to its ability to produce complex anatomically-shaped substrates without the use of a chemical solvent. In addition, it allows for precise control of both pore size and internal architectures of the substrates. Thus, the direct-3DP was considered to be superior than the indirect-3DP as a fabrication method. In the alternative CNC machining approach to fabrication, the ability to machine the CPP ceramic was feasible and by careful selection of the machining conditions, anatomically-shaped CPP substrates were produced. To develop strategies for optimizing the machining process, a mechanistic model was developed based on curve fitting the average cutting forces to determine the cutting coefficients for CPP. These cutting coefficients were functions of workpiece material, axial depth of cut, chip width, and cutter geometry. To explore the utility of this modelling approach, cutting forces were predicted for a helical ball-end mill and compared with experimental results. The cutting force simulation exhibits good agreement in predicting the fundamental force magnitude and general shape of the actual forces. However, there were some discrepancies between the predicted and measured forces. These differences were attributed to internal microstructure defects, density gradients, and the use of a shear plane model in force prediction that was not entirely appropriate for brittle materials such as CPP. The present study successfully developed 3DP and CNC fabrication methods for manufacturing anatomically-shaped CPP substrates. Future studies were recommended to explore further optimization of these fabrication methods and to demonstrate the utility of accurate substrates shapes to the clinical application of focal defect repair implants.

The purpose of the present study is to develop techniques for manufacturing anatomically-shaped substrates of implants made from calcium polyphosphate (CPP) ceramic. These substrates have tissue-engineered cartilage growing on their top surfaces and can be used as implants for osteochondral focal defect repair. While many research groups have been fabricating such substrates using standard material shapes, e.g., rectangles and circular discs, it is considered beneficial to develop methods that can be integrated in the substrate fabrication process to produce an implant that is specific to a patient’s own anatomy (as obtained from computer tomography data) to avoid uneven and/or elevated stress distribution that can affect the survival of cartilage. The custom-made, porous CPP substrates were fabricated with three-dimensional printing (3DP) and computer numerically controlled (CNC) machining for the first time to the best of the author’s knowledge. The 3DP technique was employed in two routines: indirect- and direct-3DP. In the former, 3DP was used to fabricate molds for pre-shaping of the CPP substrates from two different powder size ranges (<75 μm and 106-150 μm). In the latter, CPP substrates were produced directly from the retrofitted 3DP apparatus in a layer-by-layer fashion from 45-75 μm CPP powder with a polymeric binder. The prototyped samples were then sintered to obtain the required porosity and mechanical properties. These substrates were characterized in terms of their dimensional shrinkage and density. Also, SEM images were used to assess the particle distribution and neck and bond formations. The substrates produced using the indirect-3DP method yielded densities (<75 μm: 66.28 ± 11.62% and 106-150 μm: 65.87 ± 6.12%), which were comparable to the substrates used currently and with some success in animal studies. Geometric adjustment factors were devised to compensate for the slight expansion inherent in the 3DP mold fabricating process. These equations were used to bring the plaster molds into true dimension. The direct-3DP method has proven to be the ultimate choice due to its ability to produce complex anatomically-shaped substrates without the use of a chemical solvent. In addition, it allows for precise control of both pore size and internal architectures of the substrates. Thus, the direct-3DP was considered to be superior than the indirect-3DP as a fabrication method. In the alternative CNC machining approach to fabrication, the ability to machine the CPP ceramic was feasible and by careful selection of the machining conditions, anatomically-shaped CPP substrates were produced. To develop strategies for optimizing the machining process, a mechanistic model was developed based on curve fitting the average cutting forces to determine the cutting coefficients for CPP. These cutting coefficients were functions of workpiece material, axial depth of cut, chip width, and cutter geometry. To explore the utility of this modelling approach, cutting forces were predicted for a helical ball-end mill and compared with experimental results. The cutting force simulation exhibits good agreement in predicting the fundamental force magnitude and general shape of the actual forces. However, there were some discrepancies between the predicted and measured forces. These differences were attributed to internal microstructure defects, density gradients, and the use of a shear plane model in force prediction that was not entirely appropriate for brittle materials such as CPP. The present study successfully developed 3DP and CNC fabrication methods for manufacturing anatomically-shaped CPP substrates. Future studies were recommended to explore further optimization of these fabrication methods and to demonstrate the utility of accurate substrates shapes to the clinical application of focal defect repair implants.

Previous studies proposed that Neandertals had one third higher energetic cost of locomotion than anatomically modern humans. Greater cost of locomotion could disadvantage Neandertals in competition with anatomically modern humans and could be a factor in their extinction. Greater cost of Neandertal locomotion was ascribed to their shorter lower limb and greater body mass. However, Neandertals differed also in other morphological parameters that were not considered in estimation of their locomotor cost. In this dissertation we model locomotor cost of Neandertals and anatomically modern humans using previously described relation between muscle force production and energetic cost of movement. We estimate the key locomotor parameters using a model developed by us from osteometric data from literature (n =50) and from our measurement (n = 21), and from kinematic data of 26 individuals. Further, we analyze the effect of relative lower limb length (in relation to body mass) and crural index on energetic cost of locomotion. Our results suggest that walking of Neandertal males was 9-14% energetically more demanding than walking of anatomically modern males. Nevertheless, the walking cost of Neandertal females was similar to that of anatomically modern females. Inclusion of lower limb proportions into the...

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Recent advances in deep learning have greatly improved the ability to generate analysis models from medical images. In particular, great attention is focused on quickly generating models of the left ventricle from cardiac magnetic resonance imaging (cMRI) to improve the diagnosis and prognosis of millions of patients. However, even state-of-the-art frameworks present challenges, such as discontinuities of the cardiac tissue and excessive jaggedness along the myocardial walls. These geometrical features are often anatomically incorrect and may lead to unrealistic results once the geometrical models are employed in computational analyses. In this research, we propose an end-to-end pipeline for a subject-specific model of the heart's left ventricle from Cine cMRI. Our novel pipeline incorporates the uncertainty originating from the segmentation methods in the estimation of cardiac indices, such as ejection fraction, myocardial volume changes, and global radial and longitudinal strain, during the cardiac cycle. First, we propose an anatomically-guided deep learning model to overcome the common segmentation challenges while preserving the advantages of state-of-the-art frameworks, such as computational efficiency, robustness, and abstraction capabilities. Our anatomically-guided neural networks include a B-spline head, which acts as a regularization layer during training. In addition, the introduction of the B-spline head contributes to achieving a robust uncertainty quantification of the left ventricle inner and outer walls. We validate our approach using human short-axis (SA) cMRI slices and later apply transfer learning to verify its generalization capabilities in swine long-axis (LA) cMRI slices. Finally, we use the SA and LA contours to build a Gaussian Process (GP) model to create inner and outer walls 3D surfaces, which are then used to compute global indices of cardiac functions. Our results show that the proposed pipeline generates anatomically consistent geometries while also providing a robust tool for quantifying uncertainty in the geometry and the derived cardiac indices.

Doctorat effectué en cotutelle Pour le département d'histoire de l'Université de Montréal, M.M. Jacques G. Ruelland et Othmar Keel, Pour le laboratoire P.A.C.E.A.– U.M.R. 5199. C.N.R.S., de l'École doctorale des sciences Terre-Mer, directeurs successifs, M. P.-Y. Demars, puis M. Michel Lenoir. Thèse soutenue à Bordeaux le 6 juin 2012. / Cette thèse a pour objectif d’étudier sur le plan historique une controverse scientifique persistante en préhistoire : le problème de la transition entre Paléolithiques moyen et supérieur, en tentant d’en expliquer la durée en termes de construction et de transformation des modèles antagoniques, ainsi que le rôle de cette controverse dans l’acquisition de connaissances, afin d’élucider comment s’est produit le déplacement des enjeux que présente son état actuel. Il s’agit de dresser un historique de la controverse entourant la transition entre Paléolithiques moyen et supérieur afin de circonscrire sur le plan chronologique les persistances et l’évolution des positions antagonistes dans leurs composantes épistémologiques. Pour clarifier cette démarche, il faut d’abord caractériser ce qui constitue cette controverse particulière pour les préhistoriens à l’aide de l’apport de l’histoire des sciences, et quelle méthode d’analyse sera utilisée dans le présent travail. Il sera ainsi possible de relier ces éléments au problème scientifique choisi comme sujet d’étude, présenté dans ses caractères généraux et spécifiques, pour modéliser la définition structurale des modèles explicatifs protagonistes au débat sur la transition entre Paléolithiques moyen et supérieur. La méthodologie proposée sera ensuite appliquée à la controverse, pour découper son déroulement chronologique en trois phases historiques distinctes par leur axe de recherche spécifique, chacune des phases étant décrite sur trois niveaux structuraux (données et méthodologie, paradigmes opératoires, paradigme métaphysique), afin d’isoler les constantes et les inflexions, et d’établir un modèle explicatif de sa dynamique historique jusqu’à son état actuel. L’ambition de cette thèse est de s’appuyer sur l’histoire des sciences pour clarifier sur le plan théorique pour les préhistoriens la dynamique historique de cette controverse centrale à l’étude du changement culturel en préhistoire, et des modèles qui s’y confrontent toujours, et tenter, à partir de l’étude de ce problème d’archéologie préhistorique, d’ébaucher en retour un modèle historique et structural d’étude de cas d’une controverse spécifique et de son apport au niveau du changement conceptuel en science qui pourrait être utile à l’histoire des sciences. / This thesis’ main object is to study on an historical level a long-lasting scientific controversy in Prehistoric archaeology, the Middle to Upper Palaeolithic transition, by attempting to explain the persistence of that debate in terms of construction and transformation of antagonistic models of explanation, and by showing how that controversy had play a role on the acquisition of knowledge, to elucidate how the debate itself had change since its origin. On a chronological scale, the evolution of some epistemological elements inside the confrontation of opposed hypothesis could be contrasted with conservative notions. To make that process clear, it is necessary to characterize what constitute that specific controversy for prehistorians with the tool given by the history of sciences, and what kind of analytical methodology can be call upon for doing so. Then, it will be possible to link those elements with the scientific problem itself to establish a structural model of this debate’s theoretical positions of the protagonists. This methodology could then be use to separate the history of that debate in three sections, each with its specific research axis, each phase in three structural level (data and methods, paradigms, meta-paradigm) to create a general model of the evolution of that controversy. The ambition of that thesis is to use history of science’s contribution as a way to clarify on a theoretical level the goals of that debate, and its implication on the study of cultural change for prehistorical archaeologists community, and to initiate for science’s historians a historical and structural model of scientific controversies, and their weight on conceptual change base on a specific case study.