Image morphology: from perception to rendering

Complete image ontology can be obtained by formalising a top-down meta-language wich must address all possibilities, from global message and composition to objects and local surface properties.

Dinâmica espacial e temporal do ravinamento na margem esquerda da bacia do Baixo Tejo : formas, processos e factores

Tese de doutoramento, Geografia (Geografia Física), Universidade de Lisboa, Instituto de Geografia e Ordenamento do Território, 2014

Identifying the Influence of Channel Morphology on Physical Habitat Availability for Native Fish: Application to the Two-spined Blackfish (Gadopsis bispinosus) in the Cotter River, Australia.

The impact of channel morphology and flow on physical habitat availability for the two-spined blackfish (Gadopsis bispinosus) was assessed in the Cotter River, ACT, Australia. Physical habitat requirements for three life stages were identified based on previous field sampling in the Cotter River. Two sites were selected with contrasting channel morphology: Spur Hole, with a moderate gradient and runs and glides, and Vanity’s Crossing, with a steeper gradient, rapids, and fast-flowing pools. Physical Habitat Simulation System (PHABSIM) was used to simulate the flow v. physical habitat availability relationship for each life stage at both sites. Clear differences were apparent between sites, with Spur Hole characterised by increasing habitat with increasing flow and Vanity’s Crossing showing the opposite relationship. The nature of the channel morphology determined this difference, with Spur Hole characterised by marginal zones becoming inundated at higher flows and providing additional suitable physical habitat as discharge increases. Vanity’s Crossing does not contain similar marginal zones. Further analysis demonstrated that high water velocity was the most important factor limiting physical habitat availability at both sites. This approach demonstrates the importance of channel morphology in determining physical habitat availability and an alternative use of PHABSIM to highlight limiting factors for target species.

Quantifying Submerged Fluvial Topography Using Hyperspatial Resolution UAS Imagery and Structure From Motion Photogrammetry.

Quantifying the topography of rivers and their associated bedforms has been a fundamental concern of fluvial geomorphology for decades. Such data, acquired at high temporal and spatial resolutions, are increasingly in demand for process-oriented investigations of flow hydraulics, sediment dynamics and in-stream habitat. In these riverine environments, the most challenging region for topographic measurement is the wetted, submerged channel. Generally, dry bed topography and submerged bathymetry are measured using different methods and technology. This adds to the costs, logistical challenges and data processing requirements of comprehensive river surveys. However, some technologies are capable of measuring the submerged topography. Through-water photogrammetry and bathymetric LiDAR are capable of reasonably accurate measurements of channel beds in clear water. Whilst the cost of bathymetric LiDAR remains high and its resolution relatively coarse, the recent developments in photogrammetry using Structure from Motion (SfM) algorithms promise a fundamental shift in the accessibility of topographic data for a wide range of settings. Here we present results demonstrating the potential of so called SfM-photogrammetry for quantifying both exposed and submerged fluvial topography at the mesohabitat scale. We show that imagery acquired from a rotary-winged Unmanned Aerial System (UAS) can be processed in order to produce digital elevation models (DEMs) with hyperspatial resolutions (c. 0.02 m) for two different river systems over channel lengths of 50-100 m. Errors in submerged areas range from 0.016 m to 0.089 m, which can be reduced to between 0.008 m and 0.053 m with the application of a simple refraction correction. This work therefore demonstrates the potential of UAS platforms and SfM-photogrammetry as a single technique for surveying fluvial topography at the mesoscale (defined as lengths of channel from c.10 m to a few hundred metres). This article is protected by copyright. All rights reserved.

Effects of fluvial and marine processes on nearshore suspended sediment concentrations off the Elwha River

Senior thesis written for Oceanography 444

Modulation of a cytoskeletal calpain-like protein induces major transitions in trypanosome morphology

Individual eukaryotic microbes, such as the kinetoplastid parasite Trypanosoma brucei, have a defined size, shape, and form yet transition through life cycle stages, each having a distinct morphology. In questioning the structural processes involved in these transitions, we have identified a large calpain-like protein that contains numerous GM6 repeats (ClpGM6) involved in determining T. brucei cell shape, size, and form. ClpGM6 is a cytoskeletal protein located within the flagellum along the flagellar attachment zone (FAZ). Depletion of ClpGM6 in trypomastigote forms produces cells with long free flagella and a shorter FAZ, accompanied by repositioning of the basal body, the kinetoplast, Golgi, and flagellar pocket, reflecting an epimastigote-like morphology. Hence, major changes in microbial cell form can be achieved by simple modulation of one or a few proteins via coordinated association and positioning of membrane and cytoskeletal components.

Transição do enchimento terciário para o encaixe fluvial quaternário na área de Vila Velha de Ródão (sector NE da Bacia do Baixo Tejo)

The geomorphologic characteristics and lithostratigraphic units of the transition from the Tertiary filling stage to the Quaternary fluvial incision in the Vila Velha de Ródão area (Lower Tagus Basin, NE sector) are presented. Several morphodynamic episodes, which had an important tectonic control, were distinguished. The same main morphosedimentary processes can be identified in other areas of this important river basin. Five periods of Quaternary fluvial incision were characterized.

In vitro engineering of human stratified urothelium: analysis of its morphology and function.

PURPOSE: Gastric or intestinal patches, commonly used for reconstructive cystoplasty, may induce severe metabolic complications. The use of bladder tissues reconstructed in vitro could avoid these complications. We compared cellular differentiation and permeability characteristics of human native with in vitro cultured stratified urothelium. MATERIALS AND METHODS: Human stratified urothelium was induced in vitro. Morphology was studied with light and electron microscopy and expression of key cellular proteins was assessed using immunohistochemistry. Permeability coefficients were determined by measuring water, urea, ammonia and proton fluxes across the urothelium. RESULTS: As in native urothelium the stratified urothelial construct consisted of basal membrane and basal, intermediate and superficial cell layers. The apical membrane of superficial cells formed villi and glycocalices, and tight junctions and desmosomes were developed. Immunohistochemistry showed similarities and differences in the expression of cytokeratins, integrin and cellular adhesion proteins. In the cultured urothelium cytokeratin 20 and integrin subunits alpha6 and beta4 were absent, and symplekin was expressed diffusely in all layers. Uroplakins were clearly expressed in the superficial umbrella cells of the urothelial constructs, however, they were also present in intermediate and basal cells. Symplekin and uroplakins were expressed only in the superficial cells of native bladder tissue. The urothelial constructs showed excellent viability, and functionally their permeabilities for water, urea and ammonia were no different from those measured in native human urothelium. Proton permeability was even lower in the constructs compared to that of native urothelium. CONCLUSIONS: Although the in vitro cultured human stratified urothelium did not show complete terminal differentiation of its superficial cells, it retained the same barrier characteristics against the principal urine components. These results indicate that such in vitro cultured urothelium, after being grown on a compliant degradable support or in coculture with smooth muscle cells, is suitable for reconstructive cystoplasty.

The impact of cyclin D1 mRNA isoforms, morphology and p53 in mantle cell lymphoma: p53 alterations and blastoid morphology are strong predictors of a high proliferation index.

BACKGROUND: Mantle cell lymphoma is a clinically heterogeneous disease characterized by overexpression of cyclin D1 protein. Blastoid morphology, high proliferation, and secondary genetic aberrations are markers of aggressive behavior. Expression profiling of mantle cell lymphoma revealed that predominance of the 3'UTR-deficient, short cyclin D1 mRNA isoform was associated with high cyclin D1 levels, a high "proliferation signature" and poor prognosis. DESIGN AND METHODS: Sixty-two cases of mantle cell lymphoma were analyzed for cyclin D1 mRNA isoforms and total cyclin D1 levels by real-time reverse transcriptase polymerase chain reaction, and TP53 alterations were assessed by immunohistochemistry and molecular analysis. Results were correlated with proliferation index and clinical outcome. RESULTS: Predominance of the short cyclin D1 mRNA was found in 14 (23%) samples, including four with complete loss of the standard transcript. TP53 alterations were found in 15 (24%) cases. Predominance of 3'UTR-deficient mRNA was significantly associated with high cyclin D1 mRNA levels (P=0.009) and more commonly found in blastoid mantle cell lymphoma (5/11, P=0.060) and cases with a proliferation index of >20% (P=0.026). Both blastoid morphology (11/11, P<0.001) and TP53 alterations (15/15, P<0.001) were significantly correlated with a high proliferation index. A proliferation index of 10% was determined to be a significant threshold for survival in multivariate analysis (P=0.01). CONCLUSIONS: TP53 alterations are strongly associated with a high proliferation index and aggressive behavior in mantle cell lymphoma. Predominance of the 3'UTR-deficient transcript correlates with higher cyclin D1 levels and may be a secondary contributing factor to high proliferation, but failed to reach prognostic significance in this study.

Hydraulic and fluvial geomorphological models for a bedrock channel reach of the Twenty Mile Creek /

Bedrock channels have been considered challenging geomorphic settings for the application of numerical models. Bedrock fluvial systems exhibit boundaries that are typically less mobile than alluvial systems, yet they are still dynamic systems with a high degree of spatial and temporal variability. To understand the variability of fluvial systems, numerical models have been developed to quantify flow magnitudes and patterns as the driving force for geomorphic change. Two types of numerical model were assessed for their efficacy in examining the bedrock channel system consisting of a high gradient portion of the Twenty Mile Creek in the Niagara Region of Ontario, Canada. A one-dimensional (1-D) flow model that utilizes energy equations, HEC RAS, was used to determine velocity distributions through the study reach for the mean annual flood (MAF), the 100-year return flood and the 1,000-year return flood. A two-dimensional (2-D) flow model that makes use of Navier-Stokes equations, RMA2, was created with the same objectives. The 2-D modeling effort was not successful due to the spatial complexity of the system (high slope and high variance). The successful 1 -D model runs were further extended using very high resolution geospatial interpolations inherent to the HEC RAS extension, HEC geoRAS. The modeled velocity data then formed the basis for the creation of a geomorphological analysis that focused upon large particles (boulders) and the forces needed to mobilize them. Several existing boulders were examined by collecting detailed measurements to derive three-dimensional physical models for the application of fluid and solid mechanics to predict movement in the study reach. An imaginary unit cuboid (1 metre by 1 metre by 1 metre) boulder was also envisioned to determine the general propensity for the movement of such a boulder through the bedrock system. The efforts and findings of this study provide a standardized means for the assessment of large particle movement in a bedrock fluvial system. Further efforts may expand upon this standardization by modeling differing boulder configurations (platy boulders, etc.) at a high level of resolution.

Differentiation of morphology and reproductive traits in the house finch (Carpodacus mexicanus): a comparison between native and introduced populations

House Finches (CarpQdacqs mexiCAnuS) were introduced to Long Island, New York from southern'California in 1940. Apparently, an initial sample of less than 100 birds has given rise to a population that now occupies much of the eastern United States. This study was to determine if morphological and reproductive changes have taken place in introduced eastern birds, which have colonized a novel environment. A study area in Goleta, California (CAL) represented the parental population whereas for comparison, House Finches in St. Catharines, Ontario (ONT) represented the introduced population. Interlocality variation in 25 morphometric characters of 100 adult House Finches was examined statistically. Singleclassification analysis of variance revealed significant interlocality differentiation in seven characters of males and nine of females. Females showed differentiation in more limb elements than males. Analysis of character variation using discriminant and principal component analysis distinguished samples on the basis of variation in shape. Compared to CAL, aNT birds (especially females) had smaller extremities relative to certain core parts and weight. Females showed similar patterns of character covariation in each locality on the second principal component, which suggests that differentiation of the ONT population may not be solely environmentally induced. Sexual dimorphism was evident in four charaoters in aNT and five in CAL. Disoriminant analysis distinguished sex on the basis of variation in shape. Males possessed a relatively larger flying apparatus and small.er hind limbs than females. The dearee of sexual dimorphism did not vary sicnifioantly between looalities. 3 Data on reproduotive parameters were oolleoted in 1983 and 1984 in ONT, and 1984 in CAL. In 1984, Bouse Finohes began breedina approximately three months earlier in CAL than in ONT. In ONT, there was no sianifioant differenoe in mean olutoh initiation date between 1983 and 1984. In both looalities most nests oontained either four or five ea",s, and olutoh size differenoes between looalites were not signifioant. Seasonal deolines in olutch size were evident in ONT but not in CAL. Intralooality variation in e.g weight and size was not related to clutch size. E",g weiaht showed no seasonal trend in ONT, but inoreased sianifioantly with breed ina season in OAL. In both looalities e8'''' weiaht increased sipifioantly with order of layina in olutohes of four but not in clutohes of five. Eag's in ONT in 1983 and 1984 were sip.ificantly larser than in CAL in 1984. The modal inoubation period was 13 days and did not vary sip.ifioantly between localites. In both looalities nestling weiaht on the day of hatohing was oorrelated to fresh ega welaht. For muoh of the period between hatohing and 14 days post-hatoh, ONT nestlinas were signifioantly laraer than CAL nestlings in terms of weiaht. bill length, bill depth, and manus length.

Numerical modelling of the impact of climate change on the morphology of Saint-Lawrence tributaries

Cette thèse examine les impacts sur la morphologie des tributaires du fleuve Saint-Laurent des changements dans leur débit et leur niveau de base engendrés par les changements climatiques prévus pour la période 2010–2099. Les tributaires sélectionnés (rivières Batiscan, Richelieu, Saint-Maurice, Saint-François et Yamachiche) ont été choisis en raison de leurs différences de taille, de débit et de contexte morphologique. Non seulement ces tributaires subissent-ils un régime hydrologique modifié en raison des changements climatiques, mais leur niveau de base (niveau d’eau du fleuve Saint-Laurent) sera aussi affecté. Le modèle morphodynamique en une dimension (1D) SEDROUT, à l’origine développé pour des rivières graveleuses en mode d’aggradation, a été adapté pour le contexte spécifique des tributaires des basses-terres du Saint-Laurent afin de simuler des rivières sablonneuses avec un débit quotidien variable et des fluctuations du niveau d’eau à l’aval. Un module pour simuler le partage des sédiments autour d’îles a aussi été ajouté au modèle. Le modèle ainsi amélioré (SEDROUT4-M), qui a été testé à l’aide de simulations à petite échelle et avec les conditions actuelles d’écoulement et de transport de sédiments dans quatre tributaires du fleuve Saint-Laurent, peut maintenant simuler une gamme de problèmes morphodynamiques de rivières. Les changements d’élévation du lit et d’apport en sédiments au fleuve Saint-Laurent pour la période 2010–2099 ont été simulés avec SEDROUT4-M pour les rivières Batiscan, Richelieu et Saint-François pour toutes les combinaisons de sept régimes hydrologiques (conditions actuelles et celles prédites par trois modèles de climat globaux (MCG) et deux scénarios de gaz à effet de serre) et de trois scénarios de changements du niveau de base du fleuve Saint-Laurent (aucun changement, baisse graduelle, baisse abrupte). Les impacts sur l’apport de sédiments et l’élévation du lit diffèrent entre les MCG et semblent reliés au statut des cours d’eau (selon qu’ils soient en état d’aggradation, de dégradation ou d’équilibre), ce qui illustre l’importance d’examiner plusieurs rivières avec différents modèles climatiques afin d’établir des tendances dans les effets des changements climatiques. Malgré le fait que le débit journalier moyen et le débit annuel moyen demeurent près de leur valeur actuelle dans les trois scénarios de MCG, des changements importants dans les taux de transport de sédiments simulés pour chaque tributaire sont observés. Ceci est dû à l’impact important de fortes crues plus fréquentes dans un climat futur de même qu’à l’arrivée plus hâtive de la crue printanière, ce qui résulte en une variabilité accrue dans les taux de transport en charge de fond. Certaines complications avec l’approche de modélisation en 1D pour représenter la géométrie complexe des rivières Saint-Maurice et Saint-François suggèrent qu’une approche bi-dimensionnelle (2D) devrait être sérieusement considérée afin de simuler de façon plus exacte la répartition des débits aux bifurcations autour des îles. La rivière Saint-François est utilisée comme étude de cas pour le modèle 2D H2D2, qui performe bien d’un point de vue hydraulique, mais qui requiert des ajustements pour être en mesure de pleinement simuler les ajustements morphologiques des cours d’eau.