Clustering algorithms and shape factor methods to discriminate among small GTPase phenotypes using DIC image analysis.

Naïvement perçu, le processus d’évolution est une succession d’événements de duplication et de mutations graduelles dans le génome qui mènent à des changements dans les fonctions et les interactions du protéome. La famille des hydrolases de guanosine triphosphate (GTPases) similaire à Ras constitue un bon modèle de travail afin de comprendre ce phénomène fondamental, car cette famille de protéines contient un nombre limité d’éléments qui diffèrent en fonctionnalité et en interactions. Globalement, nous désirons comprendre comment les mutations singulières au niveau des GTPases affectent la morphologie des cellules ainsi que leur degré d’impact sur les populations asynchrones. Mon travail de maîtrise vise à classifier de manière significative différents phénotypes de la levure Saccaromyces cerevisiae via l’analyse de plusieurs critères morphologiques de souches exprimant des GTPases mutées et natives. Notre approche à base de microscopie et d’analyses bioinformatique des images DIC (microscopie d’interférence différentielle de contraste) permet de distinguer les phénotypes propres aux cellules natives et aux mutants. L’emploi de cette méthode a permis une détection automatisée et une caractérisation des phénotypes mutants associés à la sur-expression de GTPases constitutivement actives. Les mutants de GTPases constitutivement actifs Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V ont été analysés avec succès. En effet, l’implémentation de différents algorithmes de partitionnement, permet d’analyser des données qui combinent les mesures morphologiques de population native et mutantes. Nos résultats démontrent que l’algorithme Fuzzy C-Means performe un partitionnement efficace des cellules natives ou mutantes, où les différents types de cellules sont classifiés en fonction de plusieurs facteurs de formes cellulaires obtenus à partir des images DIC. Cette analyse démontre que les mutations Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V induisent respectivement des phénotypes amorphe, allongé, rond et large qui sont représentés par des vecteurs de facteurs de forme distincts. Ces distinctions sont observées avec différentes proportions (morphologie mutante / morphologie native) dans les populations de mutants. Le développement de nouvelles méthodes automatisées d’analyse morphologique des cellules natives et mutantes s’avère extrêmement utile pour l’étude de la famille des GTPases ainsi que des résidus spécifiques qui dictent leurs fonctions et réseau d’interaction. Nous pouvons maintenant envisager de produire des mutants de GTPases qui inversent leur fonction en ciblant des résidus divergents. La substitution fonctionnelle est ensuite détectée au niveau morphologique grâce à notre nouvelle stratégie quantitative. Ce type d’analyse peut également être transposé à d’autres familles de protéines et contribuer de manière significative au domaine de la biologie évolutive.

A method for the digital image analysis of ceramic grains based on shape factor segmentation

A very simple and robust method for ceramics grains quantitative image analysis is presented. Based on the use of optimal imaging conditions for reflective light microscopy of bulk samples, a digital image processing routine was developed for shading correction, noise suppressing and contours enhancement. Image analysis was done for grains selected according to their concavities, evaluated by perimeter ratio shape factor, to avoid consider the effects of breakouts and ghost boundaries due to ceramographic preparation limitations. As an example, the method was applied for two ceramics, to compare grain size and morphology distributions. In this case, most of artefacts introduced by ceramographic preparation could be discarded due to the use of perimeter ratio exclusion range.

Measuring the effective focal length and shape factor of a thick lens using a microscope

The optical power of a thick spherical lens and its Coddington shape factor are essential magnitudes that characterize its image quality. Here, we propose an experimental procedure and apparatus that allow accurate determination of those magnitudes for any spherical lens from geometrical measurements. The performance of the technique and the used instruments are simple since it only requires a microscope and an optical mouse. The propose overcomes the drawbacks of other devices that need of the refractive index or may damage the lens surfaces, like spherometers, and provides similar results to those from commercial lensmeters.

What is the shape of an air bubble on a liquid surface?

We have calculated the equilibrium shape of the axially symmetric meniscus along which a spherical bubble contacts a flat liquid surface by analytically integrating the Young-Laplace equation in the presence of gravity, in the limit of large Bond numbers. This method has the advantage that it provides semianalytical expressions for key geometrical properties of the bubble in terms of the Bond number. Results are in good overall agreement with experimental data and are consistent with fully numerical (Surface Evolver) calculations. In particular, we are able to describe how the bubble shape changes from hemispherical, with a flat, shallow bottom, to lenticular, with a deeper, curved bottom, as the Bond number is decreased.

What is the shape of an air bubble on a liquid surface?

We have calculated the equilibrium shape of the axially symmetric meniscus along which a spherical bubble contacts a flat liquid surface, by analytically integrating the Young-Laplace equation in the presence of gravity, in the limit of large Bond numbers. This method has the advantage that it provides semi-analytical expressions for key geometrical properties of the bubble in terms of the Bond number. Results are in good overall agreement with experimental data and are consistent with fully numerical (Surface Evolver) calculations. In particular, we are able to describe how the bubble shape changes from hemispherical, with a shallow flat bottom, to lenticular, with a deeper, curved bottom, as the Bond number is decreased.

Characterisation of polyethylene powders for rotational moulding and effect of powder size and shape on densification behaviour

The particle size, shape and distribution of a range of rotational moulding polyethylenes (PEs) ground to powder was investigated using a novel visual data acquisition and analysis system (TP Picture®), developed by Total Petrochemicals. Differences in the individual particle shape factors of the powder samples were observed and correlations with the grinding conditions were determined. When heated, the bubble dissolution behaviour of the same powders was investigated and the shape factor correlated with densification rate, bubble size and bubble distribution.

An automatic methodology for obtaining optimum shape factors for the radial point interpolation method

In this letter, a methodology is proposed for automatically (and locally) obtaining the shape factor c for the Gaussian basis functions, for each support domain, in order to increase numerical precision and mainly to avoid matrix inversion impossibilities. The concept of calibration function is introduced, which is used for obtaining c. The methodology developed was applied for a 2-D numerical experiment, which results are compared to analytical solution. This comparison revels that the results associated to the developed methodology are very close to the analytical solution for the entire bandwidth of the excitation pulse. The proposed methodology is called in this work Local Shape Factor Calibration Method (LSFCM).

Comparative analysis of the relationship between anterior and posterior corneal shape analyzed by Scheimpflug photography in normal and keratoconus eyes

Background To analyze and compare the relationship between anterior and posterior corneal shape evaluated by a tomographic system combining the Scheimpflug photography and Placido-disc in keratoconus and normal healthy eyes, as well as to evaluate its potential diagnostic value. Methods Comparative case series including a sample of 161 eyes of 161 subjects with ages ranging from 7 to 66 years and divided into two groups: normal group including 100 healthy eyes of 100 subjects, and keratoconus group including 61 keratoconus eyes of 61 patients. All eyes received a comprehensive ophthalmologic examination including an anterior segment analysis with the Sirius system (CSO). Antero-posterior ratios for corneal curvature (k ratio) and shape factor (p ratio) were calculated. Logistic regression analysis was used to evaluate if some antero–posterior ratios combined with other clinical parameters were predictors of the presence of keratoconus. Results No statistically significant differences between groups were found in the antero–posterior k ratios for 3-, 5- and 7-mm diameter corneal areas (p ≥ 0.09). The antero–posterior p ratio for 4.5- and 8-mm diameter corneal areas was significantly higher in the normal group than in the keratoconus group (p < 0.01). The k ratio for 3, 5, and 7 mm was significantly higher in the keratoconus grade IV subgroup than in the normal group (p < 0.01). Furthermore, significant differences were found in the p ratio between the normal group and the keratoconus grade II subgroup (p ≤ 0.01). Finally, the logistic regression analysis identified as significant independent predictors of the presence of keratoconus (p < 0.01) the 8-mm anterior shape factor, the anterior chamber depth, and the minimal corneal thickness. Conclusions The antero-posterior k and p ratios are parameters with poor prediction ability for keratoconus, in spite of the trend to the presence of more prolate posterior corneal surfaces compared to the anterior in keratoconus eyes.

Correlation of Anterior and Posterior Corneal Shape in Keratoconus

Purpose: To evaluate the correlation of the mean curvature and shape factors of both corneal surfaces for different corneal diameters measured with the Scheimpflug photography–based system in keratoconus eyes. Methods: A total of 61 keratoconus eyes of 61 subjects, aged 14 to 64 years, were included in this study. All eyes received a comprehensive ophthalmologic examination including anterior segment and corneal analysis with the Sirius system (CSO): anterior and posterior mean corneal radius for 3, 5, and 7 mm (aKM, pKM), anterior and posterior mean shape factor for 4.5 and 8 mm (ap, pp), central and minimal corneal thickness, and anterior chamber depth. Results: Mean aKM/pKM ratio around 1.20 (range, 0.95–1.48) was found for all corneal diameters (P = 0.24). Weak but significant correlations of this ratio with pachymetric parameters were found (r between −0.28 and −0.34, P < 0.04). The correlation coefficient between aKM and pKM was ≥0.92 for all corneal diameters. A strong and significant correlation was also found between ap and pp (r ≥ 0.86, P < 0.01). The multiple regression analysis revealed that central pKM was significantly correlated with aKM, central corneal thickness, anterior chamber depth, and spherical equivalent (R2 ≥ 0.88, P < 0.01) and that 8 mm pp was significantly correlated with 8 mm ap and age (R2 = 0.89, P < 0.01). Conclusions: Central posterior corneal curvature and shape factor in the keratoconus eye can be consistently predicted from the anterior corneal curvature and shape factor, respectively, in combination with other anatomical and ocular parameters.

Solids mixing and segregation in a gas spout-fluid bed-effect of the distributor design

This work is concerned with the assessment of a newer version of the spout-fluid bed where the gas is supplied from a common plenum and the distributor controls the operational phenomenon. Thus the main body of the work deals with the effect of the distributor design on the mixing and segregation of solids in a spout-filled bed. The effect of distributor design in the conventional fluidised bed and of variation of the gas inlet diameter in a spouted bed were also briefly investigated for purpose of comparison. Large particles were selected for study because they are becoming increasingly important in industrial fluidised beds but have not been thoroughly investigated. The mean particle diameters of the fraction ranged from 550 to 2400 mm, and their specific gravity from 0.97 to 2.45. Only work carried out with binary systems is reported here. The effect of air velocity, particle properties, bed height, the relative amount of jetsam and flotsam and initial conditions on the steady-state concentration profiles were assessed with selected distributors. The work is divided into three sections. Sections I and II deal with the fluidised bed and spouted bed systems. Section III covers the development of the spout-filled bed and its behaviour with reference to distributor design and it is shown how benefits of both spouting and fluidising phenomena can be exploited. In the fluidisation zone, better mixing is achieved by distributors which produce a large initial bubble diameter. Some common features exist between the behaviour of unidensity jetsam-rich systems and different density flotsam-rich systems. The shape factor does not seem to have an affect as long as it is only restricted to the minor component. However, in the case of the major component, particle shape significantly affects the final results. Studies of aspect ratio showed that there is a maximum (1.5) above which slugging occurs and the effect of the distributor design is nullified. A mixing number was developed for unidensity spherical rich systems, which proved to be extremely useful in quantifying the variation in mixing and segregation with changes in distributor design.

Thixocasting of an A356 alloy: Fluidity, porosity distribution and thermomechanical fatigue behavior

An extensive set of experiments was performed on a semi-solid A356 alloy in order to assess its flow behavior, mechanical properties, microstructural evolution and porosity level. Three different microstructural conditioning techniques (raw material preparation) were employed: deformation recrystallization, magnetohydrodynamic stirring and low temperature pouring. Measurement of microstructural parameters such as Al-alpha particle size, shape factor, contiguity and entrapped liquid showed a relative equivalency among the various conditioning techniques. It was found that the strongest influence on semi-solid slurry fluidity is exerted by the mould temperature. Tensile properties and porosity levels were measured on a demonstration part produced with different slurry ingate velocities. Results showed similar strength levels among all thixocast samples, a strong correlation between elongation and pore volume fraction and porosity levels much lower than the typical figure for permanent mould or die cast Al-Si alloys. Finally, thermomechanical fatigue tests results were much more favorable to the semi-solid material when compared with the conventionally cast alloy, a result attributed to lower porosity, spheroidal shape of the Al-alpha phase, and refined Si eutectic particles. alpha 2007 Elsevier B.V. All rights reserved.

Effects of viscous dissipation and boundary conditions on forced convection in a channel occupied by a saturated porous medium

Forced convection with viscous dissipation in a parallel plate channel filled by a saturated porous medium is investigated numerically. Three different viscous dissipation models are examined. Two different sets of wall conditions are considered: isothermal and isoflux. Analytical expressions are also presented for the asymptotic temperature profile and the asymptotic Nusselt number. With isothermal walls, the Brinkman number significantly influences the developing Nusselt number but not the asymptotic one. At constant wall heat flux, both the developing and the asymptotic Nusselt numbers are affected by the value of the Brinkman number. The Nusselt number is sensitive to the porous medium shape factor under all conditions considered.

Effects of viscous dissipation and boundary conditions on forced convection in a channel occupied by a saturated porous medium

Forced convection with viscous dissipation in a parallel plate channel filled by a saturated porous medium is investigated numerically. Three different viscous dissipation models are examined. Two different sets of wall conditions are considered: isothermal and isoflux. Analytical expressions are also presented for the asymptotic temperature profile and the asymptotic Nusselt number. With isothermal walls, the Brinkman number significantly influences the developing Nusselt number but not the asymptotic one. At constant wall heat flux, both the developing and the asymptotic Nusselt numbers are affected by the value of the Brinkman number. The Nusselt number is sensitive to the porous medium shape factor under all conditions considered.

Biopolttoaineiden leijutusominaisuuksien karakterisointi

Tässä diplomityössä selvitettiin biopolttoaineiden ominaisuuksia leijutuksen kannalta. Ensiksi tutkittavat biopolttoaineet, hake ja turve, seulottiin ja seulotut näytteet analysoitiin. Seuraavaksi turvetta ja haketta leijutettiin eri nopeuksilla ja eri leijutusnopeuksilla saadut näytteet analysoitiin kuva-analysilla. Partikkeleista selvitettiin runsaasti mittoja, kuten keskihalkaisija, pinta-ala ja muotokerroin. Kirjallisuudesta löytyvien korrelaatioiden avulla laskettiin leijutettujen partikkelien vastuskertoimet ja terminaalinopeudet. Korrelaatioiden tuloksia verrattiin mittaustuloksiin. Tässä työssä myös laskettiin kyseisiin biopolttoaineisiin vaikuttavat ominaisvoimat leijutuksessa sekä laskettiin korjauskerroin, jota käytettiin ominaisvoimien korjaamiseen. Referenssiaineina käytettiin hiekkaa ja lasikuulia.

Self-organisation in the assembly of gels from mixtures of different dendritic peptide building blocks

This paper investigates dendritic peptides capable of assembling into nanostructured gels, and explores the effect on self-assembly of mixing different molecular building blocks. Thermal measurements, small angle Xray scattering (SAXS) and circular dichroism (CD) spectroscopy are used to probe these materials on macroscopic, nanoscopic and molecular length scales. The results from these investigations demonstrate that in this case, systems with different "size" and "chirality" factors can self-organise, whilst systems with different "shape" factors cannot. The "size" and "chirality" factors are directly connected with the molecular information programmed into the dendritic peptides, whilst the shape factor depends on the group linking these peptides together-this is consistent with molecular recognition hydrogen bond pathways between the peptidic building blocks controlling the ability of these systems to self-recognise. These results demonstrate that mixtures of relatively complex peptides, with only subtle differences on the molecular scale, can self-organise into nanoscale structures, an important step in the spontaneous assembly of ordered systems from complex mixtures.