Community-acquired Clostridium difficile infections have recently been increasing in incidence and severity. Several studies have isolated C. difficile spores from livestock and retail meats, suggesting that food may play a role in transmission. No research has been done, however, on what food conditions might allow for the survival and/or growth of the bacterium. We therefore modelled the minimum thresholds for C. difficile growth under low pH, water activity (aw), and temperature. We also sampled retail ground meats, cheese, and milk for the presence of C. difficile spores and subtyped food isolates for comparison with clinical strains. We found that C. difficile growth could be prevented by refrigeration temperatures. C. difficile spores were also detected for the first time in Canada in ground lamb, ground turkey, ground chicken, cheese and milk. The majority of these food isolates were genetically similar to epidemic strain NAP7/078, suggesting that food may not be a direct vector for C. difficile transmission, but could still be clinically relevant.

To develop or engineer artificial tissues in tissue engineering, a detailed knowledge of the in vitro culture process including cell and tissue growth inside porous scaffolds, nutrient transport, and the shear stress acting on the cells is of great advantage. It has been shown that obtaining such information by means of experimental techniques is exceedingly difficult and in some ways impossible. Mathematical modelling and computational simulation based on computational fluid dynamics (CFD) has emerged recently to be a promising tool to characterize the culture process. However, due to the complicated structure of porous scaffolds, modelling and simulation of the in vitro cell culture process has been shown to be a challenging task. Furthermore, due to the cell growth during the culture process, the geometry of the scaffold structure is not constant, but changes with time, which makes the task even more challenging. To overcome these challenges, the research presented in this thesis is aimed at developing a CFD-based mathematical model and multi-time scale computational framework for culturing cell-scaffold constructs placed in perfusion bioreactors. To predict the three-dimensional (3D) cell growth in a porous tissue scaffold placed inside a perfusion bioreactor, a model is developed based on the continuity and momentum equations, a convection-diffusion equation and a suitable cell growth equation, which characterize the fluid flow, nutrient transport and cell growth, respectively. To solve these equations in a coupled fashion, an in-house FORTRAN code is developed based on the multiple relaxation time lattice Boltzmann method (MRT LBM), where the D3Q19 MRT LBM and D3Q7 MRT LBM models have been used for the fluid flow and mass transfer simulation, respectively. In the model cell growth equation, the transport of nutrients, i.e. oxygen and glucose, as well as the shear stress induced on the cells are considered for predicting the cell growth rate. In the developed model and computational framework, the influence of the dynamic strand surface on the local flow and nutrient concentration has been addressed by using a two-way coupling between the cell growth and local flow field and nutrient concentration, where a control-volume method within the LBM framework is applied. The simulation results provide quantification of the biomechanical environment, i.e. fluid velocity, shear stress and nutrient concentration inside the bioreactor. The final simulation applied the cell growth model to the culture of a three-zone tissue scaffold where the scaffold strands were initially seeded with cells. The prediction for the 3D cell growth rate indicates that the increase in the cell volume fraction is much higher in the front region of the scaffold due to the higher nutrient supply. The higher cell growth in the front zone reduces the permeability of the porous scaffold and significantly reduces the nutrient supply to the middle and rear regions of the scaffold, which in turn limit the cell growth in those regions. However, implementation of a bi-directional perfusion approach, which reverses the flow direction for second half of the culture period, is shown to significantly improve the nutrient transport inside the scaffold and increase the cell growth in the rear zone of the scaffold. The results in this study also demonstrate that the developed mathematical model and computational framework are capable of realistically simulating the 3D cell growth over extended culture periods. As such, they represent a promising tool for enhancing the growth of tissues in perfusion bioreactors.

In order to understand how bunchgrasses achieve dominance over other plant growth forms and how they achieve dominance over one another in different environments, it is first necessary to develop a detailed understanding of how their growth strategy interacts with the resource limits of their environment. Two properties which have been studied separately in limited detail are architecture and disproportionate resource allocation. Architecture is the structural layout of organs and objects at different hierarchical levels. Disproportionate resource allocation is the manner in which resources are allocated across objects at each level of hierarchy. Clonal architecture and disproportionate resource allocation may interact significantly to determine the growth ability of clonal plants. These interactions have not been researched in bunchgrasses. This thesis employs a novel simulation technique, functional-structural plant modelling, to investigate how bunchgrasses interact with the resource constraints imposed in humid grasslands. An appropriate functional-structural plant model, the TILLERTREE model, is developed that integrates the architectural growth of bunchgrasses with environmental resource capture and disproportionate resource allocation. Simulations are conducted using a chosen model species Themeda triandra, and the environment is parameterised using characteristics of the Southern Tall Grassveld, a humid grassland type found in South Africa. Behaviour is considered at two levels, namely growth of single ramets and growth of multiple ramets on single bunchgrass clones. In environments with distinct growing and non-growing seasons, bunchgrasses are subjected to severe light depletion during regrowth at the start of each growing season because of the accumulation of dead material in canopy caused by the upright, densely packed manner in which they grow. Simulations conducted here indicate that bunchgrass tillers overcome this resource bottleneck through structural adaptations (etiolation, nonlinear blade mass accretion, residual live photosynthetic surface) and disproportionate resource allocation between roots and shoots of individual ramets that together increase the temporal resource efficiency of ramets by directing more resources to shoot growth and promoting extension of new leaves through the overlying dead canopy. The architectural arrangement of bunchgrasses as collections of tillers and ramets directly leads to consideration of a critical property of clonal bunchgrasses: tiller recruitment. Tiller recruitment is a fundamental discrete process limiting the vegetative growth of bunchgrass clones. Tiller recruitment occurs when lateral buds on parent tillers are activated to grow. The mechanism that controls bud outgrowth has not been elucidated. Based on a literature review, it is here proposed that lateral bud outgrowth requires suitable signals for both carbohydrate and nitrogen sufficiency. Subsequent simulations with the model provide corroborative evidence, in that greatest clonal productivity is achieved when both signals are present. Resource allocation between live structures on clones may be distributed proportionately in response to sink demand or disproportionately in response to relative photosynthetic productivity. Model simulations indicate that there is a trade-off between total clonal growth and individual tiller growth as the level of disproportionate allocation between ramets on ramet groups and between tillers on ramets increases, because disproportionate allocation reduces tiller population size and clonal biomass, but increases individual tiller performance. Consequently it is proposed that different life strategies employed by bunchgrasses, especially annual versus perennial life strategies, may follow more proportionate and less proportionate allocation strategies respectively, because the former favours maximal resource capture and seed production while the latter favours individual competitive ability. Structural disintegration of clones into smaller physiologically integrated units (here termed ramet groups) that compete with one another for resources is a documented property of bunchgrasses. Model simulations in which complete clonal integration is enforced are unable to survive for long periods because resource bottlenecks compromise all structures equally, preventing them from effectively overcoming resource deficits during periods when light is restrictive to growth. Productivity during the period of survival is also reduced on bunchgrass clones with full integration relative to clones that disintegrate because of the inefficient allocation of resources that arises from clonal integration. This evidence indicates that clonal disintegration allows bunchgrass clones both to increase growth efficiency and pre-empt potential death, by promoting the survival of larger ramet groups and removing smaller ramet groups from the system. The discrete nature of growth in bunchgrasses and the complex population dynamics that arise from the architectural growth and the temporal resource dynamics of the environment, may explain why different bunchgrass species dominate under different environments. In the final section this idea is explored by manipulating two species tiller traits that have been shown to be associated with species distributions across non-selective in defoliation regimes, namely leaf organ growth rate and tiller size (mass or height). Simulations with these properties indicate that organ growth rate affects daily nutrient demands and therefore the rate at which tillers are terminated, but had only a small effect on seasonal resource capture. Tiller mass size affects the size of the live tiller population where smaller tiller clones maintain greater numbers of live tillers, which allows them to them to sustain greater biomass over winter and therefore to store more reserves for spring regrowth, suggesting that size may affect seasonal nitrogen capture. The greatest differences in clonal behaviour are caused by tiller height, where clones with shorter tillers accumulate substantially more resources than clones with taller tillers. This provides strong evidence there is trade-off for bunchgrasses between the ability to compete for light and the ability to compete for nitrogen, which arises from their growth architecture. Using this evidence it is proposed that bunchgrass species will be distributed across environments in response to the nitrogen productivity. Shorter species will dominate at low nitrogen productivity, while taller species dominate at high nitrogen productivity. Empirical evidence is provided in support of this proposal. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2005.

Community-acquired Clostridium difficile infections have recently been increasing in incidence and severity. Several studies have isolated C. difficile spores from livestock and retail meats, suggesting that food may play a role in transmission. No research has been done, however, on what food conditions might allow for the survival and/or growth of the bacterium. We therefore modelled the minimum thresholds for C. difficile growth under low pH, water activity (aw), and temperature. We also sampled retail ground meats, cheese, and milk for the presence of C. difficile spores and subtyped food isolates for comparison with clinical strains. We found that C. difficile growth could be prevented by refrigeration temperatures. C. difficile spores were also detected for the first time in Canada in ground lamb, ground turkey, ground chicken, cheese and milk. The majority of these food isolates were genetically similar to epidemic strain NAP7/078, suggesting that food may not be a direct vector for C. difficile transmission, but could still be clinically relevant.

Community-acquired Clostridium difficile infections have recently been increasing in incidence and severity. Several studies have isolated C. difficile spores from livestock and retail meats, suggesting that food may play a role in transmission. No research has been done, however, on what food conditions might allow for the survival and/or growth of the bacterium. We therefore modelled the minimum thresholds for C. difficile growth under low pH, water activity (aw), and temperature. We also sampled retail ground meats, cheese, and milk for the presence of C. difficile spores and subtyped food isolates for comparison with clinical strains. We found that C. difficile growth could be prevented by refrigeration temperatures. C. difficile spores were also detected for the first time in Canada in ground lamb, ground turkey, ground chicken, cheese and milk. The majority of these food isolates were genetically similar to epidemic strain NAP7/078, suggesting that food may not be a direct vector for C. difficile transmission, but could still be clinically relevant.

The Mississippi Institute for Forest Inventory (MIFI) multi-product forest inventory divides Mississippi into five inventory regions with one region inventoried each year on a rotating basis. Resource analyses that overlap these temporally separated regions require adjustment to a common comparative time base by applying appropriate forest stand growth and harvest allocation models to the portions of a selected area not inventoried at the desired common time base. Currently the Mississippi Dynamic Inventory Reporter (MDIR) does not make adjustments to temporally synchronize portions of user selected working circles, polygons, or counties that occur in separate inventory regions. Separate inventory reports for each overlap area must be prepared to which growth and harvest are manually allocated to bring each area to the same point in time. The study objective was to provide an automated solution to temporal reconciliation by developing a growth and yield system that reconciles modeled timber volume growth, mortality, and harvests with known values from previous successive inventories and state tax records of harvested volumes at the county level. The modeling effort focused on constructing an optimized system for the Southwest MIFI 2004 and 2012 inventories. Species group specific, distance independent, tree-list models, including probability of survival and diameter growth equations, were developed through logistic and linear regressions, respectively. Probability of survival models were assessed for model performance using logistic regression concordant/discordant pairs. R2 and parameter p-values were used to evaluate diameter growth model performance. As the 2004 and 2012 datasets are each composed of randomly selected plots within the Southwest region, county totals were used for temporal comparison. County level Doyle volume calibration was within 150 units of tolerance for all counties in the Southwest region. The resulting growth and yield system represents a successful effort to develop a methodology for bridging temporally separated MIFI inventory analyses, while providing newly developed diameter and mortality equations for the state. The accompanying computer application allows the addition of both enhanced growth and yield and stand table projection models. System implementation will greatly reduce the time required for producing multi-temporal analyses and, thus, increase their usability and functionality.

Despite the phenomena of fracture and fatigue having been the focus of academic research for more than 150 years, it remains in effect an empirical science lacking a complete and comprehensive set of predictive solutions. In this regard, the focus of the research in this thesis is on the development of new cohesive-zone models for fracture and fatigue that are afforded an ability to capture strain-rate effects. For the case of monotonic fracture in ductile material, different combinations of material response are examined with rate effects appearing either in the bulk material or localised to the cohesive-zone or in both. The development of a new rate-dependent CZM required first an analysis of two existing methods for incorporating rate dependency, i.e.either via a temporal critical stress or a temporal critical separation. The analysis revealed unrealistic crack behaviour at high loading rates. The new rate-dependent cohesive model introduced in the thesis couples the temporal responses of critical stress and critical separation and is shown to provide a stable and realistic solution to dynamic fracture. For the case of fatigue, a new frequency-dependent cohesive-zone model (FDCZM) has been developed for the simulation of both high and low-cycle fatigue-crack growth in elasto-plastic material. The developed model provides an alternative approach that delivers the accuracy of the loading-unloading hysteresis damage model along with the computational efficiency of the equally well-established envelope load-damage model by incorporating a fast-track feature. With the fast-track procedure, a particular damage state for one loading cycle is 'frozen in' over a predefined number of cycles. Stress and strain states are subsequently updated followed by an update on the damage state in the representative loading cycle which again is 'frozen in' and applied over the same number of cycles. The process is repeated up to failure. The technique is shown to be highly efficient in terms of time and cost and is particularly effective when a large number of frozen cycles can be applied without significant loss of accuracy. To demonstrate the practical worth of the approach, the effect that the frequency has on fatigue crack growth in austenitic stainless-steel 304 is analysed. It is found that the crack growth rate (da/dN) decreases with increasing frequency up to a frequency of 5 Hz after which it levels off. The behaviour, which can be linked to martensitic phase transformation, is shown to be accurately captured by the new FDCZM.

Dans le cadre de cette thèse, nous présentons un aperçu général des surfaces du silicium micro et nano structurées, appelées silicium noir (BSi), et obtenues par la gravure ionique réactive cryogénique (cryo-DRIE). Ces surfaces auto-générées peuvent être fabriquées dans un procédé en une seule étape fournissant de grandes surfaces à faible réflectivité sur une large gamme de longueurs d'onde et d'angles d'incidence. Nous examinons plusieurs aspects des surfaces du BSi, incluant les méthodes de fabrication, les applications, les méthodes de caractérisation de sa topographie, les techniques de modélisation pour les simulations optiques, et les mécanismes de croissance. Nous développons ensuite trois principales contributions que cette thèse apporte à l'état de l'art : une meilleure compréhension de la topographie du BSi, la modélisation de son comportement optique et un aperçu de ses mécanismes de formation. Nous développons une nouvelle technique de caractérisation topographique du BSi, utilisant un faisceau ionique localisé dans le plan de l'échantillon pour réaliser une nanotomographie qui reproduit les détails de structure avec une précision inférieure au micron. Nous présentons ensuite différentes méthodes de modélisation de cellules unitaires du BSi basées soit sur la topographie de la surface réelle obtenue, ou sur des formes géométriques équivalentes qui sont statistiquement représentatives de la topographie du BSi. Nous sommes capables d'obtenir une excellente concordance entre les simulations et les données expérimentales. Nous présentons également un modèle capable de simuler toute l'évolution de la surface du BSi allant d'un substrat plat jusqu'à sa topographie entièrement développée, en concordance avec des données obtenues expérimentalement. On produit un diagramme de phase qui saisit les combinaisons de paramètres responsables de la formation du BSi. Nous sommes en mesure de reproduire dans notre modèle, un certain nombre d'effets subtils qui mènent à la densification du motif observé, responsable de la formation du BSi pendant cryo-DRIE / In this thesis, we present a general overview of silicon micro and nanostructured surfaces, known as black silicon (BSi), fabricated with cryogenic deep reactive ion etching (cryo-DRIE). These self-generated surfaces can be fabricated in a single step procedure and provide large surfaces with reduced reflectance over a broad range of wavelengths and angles of incidence. We review several aspects of BSi surfaces, such as its fabrication methods, applications, topography characterization methods, modelling techniques for optical simulations, and growth mechanisms. We then develop three main contributions that this thesis brings to the state of the art: a better understanding of BSi topography, modelling of its optical behaviour and insights into its formation mechanism. We develop a novel BSi topographical characterisation technique which is based on in-plane focused ion beam nanotomography and can reproduce sample details with submicron accuracy. We then present different methods of modelling BSi unit cells, based either on real surface topography obtained using the aforementioned technique, or on equivalent geometric shapes that are statistically representative for BSi topography. We are capable to obtain excellent matching between simulations and experimental data. Finally, we present an experimentally-backed phenomenological model that is capable of simulating the entire evolution of a surface from a planar substrate to fully developed BSi topography. We produce a phase diagram which captures the parameter combinations responsible for BSi formation. We also observe experimentally, and are able to reproduce within our model, a number of subtle effects that lead to the observed pattern densification that is responsible for BSi formation during cryo-DRIE

No description available.

Cette étude propose d’analyser l’influence de l’architecture du palmier à huile sur sa capacité à intercepter la lumière, en se basant sur des reconstructions 3D de palmiers et en établissant un bilan radiatif sur ses structures végétales reconstruites in silico. Le premier objectif de l’étude était de caractériser et modéliser la variabilité génétique de l’architecture du palmier à huile et de son interception lumineuse. Dans un deuxième objectif l’amélioration potentielle de l’interception de la lumière et de l’assimilation carbonée a été évaluée en modifiant les traits morphologiques et géométriques des feuilles et des idéotypes architecturaux de palmiers à huile ont été proposés.Des relations allométriques ont été utilisées pour modéliser les traits architecturaux en fonction de gradients ontogénétique et de topologie des feuilles dans la couronne. La méthode permet de reconstruire des palmiers à huile virtuels à différents âges au cours du développement. De plus, l’approche allométrique a été couplée à des modèles à effets mixtes pour intégrer au travers de paramètres la variabilité entre et au sein des cinq progénies. Le modèle permet ainsi de simuler les spécificités architecturales des cinq progenies en incluant les variabilités entre individus observés. Le modèle architectural, paramétré pour les différentes progénies, a ensuite été implémenté dans AMAPstudio pour générer des maquettes 3D de palmiers et ainsi estimer leur interception lumineuse, de l’individu à la parcelle entière.Les résultats de ces analyses ont révélé des différences significatives entre et au sein des progenies, dans la géométrie des feuilles (longueur du pétiole, densité de folioles sur le rachis, et courbure du rachis) et dans la morphologie des folioles (gradients de longueurs et largeurs le long du rachis). La comparaison virtuelle des différentes progénies ont aussi montré des efficacités distinctes de l’interception lumineuse.Des analyses de sensibilité ont ensuite été réalisées pour identifier les traits architecturaux influençant l’interception lumineuse et l’assimilation potentielle à différents âges de la plante. Les paramètres les plus sensibles au cours du développement furent ceux reliés à la surface totale foliaire (longueur des rachis, nombre de folioles, morphologie des folioles), mais les attributs géométriques plus fins de la feuille ont montré un effet croissant avec la fermeture de la canopée. Sur un couvert adulte, l’optimum en assimilation carbonée est atteint pour des indices de surfaces foliaires (LAI) entre 3,2 et 5,5 m2.m−2, avec des feuilles érigées, de courts pétioles et rachis et un nombre important de folioles sur le rachis. Quatre idéotypes architecturaux pour l’assimilation carbonée ont été proposés et présentent des combinaisons spécifiques de traits géométriques, limitant l’ombrage mutuel des plantes et optimisant la distribution de la lumière dans la couronne.En conclusion, le modèle 3D de palmiers à huile, dans sa conception et son application, a permis de détecter les traits architecturaux génétiquement déterminés et influençant l’interception lumineuse. Ainsi, le nombre limité de traits dégagés par l’analyse de sensibilité ainsi que les combinaisons de traits révélées au travers des idéotypes pourraient être pris en compte dans de futurs programmes de sélection. En perspective, des travaux dédiés à intégrer dans ce modèle d’autres processus physiologiques, tels que la régulation de la conductance stomatique et le partitionnement du carbone dans la plante, sont à envisager. Ce nouvel FSPM pourrait alors être utilisé pour tester différents scénarii, comme par exemple dans un contexte de changement climatique avec de faibles radiations et des périodes de sécheresse fréquentes. De même, ce modèle pourrait être utilisé pour étudier différentes configurations de plantation et des systèmes de cultures intercalaires, et ainsi proposer de nouveaux idéotypes multicritères / In this study we proposed to investigate the influence of oil palm architecture on the capacity of the plant to intercept light, by using 3D reconstructions and model-assisted evaluation of radiation-use efficiency. The first objective of this study was to analyse and model oil palm architecture and light interception taking into account genetic variability. A second objective was to explore the potential improvements in light capture and carbon assimilation by manipulating oil palm leaf traits and propose architectural ideotypes.Allometric relationships were applied to model these traits according to ontogenetic gradients and leaf position within the crown. The methodology allowed reconstructing virtual oil palms at different stages over plant development. Additionally, the allometric-based approach was coupled to mixed-effect models in order to integrate inter and intra progeny variability through progeny-specific parameters. The model thus allowed simulating the specificity of plant architecture for a given progeny while including observed inter-individual variability. The architectural model, parameterized for the different progenies, was then implemented in AMAPstudio to generate 3D mock-ups and estimate light interception efficiency, from individual to stand scales.Significant differences in leaf geometry (petiole length, density of leaflets and rachis curvature) and leaflets morphology (gradients of leaflets length and width) were detected between and within progenies, and were accurately simulated by the modelling approach. Besides, light interception estimated from the validated 3D mock-ups showed significant variations among the five progenies.Sensitivity analyses were then performed on a subset of architectural parameters to identify the architectural traits impacting on light interception efficiency and potential carbon assimilation over plant development. The most sensitive parameters over plant development were those related to leaf area (rachis length, number of leaflets, leaflets morphology), but fine attribute related to leaf geometry showed increasing influence when canopy got closed. In adult stand, optimized carbon assimilation was estimated on plants presenting a leaf area index (LAI) between 3.2 and 5.5 m2.m−2, with erected leaves, short rachis and petiole and high number of leaflet on rachis. Four architectural ideotypes for carbon assimilation were proposed based on specific combinations of organs geometry, limiting mutual shading and optimizing light distribution within plant crown.In conclusion, this study highlighted how a functional-structural plant model (FSPM) can be used to virtually explore plant biology. In our case of study, the 3D model of oil palm, in its conception and its application, permitted to detect the architectural traits genetically determined and influencing light interception. The limited number of traits revealed in the sensitivity analysis and the combination of traits proposed through ideotypes could guide further breeding programs. Forthcoming work will be dedicated to integrate in the modeling approach other physiological processes such as stomatal conductance and carbon partitioning. The improved FSPM could then be used to test different scenarios, for instance in climate change context with low radiations or frequent drought events. Similarly, the model could be used to investigate different planting patterns and intercropping systems, and proposed new multi-criteria ideotypes of oil palm.