Retinal Image Analysis Using Machine Vision

The topic of this thesis is studying how lesions in retina caused by diabetic retinopathy can be detected from color fundus images by using machine vision methods. Methods for equalizing uneven illumination in fundus images, detecting regions of poor image quality due toinadequate illumination, and recognizing abnormal lesions were developed duringthe work. The developed methods exploit mainly the color information and simpleshape features to detect lesions. In addition, a graphical tool for collecting lesion data was developed. The tool was used by an ophthalmologist who marked lesions in the images to help method development and evaluation. The tool is a general purpose one, and thus it is possible to reuse the tool in similar projects.The developed methods were tested with a separate test set of 128 color fundus images. From test results it was calculated how accurately methods classify abnormal funduses as abnormal (sensitivity) and healthy funduses as normal (specificity). The sensitivity values were 92% for hemorrhages, 73% for red small dots (microaneurysms and small hemorrhages), and 77% for exudates (hard and soft exudates). The specificity values were 75% for hemorrhages, 70% for red small dots, and 50% for exudates. Thus, the developed methods detected hemorrhages accurately and microaneurysms and exudates moderately.

Cross-scale analysis of the region effect on vascular plant species diversity in southern and northern European mountain ranges.

Background: The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities?Methodology/Principal Findings: We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total gamma-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific gamma-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot beta-diversity) and (iv) number of species present per plot (plot gamma-diversity). We found strong region effects on total gamma-diversity, habitat-specific gamma-diversity and plot-to-plot beta-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot alpha-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots.Conclusions/Significance: We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges,but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Because different processes can lead to a similar pattern, we discuss the consistency of our results with Quaternary history and other divergent features between the two regions such as habitat connectivity, selection for vagility and environmental differences not accounted for in our analyses

The class basis of the cleavage between the New Left and the radical right: An analysis for Austria, Denmark, Norway and Switzerland

This chapter argues that the electoral competition between the New Left and the Radical Right is best understood as a cultural divide anchored in different class constituencies. Based on individual-level data from the European Social Survey, we analyze the links between voters' class position, their economic and cultural preferences and their party choice for four small and affluent European countries. We find a striking similarity in the class pattern across countries. Everywhere, the New Left attracts disproportionate support from socio-cultural professionals and presents a clear-cut middle-class profile, whereas the Radical Right is most successful among production and service workers and receives least support from professionals. In general, the Radical Right depends on the votes of lowereducated men and older citizens and has turned into a new type of working-class party. However, its success within the working-class is not due to economic, but to cultural issues. The voters of the Radical Right collide with those of the New Left over a cultural conflict of identity and community - and not over questions of redistribution. A full-grown cleavage has thus emerged in the four countries under study, separating a libertarian-universalistic pole from an authoritarian-communitarian pole and going along with a process of class realignment.

Analysis of a finite volume method for a cross-diffusion model in population dynamics

The main goal of this paper is to propose a convergent finite volume method for a reactionâeuro"diffusion system with cross-diffusion. First, we sketch an existence proof for a class of cross-diffusion systems. Then the standard two-point finite volume fluxes are used in combination with a nonlinear positivity-preserving approximation of the cross-diffusion coefficients. Existence and uniqueness of the approximate solution are addressed, and it is also shown that the scheme converges to the corresponding weak solution for the studied model. Furthermore, we provide a stability analysis to study pattern-formation phenomena, and we perform two-dimensional numerical examples which exhibit formation of nonuniform spatial patterns. From the simulations it is also found that experimental rates of convergence are slightly below second order. The convergence proof uses two ingredients of interest for various applications, namely the discrete Sobolev embedding inequalities with general boundary conditions and a space-time $L^1$ compactness argument that mimics the compactness lemma due to Kruzhkov. The proofs of these results are given in the Appendix.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Coordination pattern adaptability: energy cost of degenerate behaviors.

This study investigated behavioral adaptability, which could be defined as a blend between stability and flexibility of the limbs movement and their inter-limb coordination, when individuals received informational constraints. Seven expert breaststroke swimmers performed three 200-m in breaststroke at constant submaximal intensity. Each trial was performed randomly in a different coordination pattern: 'freely-chosen', 'maximal glide' and 'minimal glide'. Two underwater and four aerial cameras enabled 3D movement analysis in order to assess elbow and knee angles, elbow-knee pair coordination, intra-cyclic velocity variations of the center of mass, stroke rate and stroke length and inter-limb coordination. The energy cost of locomotion was calculated from gas exchanges and blood lactate concentration. The results showed significantly higher glide, intra-cyclic velocity variations and energy cost under 'maximal glide' compared to 'freely-chosen' instructional conditions, as well as higher reorganization of limb movement and inter-limb coordination (p<0.05). In the 'minimal glide' condition, the swimmers did not show significantly shorter glide and lower energy cost, but they exhibited significantly lower deceleration of the center of mass, as well as modified limb movement and inter-limb coordination (p<0.05). These results highlight that a variety of structural adaptations can functionally satisfy the task-goal.

Experimental and Numerical Analysis of Different Volutes in a Centrifugal Compressor

In a centrifugal compressor the flow around the diffuser is collected and led to the pipe system by a spiral-shaped volute. In this study a single-stage centrifugal compressor with three different volutes is investigated. The compressorwas first equipped with the original volute, the cross-section of which was a combination of a rectangle and semi-circle. Next a new volute with a fully circular cross-section was designed and manufactured. Finally, the circular volute wasmodified by rounding the tongue and smoothing the tongue area. The overall performance of the compressor as well as the static pressure distribution after the impeller and on the volute surface were measured. The flow entering the volute was measured using a three-hole Cobra-probe, and flow visualisations were carriedout in the exit cone of the volute. In addition, the radial force acting on theimpeller was measured using magnetic bearings. The complete compressor with thecircular volute (inlet pipe, full impeller, diffuser, volute and outlet pipe) was also modelled using computational fluid dynamics (CFD). A fully 3-D viscous flow was solved using a Navier-Stokes solver, Finflo, developed at Helsinki University of Technology. Chien's k-e model was used to take account of the turbulence. The differences observed in the performance of the different volutes were quite small. The biggest differences were at low speeds and high volume flows,i.e. when the flow entered the volute most radially. In this operating regime the efficiency of the compressor with the modified circular volute was about two percentage points higher than with the other volutes. Also, according to the Cobra-probe measurements and flow visualisations, the modified circular volute performed better than the other volutes in this operating area. The circumferential static pressure distribution in the volute showed increases at low flow, constant distribution at the design flow and decrease at high flow. The non-uniform static pressure distribution of the volute was transmitted backwards across the vaneless diffuser and observed at the impeller exit. At low volume flow a strong two-wave pattern developed into the static pressure distribution at the impeller exit due to the response of the impeller to the non-uniformity of pressure. The radial force of the impeller was the greatest at the choke limit, the smallest atthe design flow, and moderate at low flow. At low flow the force increase was quite mild, whereas the increase at high flow was rapid. Thus, the non-uniformityof pressure and the force related to it are strong especially at high flow. Theforce caused by the modified circular volute was weaker at choke and more symmetric as a function of the volume flow than the force caused by the other volutes.

Analysis of vineyard differential management zones and relation to vine development, grape maturity and quality

The objective of research was to analyse the potential of Normalized Difference Vegetation Index (NDVI) maps from satellite images, yield maps and grapevine fertility and load variables to delineate zones with different wine grape properties for selective harvesting. Two vineyard blocks located in NE Spain (Cabernet Sauvignon and Syrah) were analysed. The NDVI was computed from a Quickbird-2 multi-spectral image at veraison (July 2005). Yield data was acquired by means of a yield monitor during September 2005. Other variables, such as the number of buds, number of shoots, number of wine grape clusters and weight of 100 berries were sampled in a 10 rows × 5 vines pattern and used as input variables, in combination with the NDVI, to define the clusters as alternative to yield maps. Two days prior to the harvesting, grape samples were taken. The analysed variables were probable alcoholic degree, pH of the juice, total acidity, total phenolics, colour, anthocyanins and tannins. The input variables, alone or in combination, were clustered (2 and 3 Clusters) by using the ISODATA algorithm, and an analysis of variance and a multiple rang test were performed. The results show that the zones derived from the NDVI maps are more effective to differentiate grape maturity and quality variables than the zones derived from the yield maps. The inclusion of other grapevine fertility and load variables did not improve the results.

'Herbal' but potentially hazardous: an analysis of the constituents and smoke emissions of tobacco-free waterpipe products and the air quality in the cafes where they are served

BACKGROUND: There are limited data on the composition and smoke emissions of 'herbal' shisha products and the air quality of establishments where they are smoked. METHODS: Three studies of 'herbal' shisha were conducted: (1) samples of 'herbal' shisha products were chemically analysed; (2) 'herbal' and tobacco shisha were burned in a waterpipe smoking machine and main and sidestream smoke analysed by standard methods and (3) the air quality of six waterpipe cafes was assessed by measurement of CO, particulate and nicotine vapour content. RESULTS: We found considerable variation in heavy metal content between the three products sampled, one being particularly high in lead, chromium, nickel and arsenic. A similar pattern emerged for polycyclic aromatic hydrocarbons. Smoke emission analyses indicated that toxic byproducts produced by the combustion of 'herbal' shisha were equivalent or greater than those produced by tobacco shisha. The results of our air quality assessment demonstrated that mean PM2.5 levels and CO content were significantly higher in waterpipe establishments compared to a casino where cigarette smoking was permitted. Nicotine vapour was detected in one of the waterpipe cafes. CONCLUSIONS: 'Herbal' shisha products tested contained toxic trace metals and PAHs levels equivalent to, or in excess of, that found in cigarettes. Their mainstream and sidestream smoke emissions contained carcinogens equivalent to, or in excess of, those of tobacco products. The content of the air in the waterpipe cafes tested was potentially hazardous. These data, in aggregate, suggest that smoking 'herbal' shisha may well be dangerous to health.

Analysis of flow dynamics in right ventricular outflow tract.

BACKGROUND: The mechanism behind early graft failure after right ventricular outflow tract (RVOT) reconstruction is not fully understood. Our aim was to establish a three-dimensional computational fluid dynamics (CFD) model of RVOT to investigate the hemodynamic conditions that may trigger the development of intimal hyperplasia and arteriosclerosis. METHODS: Pressure, flow, and diameter at the RVOT, pulmonary artery (PA), bifurcation of the PA, and left and right PAs were measured in 10 normal pigs with a mean weight of 24.8 ± 0.78 kg. Data obtained from the experimental scenario were used for CFD simulation of pressure, flow, and shear stress profile from the RVOT to the left and right PAs. RESULTS: Using experimental data, a CFD model was obtained for 2.0 and 2.5-L/min pulsatile inflow profiles. In both velocity profiles, time and space averaged in the low-shear stress profile range from 0-6.0 Pa at the pulmonary trunk, its bifurcation, and at the openings of both PAs. These low-shear stress areas were accompanied to high-pressure regions 14.0-20.0 mm Hg (1866.2-2666 Pa). Flow analysis revealed a turbulent flow at the PA bifurcation and ostia of both PAs. CONCLUSIONS: Identified local low-shear stress, high pressure, and turbulent flow correspond to a well-defined trigger pattern for the development of intimal hyperplasia and arteriosclerosis. As such, this real-time three-dimensional CFD model may in the future serve as a tool for the planning of RVOT reconstruction, its analysis, and prediction of outcome.

Analysis of the genetic basis of periodic fever with aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome.

PFAPA syndrome is the most common autoinflammatory syndrome in children from Western countries. In spite of its strong familial clustering, its genetic basis and inheritance pattern are still unknown. We performed a comprehensive genetic study on 68 individuals from 14 families. Linkage analysis suggested a susceptibility locus on chromosome 8, but direct molecular sequencing did not support this initial statistical finding. Exome sequencing revealed the absence of any gene that was mutated in all patients. Exhaustive screening of genes involved in other autoinflammatory syndromes or encoding components of the human inflammasome showed no DNA variants that could be linked to PFAPA molecular pathology. Among these, the previously-reported missense mutation V198M in the NLRP3 gene was clearly shown not to co-segregate with PFAPA. Our results on this relatively large cohort indicate that PFAPA syndrome is unlikely to be a monogenic condition. Moreover, none of the several genes known to be involved in inflammation or in autoinflammatory disorders seem to be relevant, alone, to its etiology, suggesting that PFAPA results from oligogenic or complex inheritance of variants in multiple disease genes and/or non-genetic factors.

Particle Size Analysis of Pharmaceutical Powders by Laser Diffraction

Raaka-aineen hiukkaskoko on lääkekehityksessä keskeinen materiaaliparametri. Lääkeaineen partikkelikoko vaikuttaa moneen lääketuotteen tärkeään ominaisuuteen, esimerkiksi lääkkeen biologiseen hyväksikäytettävyyteen. Tässä diplomityössä keskityttiin jauhemaisten lääkeaineiden hiukkaskoon määrittämiseen laserdiffraktiomenetelmällä. Menetelmä perustuu siihen, että partikkeleista sironneen valon intensiteetin sirontakulmajakauma on riippuvainen partikkelien kokojakaumasta. Työn kirjallisuusosassa esiteltiin laserdiffraktiomenetelmän teoriaa. PIDS (Polarization Intensity Differential Scattering) tekniikka, jota voidaan käyttää laserdiffraktion yhteydessä, on myös kuvattu kirjallisuusosassa. Muihin menetelmiin perustuvista analyysimenetelmistä tutustuttiin mikroskopiaan sekä aerodynaamisen lentoajan määrittämiseen perustuvaan menetelmään. Kirjallisuusosassa esiteltiin myös partikkelikoon yleisimpiä esitystapoja. Työn kokeellisen osan tarkoituksena oli kehittää ja validoida laserdiffraktioon perustuva partikkelikoon määritysmenetelmä tietylle lääkeaineelle. Menetelmäkehitys tehtiin käyttäen Beckman Coulter LS 13 320 laserdiffraktoria. Laite mahdollistaa PIDS-tekniikan käytön laserdiffraktiotekniikan ohella. Menetelmäkehitys aloitettiin arvioimalla, että kyseinen lääkeaine soveltuu parhaiten määritettäväksi nesteeseen dispergoituna. Liukoisuuden perusteella väliaineeksi valittiin tällä lääkeaineella kyllästetty vesiliuos. Dispergointiaineen sekä ultraäänihauteen käyttö havaittiin tarpeelliseksi dispergoidessa kyseistä lääkeainetta kylläiseen vesiliuokseen. Lopuksi sekoitusnopeus näytteensyöttöyksikössä säädettiin sopivaksi. Validointivaiheessa kehitetyn menetelmän todettiin soveltuvan hyvin kyseiselle lääkeaineelle ja tulosten todettiin olevan oikeellisia sekä toistettavia. Menetelmä ei myöskään ollut herkkä pienille häiriöille.

Dynamic Criteria: a Longitudinal Analysis of Professional Basketball Players" Outcomes

This paper describes the fluctuations of temporal criteria dynamics in the context of professional sport. Specifically, we try to verify the underlying deterministic patterns in the outcomes of professional basketball players. We use a longitudinal approach based on the analysis of the outcomes of 94 basketball players over ten years, covering practically players" entire career development. Time series were analyzed with techniques derived from nonlinear dynamical systems theory. These techniques analyze the underlying patterns in outcomes without previous shape assumptions (linear or nonlinear). These techniques are capable of detecting an intermediate situation between randomness and determinism, called chaos. So they are very useful for the study of dynamic criteria in organizations. We have found most players (88.30%) have a deterministic pattern in their outcomes, and most cases are chaotic (81.92%). Players with chaotic patterns have higher outcomes than players with linear patterns. Moreover, players with power forward and center positions achieve better results than other players. The high number of chaotic patterns found suggests caution when appraising individual outcomes, when coaches try to find the appropriate combination of players to design a competitive team, and other personnel decisions. Management efforts must be made to assume this uncertainty.

Environmental Structural Decomposition Analysis of Italian Emissions, 1995-2005

[spa] El estudio analiza la evolución de los gases de efecto invernadero (GEI) y las emisiones de acidificación para Italia durante el periodo 1995-2005. Los datos muestran que mientras las emisiones que contribuyen a la acidificación han disminuido constantemente, las emisiones de GEI han aumentado debido al aumento de dióxido de carbono. El objetivo de este estudio es poner de relieve cómo diferentes factores económicos, en particular el crecimiento económico, el desarrollo de una tecnología menos contaminante y la estructura del consumo, han impulsado la evolución de las emisiones. La metodología propuesta es un análisis de descomposición estructural (ADE), método que permite descomponer los cambios de la variable de interés entre las diferentes fuerzas y revelar la importancia de cada factor. Por otra parte, este estudio considera la importancia del comercio internacional e intenta incluir el “problema de la responsabilidad”. Es decir, a través de las relaciones comerciales internacionales, un país podría estar exportando procesos de producción contaminantes sin una reducción real de la contaminación implícita en su patrón de consumo. Con este fin, siguiendo primero un enfoque basado en la “responsabilidad del productor”, el ADE se aplica a las emisiones causadas por la producción nacional. Sucesivamente, el análisis se mueve hacia un enfoque basado en la “responsabilidad del consumidor" y la descomposición se aplica a las emisiones relacionadas con la producción nacional o la producción extranjera que satisface la demanda interna. De esta manera, el ejercicio permite una primera comprobación de la importancia del comercio internacional y pone de relieve algunos resultados a nivel global y a nivel sectorial.

Environmental Structural Decomposition Analysis of Italian Emissions, 1995-2005

[spa] El estudio analiza la evolución de los gases de efecto invernadero (GEI) y las emisiones de acidificación para Italia durante el periodo 1995-2005. Los datos muestran que mientras las emisiones que contribuyen a la acidificación han disminuido constantemente, las emisiones de GEI han aumentado debido al aumento de dióxido de carbono. El objetivo de este estudio es poner de relieve cómo diferentes factores económicos, en particular el crecimiento económico, el desarrollo de una tecnología menos contaminante y la estructura del consumo, han impulsado la evolución de las emisiones. La metodología propuesta es un análisis de descomposición estructural (ADE), método que permite descomponer los cambios de la variable de interés entre las diferentes fuerzas y revelar la importancia de cada factor. Por otra parte, este estudio considera la importancia del comercio internacional e intenta incluir el “problema de la responsabilidad”. Es decir, a través de las relaciones comerciales internacionales, un país podría estar exportando procesos de producción contaminantes sin una reducción real de la contaminación implícita en su patrón de consumo. Con este fin, siguiendo primero un enfoque basado en la “responsabilidad del productor”, el ADE se aplica a las emisiones causadas por la producción nacional. Sucesivamente, el análisis se mueve hacia un enfoque basado en la “responsabilidad del consumidor" y la descomposición se aplica a las emisiones relacionadas con la producción nacional o la producción extranjera que satisface la demanda interna. De esta manera, el ejercicio permite una primera comprobación de la importancia del comercio internacional y pone de relieve algunos resultados a nivel global y a nivel sectorial.