The oral microbiome is a key component of the human body and has been associated with several habits and diseases. Despite its important role in health, it remains relatively understudied, compared to the gut microbiome. To deepen our understanding of the oral microbiome and its links to host conditions, the main aim of my PhD thesis was to characterize the lifestyle, environmental and genetic determinants of the salivary microbiome using data from CHRISMB, a convenience sample within the Cooperative Health Research in South Tyrol (CHRIS) study. With more than 1,900 samples, CHRISMB is one of the largest salivary microbiome data resources in the world. First, I studied the association between the salivary microbiome and smoking status and degree of exposure both from the compositional and predicted metabolism perspective. I found associations with 44 genera, 11 of which were also proportionally affected by the degree of exposure to tobacco. Intriguingly, these associations highlight a novel role of salivary microbiome metabolism in cardiovascular diseases through periodontium degeneration via the nitrate reduction and extracellular matrix degradation pathways. My second contribution focused on the role of geography, family relatedness, and genetics in shaping CHRISMB diversity. I investigated the associations between household, municipality and altitude of residence, heritability, and genetic marker associations (mbGWAS). I confirmed that cohabitation is a strong driver of microbiome similarity, while municipality and altitude of residence did not show strong associations. Siblings living apart had a more similar microbiota than unrelated and non-cohabiting individuals. Sixteen out of 142 taxa had a significant heritability component, while 34 had a significant household component. A mbGWAS Gene-level analysis resulted in one association between rare variants in the SRFBP1 and LOX genes locus and Selenomonas noxia. This work confirmed that host genetics and familial relationships has a modest but significant association with the salivary microbiome composition and that the environment and lifestyle are strongly associated. In summary, this thesis deepens our understanding of population-level factors associated with salivary microbiome variability, which can help design future hypothesis driven studies.

Since past more than hundred years, fluvial geomorphologists all across the globe have been trying to understand the basic phenomena and processes that control the behavioral patterns of streams. A large number of stream classification systems has been proposed till date, but none of them have been accepted universally. Lately, a large amount of efforts have been made to develop bankfull relations for estimating channel geometry that can be employed for stream restoration practices. Focusing on these two objectives, in this study a new stream classification system based on elevation above mean sea level has been developed and later using elevation as one of the independent and nondimensionalising parameters, universal and regional regime equations in dimensionless forms have been developed for predicting channel geometry at bankfull conditions. To accomplish the first objective, 873 field measurement values describing the hydraulic geometry and morphology of streams mainly from Canada, UK and USA were compiled and statistically analyzed. Based on similar mode values of three dimensionless channel variables (aspect ratio, sinuosity and channel slope), several fine elevations ranges were merged to produce the final five elevation ranges. These final five zones formed the basis of the new elevation based classification system and were identified with their unique modal values of dimensionless variables. Performing joint probability distributions on each of these zones, trends in the behavior of channel variables while moving from lowland to upland were observed. For the completion of second objective, 405 data points out of initial 873 points were selected and employed for the development of bankfull relations by using bankfull discharge and watershed variables as the input variables. Regression equations developed for width and depth established bankfull discharge as the only required input variable whereas all other watershed variables were proved out to be relatively insignificant. Channel slope equation did not show any dependence on bankfull discharge and was observed to be influenced only by drainage area and valley slope factors. Later when bankfull discharge was replaced by annual average rainfall as the new input variable, watershed parameters (drainage area, forest cover, urban cover etc.) became significant in bankfull width and depth regression equations. This suggested that bankfull discharge in itself encompasses the effects of all the watershed variables and associated processes and thus is sufficient for estimating channel dimensions. Indeed, bankfull discharge based regression equation demonstrated its strong dependence on watershed and rainfall variables. / Master of Science

Traumatic brain injury (TBI) is a leading cause of morbidity and mortality among young children and adults. This primary injury initiates an inflammatory response that may lead to a secondary brain injury. Nursing care in the critical care setting supports prevention or reduction of secondary injury through control of intracranial pressure (ICP), mean arterial pressure (MAP), and the subsequent cerebral perfusion pressure (CPP). While secondary injury may be preventable, some nursing interventions may contribute to increased ICP and decreased CPP. Patients with increased ICP or decreased CPP are at risk for poor clinical outcomes. This literature review examined the effort of routine nursing care interventions on outcomes of TBI patients in the critical care setting. Eleven research articles studying head of bed elevation, head and neck positioning, turning, and spacing of patient care activities were the focus of the analysis. Results typically showed positive outcomes by elevating the head of the bed to thirty degrees. CPP was also maintained at thirty degrees, but showed varied results. ICP and CPP are best controlled with the head and neck in a neutral position. Turning patients is a routine nursing intervention that contributes to increased ICP in some positions in some patients. Most studies suggest ICP is lowest in the supine position and highest in the left lateral position, but differences in findings were noted. Providing basic nursing care interventions in close succession also may contribute to increases in ICP in some patients. Results from this review provide evidence to support the importance of assessing and planning care for each TBI patient individually. It is hoped that findings from this review will provide guidance for bedside nurses to improve clinical practice and drive future research to support best practices for care of patients who suffer TBI.

Rhododendron is a monophyletic group that inhabits many different climates. One clearly defined diversification was from temperate ancestors into tropical habitats. The focus of this work was to explore leaf and stem anatomical traits in relation to habitat (temperate and tropical) and elevation of the native range. A closely-related group of Rhododendron was selected to reduce variation in genetic history and reveal environment–associated adaptive traits. Vessel anatomical traits of Rhododendron accessions were assayed for the trade of between safety (protection against catastrophic failure) and efficiency (high theoretical conductivity). Rhododendron wood and vessels were found to be relatively safe. The metrics of wood efficiency were higher for the tropical species. Thus, a trade-off between safety and efficiency was found although the wood of Rhododendron is characterized as highly safe. Leaf anatomical traits of Rhododendron were assayed for habitat and elevation. Leaves on tropical species were thicker and denser compared with temperate species. Idioblasts were always found in tropical leaves but not in temperate species. Leaves of tropical species were more xeromorphic (drought tolerant) than those of temperate species. Increasing elevation of the native range did not influence leaf anatomical traits. Idioblast abundance and leaf water relations traits were assayed for tropical Rhododendron species. Idioblast expression varied from 5% to 28% and stomatal pore index varied from 0.08 to 3.3. Idioblast expression was highly correlated with leaf succulence, and water deficit at the turgor loss point. Idioblast expression was positively associated with leaf capacitance for thin (< 0.5 mm) leaves. Thus, idioblasts can serve as a water buffer for relatively thin leaves. Synthesis–Wood traits of evergreen Rhododendron shrubs reflect adaptation for safety. Although tropical species have significantly higher efficiency, wood safety is still the dominant feature. The implication of high wood safety is constrained water flow and a potential for low water potential. Both leaf succulence and the presence of idioblasts in thin leaves enhances leaf capacitance and provides some buffering against short-term drought. These leaf adaptations in tropical Rhododendron shrubs likely reflect the abundance of epiphytes in this group. / Ph. D. / <i>Rhododendron</i> is a very diverse genus that is found in many different habitats from arctic to tropical. However, most of the species are evergreen with a slow growth rate. The goal of this study was to explore the variation in wood and leaf anatomical traits in order to explain how these plants can succeed in so many different habitats. The vessels in wood of temperate species were found to be very small. Although the size of the vessels increased for tropical species, they were still small relative to many other species. Surprisingly, leaf traits suggested greater drought tolerance for tropical species compared with temperate species. A unique anatomical trait called idioblasts was found only in leaves of tropical species. Idioblasts were very large cells, found just below the upper epidermis, which occupied up to 30% of the leaf volume. Idioblasts were found to help buffer water loss for thin tropical leaves. In summary, <i>Rhododendron</i> wood constrains water flow for plants in all habitats, which will induce water stress in warm or dry areas. Consequently, leaves have drought tolerance traits in tropical regions. Therefore, anatomical traits of wood and leaf help explain how <i>Rhododendron</i> species can occupy a wide diversity of habitats.

Sitting in a pub in Dublin, I tried to understand the architectural qualities of my so-called watering hole. The stylish wood and spatial divisions were pleasant but were not the full reasons behind why I loved being apart of the place. I started to think why architecture is not valued through our sensibilities? Or a better question, how can architecture be valued through our sensibilities? Our emotions are developed through our experiences. The movement through the pub, my actions within the space, and the senses being formed from my surroundings helped my understanding of why I enjoyed the pub. There was a function, a process, and an interpretation of senses. Our senses are developed from our immediate environments. We know ourselves in relation to other things. We know how certain things make us feel. Things have histories and we evaluate these things in relation to our own timeline. When these relationships and feelings meet we understand our surroundings through placement. Here is where we dwell in a place. Place is the building, within the building, and around the building. Place and dwelling are more cognitive than physically inhabiting within a location. Our understanding of how we love a building starts with place. How do you design a place? How do things and people belong to these places? Can a bar and brewery become one of these things on the banks of the Potomac in Old Town Alexandria? And, will it make a new and better place? Will it be loved? / Master of Architecture

This thesis analyzed the new parameter hydrodynamic demand representing the damage of tsunami waves on structures and coastlines,maximum positive amplitudes and current velocities occurred during tsunami inundation by using the numerical model TUNAMI-N2. Regular shaped basins were used with two different bottom slopes in analyses in order to understand the behaviour of tsunami wave and investigate the change of important tsunami parameters along different slopes during tsunami inundation. In application, different initial conditions were used for wave profiles such as solitary wave, leading elevation single sinusoidal wave and leading depression sinusoidal wave. Three different initial wave amplitudes were used in order to test the change of distribution of the hydrodynamic demand. The numerical results were compared and discussed with each other and with the results of existing analytical and experimental studies.

This study analyzes the parameter &ldquo / hydrodynamic demand&rdquo / that is also defined by the square of Froude Number representing the damage of tsunami waves on structures and coastlines, and other hydrodynamic parameters, i.e., the distribution of instantaneous flow depths, runup values and the direction of maximum currents, occurred during tsunami inundation by using advanced numerical modeling. The analyses are performed on regular-shaped basins with different bottom slopes and real-shaped topographies using different wave shapes, wave periods and types. Various orientation and amount of coastal and land structures are used in simulations to have results for many different cases. This study provides the opportunity to define the damage of level in residential areas and to test the performance of coastal protection structures. The behavior of tsunami hydrodynamic parameters in shallow and inundation zone is investigated and a correlation is obtained between the average maximum values of square of Froude Number with the wave characteristics and sea bottom slope. After determining hydrodynamic parameters in regular shaped basins, a case study is applied by modeling the March 11, 2011 Great East Japan Tsunami with finer resolution in nested domains. The determination of hydrodynamic parameters in inundation zone during 2011 Japan event is performed in one of the most damaged coastal city Kamaishi.

La reconstruction de bâtiments à partir de photographies aériennes et d’autres données spatiales urbaines multi-sources est une tâche qui utilise une multitude de méthodes automatisées et semi-automatisées allant des processus ponctuels au traitement classique des images et au balayage laser. Dans cette thèse, un système de relaxation itératif est développé sur la base de l'examen du contexte local de chaque bord en fonction de multiples sources d'entrée spatiales (masques optiques, d'élévation, d'ombre et de feuillage ainsi que d'autres données prétraitées, décrites au chapitre 6). Toutes ces données multisource et multirésolution sont fusionnées de manière à extraire les segments de ligne probables ou les arêtes correspondant aux limites des bâtiments. Deux nouveaux sous-systèmes ont également été développés dans cette thèse. Ils ont été conçus dans le but de fournir des informations supplémentaires, plus fiables, sur les contours des bâtiments dans une future version du système de relaxation proposé. La première est une méthode de réseau de neurones à convolution profonde (CNN) pour la détection de frontières de construction. Le réseau est notamment basé sur le modèle SRCNN (Dong C. L., 2015) de super-résolution à la pointe de la technologie. Il accepte des photographies aériennes illustrant des données de zones urbaines densément peuplées ainsi que leurs cartes d'altitude numériques (DEM) correspondantes. La formation utilise trois variantes de cet ensemble de données urbaines et vise à détecter les contours des bâtiments grâce à une nouvelle cartographie hétéroassociative super-résolue. Une autre innovation de cette approche est la conception d'une couche de perte personnalisée modifiée appelée Top-N. Dans cette variante, l'erreur quadratique moyenne (MSE) entre l'image de sortie reconstruite et l'image de vérité de sol (GT) fournie des contours de bâtiment est calculée sur les 2N pixels de l'image avec les valeurs les plus élevées. En supposant que la plupart des N pixels de contour de l’image GT figurent également dans les 2N pixels supérieurs de la reconstruction, cette modification équilibre les deux catégories de pixels et améliore le comportement de généralisation du modèle CNN. Les expériences ont montré que la fonction de coût Top-N offre des gains de performance par rapport à une MSE standard. Une amélioration supplémentaire de la capacité de généralisation du réseau est obtenue en utilisant le décrochage. Le deuxième sous-système est un réseau de convolution profonde à super-résolution, qui effectue un mappage associatif à entrée améliorée entre les images d'entrée à basse résolution et à haute résolution. Ce réseau a été formé aux données d’altitude à basse résolution et aux photographies urbaines optiques à haute résolution correspondantes. Une telle différence de résolution entre les images optiques / satellites optiques et les données d'élévation est souvent le cas dans les applications du monde réel. / Building reconstruction from aerial photographs and other multi-source urban spatial data is a task endeavored using a plethora of automated and semi-automated methods ranging from point processes, classic image processing and laser scanning. In this thesis, an iterative relaxation system is developed based on the examination of the local context of each edge according to multiple spatial input sources (optical, elevation, shadow & foliage masks as well as other pre-processed data as elaborated in Chapter 6). All these multisource and multiresolution data are fused so that probable line segments or edges are extracted that correspond to prominent building boundaries.Two novel sub-systems have also been developed in this thesis. They were designed with the purpose to provide additional, more reliable, information regarding building contours in a future version of the proposed relaxation system. The first is a deep convolutional neural network (CNN) method for the detection of building borders. In particular, the network is based on the state of the art super-resolution model SRCNN (Dong C. L., 2015). It accepts aerial photographs depicting densely populated urban area data as well as their corresponding digital elevation maps (DEM). Training is performed using three variations of this urban data set and aims at detecting building contours through a novel super-resolved heteroassociative mapping. Another innovation of this approach is the design of a modified custom loss layer named Top-N. In this variation, the mean square error (MSE) between the reconstructed output image and the provided ground truth (GT) image of building contours is computed on the 2N image pixels with highest values . Assuming that most of the N contour pixels of the GT image are also in the top 2N pixels of the re-construction, this modification balances the two pixel categories and improves the generalization behavior of the CNN model. It is shown in the experiments, that the Top-N cost function offers performance gains in comparison to standard MSE. Further improvement in generalization ability of the network is achieved by using dropout.The second sub-system is a super-resolution deep convolutional network, which performs an enhanced-input associative mapping between input low-resolution and high-resolution images. This network has been trained with low-resolution elevation data and the corresponding high-resolution optical urban photographs. Such a resolution discrepancy between optical aerial/satellite images and elevation data is often the case in real world applications. More specifically, low-resolution elevation data augmented by high-resolution optical aerial photographs are used with the aim of augmenting the resolution of the elevation data. This is a unique super-resolution problem where it was found that many of -the proposed general-image SR propositions do not perform as well. The network aptly named building super resolution CNN (BSRCNN) is trained using patches extracted from the aforementioned data. Results show that in comparison with a classic bicubic upscale of the elevation data the proposed implementation offers important improvement as attested by a modified PSNR and SSIM metric. In comparison, other proposed general-image SR methods performed poorer than a standard bicubic up-scaler.Finally, the relaxation system fuses together all these multisource data sources comprising of pre-processed optical data, elevation data, foliage masks, shadow masks and other pre-processed data in an attempt to assign confidence values to each pixel belonging to a building contour. Confidence is augmented or decremented iteratively until the MSE error fails below a specified threshold or a maximum number of iterations have been executed. The confidence matrix can then be used to extract the true building contours via thresholding.

The braided rivers and floodplains in the Upper Waitaki Basin (UWB) of the South Island of New Zealand are critical habitats for endangered and threatened fauna such as the black stilt. However, this habitat has degraded due to introduced predators, hydropower operations, and invasive weeds including Russell lupins. While conservation efforts have been made to restore these habitats, flood events may provide a natural mechanism for removal of invasive vegetation and re-creation of natural floodplain habitats. However, little is understood about the hydraulic effects of floods on vegetation and potential mortality in these dynamic systems. Therefore, this thesis analyzed the flood-induced processes that cause lupin mortality in a reach of the Ahuriri River in the UWB, and simulated various sized flood events to assess how and where these processes occurred. To determine the processes that cause lupin mortality, post-flood observations were utilized to develop the hypothesis that flood-induced drag, erosion, sediment deposition, inundation, and trauma were responsible. Field and laboratory experiments were conducted to evaluate and quantify these individual processes, and results showed that drag, erosion, sediment deposition and inundation could cause lupin mortality. Utilizing these mortality processes, mortality thresholds of velocity, water depth, inundation duration, and morphologic changes were estimated through data analysis and evaluation of various empirical relationships. Delft3D was the numerical model used to simulate 2-dimensional flood hydraulics in the study-reach and was calibrated in three stages for hydraulics, vegetation, and morphology. Hydraulic calibration was achieved using the study-reach topography captured by Structure-from-Motion (SfM) and various hydraulic data (depth, velocity, and water extent from aerial photographs). Vegetation inclusion in Delft3D was possible utilizing a function called ‘trachytopes’, which represented vegetation roughness and flow resistance and was calibrated utilizing data from a lupin-altered flow conveyance experiment. Morphologic calibration was achieved by simulating an observed near-mean annual flood event (209 m3 s-1) and adjusting the model parameters until the simulated morphologic changes best represented the observed morphologic changes captured by pre- and post-flood SfM digital elevation models. Calibration results showed that hydraulics were well represented, vegetation inclusion often improved the simulated water inundation extent accuracy at high flows, but that local erosion and sediment deposition were difficult to replicate. Simulation of morphological change was expected to be limited due to simplistic bank erosion prediction methods. Nevertheless, the model was considered adequate since simulated total bank erosion was comparable to that observed and realistic river characteristics (riffles, pools, and channel width) were produced. Flood events ranging from the 2- to 500-year flood were simulated with the calibrated model, and lupin mortality was estimated using simulation results with the lupin mortality thresholds. Results showed that various degrees of lupin mortality occurred for the different flood events, but that the dominant mortality processes fluctuated between erosion, drag, and inundation. Sediment deposition-induced mortality was minimal, but was likely under-represented in the modeling due to poor model sediment deposition replication and possibly over-restrictive deposition mortality thresholds. The research presented in this thesis provided greater understanding of how natural flood events restore and preserve the floodplain habitats of the UWB and can be used to aid current and future braided river conservation and restoration efforts.

This study demonstrates the value of historical aerial photographs as a source for monitoring long-term landslide evolution, which can be unlocked by using appropriate photogrammetric methods. The understanding of landslide mechanisms requires extensive data records; a literature review identified quantitative data on surface movements as a key element for their analysis. It is generally acknowledged that, owing to the flexibility and high degree of automation of modern digital photogrammetric techniques, it is possible to derive detailed quantitative data from aerial photographs. In spite of the relative ease of such techniques, there is only scarce research available on data quality that can be achieved using commonly available material, hence the motivation of this study. In two landslide case-studies (the Mam Tor and East Pentwyn landslides) the different types of products were explored, that can be derived from historical aerial photographs. These products comprised geomorphological maps, automatically derived elevation models (DEMs) and displacement vectors. They proved to be useful and sufficiently accurate for monitoring landslide evolution. Comparison with independent survey data showed good consistency, hence validating the techniques used. A wide range of imagery was used in terms of quality, media and format. Analysis of the combined datasets resulted in improvements to the stochastic model and establishment of a relationship between image ground resolution and data accuracy. Undetected systematic effects provided a limiting constraint to the accuracy of the derived data, but the datasets proved insufficient to quantify each factor individually. An important advancement in digital photogrammetry is image matching, which allows automation of various stages of the working chain. However, it appeared that the radiometric quality of historical images may not always assure good results, both for extracting DEMs and vectors using automatic methods. It can be concluded that the photographic archive can provide invaluable data for landslide studies, when modern photogrammetric techniques are being used. As ever, independent and appropriate checks should always be included in any photogrammetric design.