Distance Transforms on Gray-Level Surfaces

This thesis studies gray-level distance transforms, particularly the Distance Transform on Curved Space (DTOCS). The transform is produced by calculating distances on a gray-level surface. The DTOCS is improved by definingmore accurate local distances, and developing a faster transformation algorithm. The Optimal DTOCS enhances the locally Euclidean Weighted DTOCS (WDTOCS) with local distance coefficients, which minimize the maximum error from the Euclideandistance in the image plane, and produce more accurate global distance values.Convergence properties of the traditional mask operation, or sequential localtransformation, and the ordered propagation approach are analyzed, and compared to the new efficient priority pixel queue algorithm. The Route DTOCS algorithmdeveloped in this work can be used to find and visualize shortest routes between two points, or two point sets, along a varying height surface. In a digital image, there can be several paths sharing the same minimal length, and the Route DTOCS visualizes them all. A single optimal path can be extracted from the route set using a simple backtracking algorithm. A new extension of the priority pixel queue algorithm produces the nearest neighbor transform, or Voronoi or Dirichlet tessellation, simultaneously with the distance map. The transformation divides the image into regions so that each pixel belongs to the region surrounding the reference point, which is nearest according to the distance definition used. Applications and application ideas for the DTOCS and its extensions are presented, including obstacle avoidance, image compression and surface roughness evaluation.

New Distance Transforms for Gray Level Image Compression

This thesis deals with distance transforms which are a fundamental issue in image processing and computer vision. In this thesis, two new distance transforms for gray level images are presented. As a new application for distance transforms, they are applied to gray level image compression. The new distance transforms are both new extensions of the well known distance transform algorithm developed by Rosenfeld, Pfaltz and Lay. With some modification their algorithm which calculates a distance transform on binary images with a chosen kernel has been made to calculate a chessboard like distance transform with integer numbers (DTOCS) and a real value distance transform (EDTOCS) on gray level images. Both distance transforms, the DTOCS and EDTOCS, require only two passes over the graylevel image and are extremely simple to implement. Only two image buffers are needed: The original gray level image and the binary image which defines the region(s) of calculation. No other image buffers are needed even if more than one iteration round is performed. For large neighborhoods and complicated images the two pass distance algorithm has to be applied to the image more than once, typically 3 10 times. Different types of kernels can be adopted. It is important to notice that no other existing transform calculates the same kind of distance map as the DTOCS. All the other gray weighted distance function, GRAYMAT etc. algorithms find the minimum path joining two points by the smallest sum of gray levels or weighting the distance values directly by the gray levels in some manner. The DTOCS does not weight them that way. The DTOCS gives a weighted version of the chessboard distance map. The weights are not constant, but gray value differences of the original image. The difference between the DTOCS map and other distance transforms for gray level images is shown. The difference between the DTOCS and EDTOCS is that the EDTOCS calculates these gray level differences in a different way. It propagates local Euclidean distances inside a kernel. Analytical derivations of some results concerning the DTOCS and the EDTOCS are presented. Commonly distance transforms are used for feature extraction in pattern recognition and learning. Their use in image compression is very rare. This thesis introduces a new application area for distance transforms. Three new image compression algorithms based on the DTOCS and one based on the EDTOCS are presented. Control points, i.e. points that are considered fundamental for the reconstruction of the image, are selected from the gray level image using the DTOCS and the EDTOCS. The first group of methods select the maximas of the distance image to new control points and the second group of methods compare the DTOCS distance to binary image chessboard distance. The effect of applying threshold masks of different sizes along the threshold boundaries is studied. The time complexity of the compression algorithms is analyzed both analytically and experimentally. It is shown that the time complexity of the algorithms is independent of the number of control points, i.e. the compression ratio. Also a new morphological image decompression scheme is presented, the 8 kernels' method. Several decompressed images are presented. The best results are obtained using the Delaunay triangulation. The obtained image quality equals that of the DCT images with a 4 x 4

Future prospects of short distance rail based passenger transport in Northern Europe

The worlds’ population is increasing and cities have become more crowded with people and vehicles. Communities in the fringe of metropolitans’ increase the traffic done with private cars, but also increase the need for public transportation. People have typically needs traveling to work located in city centers during the morning time, and return to suburbs in the afternoon or evening. Rail based passenger transport is environmentally friendly transport mode with high capacity to transport large volume of people. Railways have been regulated markets with national incumbent having monopoly position. Opening the market for competition is believed to have a positive effect by increasing the efficiency of the industry. National passenger railway market is opened for competition only in few countries, where as international traffic in EU countries was deregulated in 2010. The objective of this study is to examine the passenger railway market of three North European countries, Sweden, Denmark and Estonia. The interest was also to get an understanding of the current situation and how the deregulation has proceeded. Theory of deregulation is unfolded with literature analyses and empirical part of the study is constructed from two parts. Customer satisfaction survey was chosen as a method to collect real life experiences from the passengers and measure their knowledge of the market situation and possible changes appeared. Interviews of experts from the industry and labor unions give more insights and able better understanding for example of social consequences caused from opening the market for competition. Expert interviews were conducted by using semi-structured theme interview. Based on the results of this study, deregulation has proceeded quite differently in the three countries researched. Sweden is the most advanced country, where the passenger railway market is open for new entrants. Denmark and Estonia are lagging behind. Opening the market is considered positive among passengers and most of the experts interviewed. Common for the interviews were the labour unions negative perspective concerning deregulation. Despite the fact deregulation is considered positive among the respondents of the customer satisfaction survey, they could not name railway undertakings operating in their country. Generally respondents were satisfied with the commuter trains. Ticket price, punctuality of trains and itinerary affect the most to customer satisfaction.

Activation of supply relationships : a study of main providers in the Turku logistics cluster

Företag inom industri och handel väljer allt oftare att låta ett logistikföretag sköta stora delar av sina logistiska processer. Logistikföretagen i sin tur överlåter utförandet av enskilda tjänster, som t.ex. olika typer av transport, till olika samarbetspartners inom branschen. I avhandlingen studeras hur logistikföretag går till väga då de väljer vilka av deras samarbetspartners som ska engageras för att delta i utförandet av ett logistiktjänstepaket, en arbetsprocess som här kallas aktivering. Fokus ligger på aktiveringens innehåll och de faktorer som inverkar på hur den går till och vilka samarbetsparter som kommer att engageras. Arbetet bygger på nätverksansatsen för studier av företagsrelationer på industriella marknader. Aktiveringsprocessen uppfattas som en rätt ordinär, rutinmässig verksamhet i företaget, men den kan också förväntas inverka på hur företagets samarbetsnätverk utvecklas över tiden, genom att vissa relationer förstärks medan andra försvagas. I den empi riska undersökningen deltog 29 logistikföretag i Åboregionen som utgående från ett diskussionsunderlag fick berätta om hur de går till väga vid aktivering.

Cellular responses to stress and kinase signaling activation : apoptosis and differentiation

Stressignaler avkänns många gånger av membranbundna proteiner som översätter signalerna till kemisk modifiering av molekyler, ofta proteinkinaser Dessa kinaser överför de avkodade budskapen till specifika transkriptionsfaktorer genom en kaskad av sekventiella fosforyleringshändelser, transkriptionsfaktorerna aktiverar i sin tur de gener som behövs för att reagera på stressen. En av de mest kända måltavlorna för stressignaler är transkriptionsfaktor AP-1 familjemedlemen c-Jun. I denna studie har jag identifierat den nukleolära proteinet AATF som en ny regulator av c-Jun-medierad transkriptionsaktivitet. Jag visar att stresstimuli inducerar omlokalisering av AATF vilket i sin tur leder till aktivering av c-Jun. Den AATF-medierad ökningen av c-Jun-aktiviteten leder till en betydande ökning av programmerad celldöd. Parallellt har jag vidarekarakteriserat Cdk5/p35 signaleringskomplexet som tidigare har identifierats i vårt laboratorium som en viktig faktor för myoblastdifferentiering. Jag identifierade den atypiska PKCξ som en uppströms regulator av Cdk5/p35-komplexet och visar att klyvning och aktivering av Cdk5 regulatorn p35 är av fysiologisk betydelse för differentieringsprocessen och beroende av PKCξ aktivitet. Jag visar att vid induktion av differentiering fosforylerar PKCξ p35 vilket leder till calpain-medierad klyvning av p35 och därmed ökning av Cdk5-aktiviteten. Denna avhandling ökar förståelsen för de regulatoriska mekanismer som styr c-Jun-transkriptionsaktiviteten och c-Jun beroende apoptos genom att identifiera AATF som en viktig faktor. Dessutom ger detta arbete nya insikter om funktionen av Cdk5/p35-komplexet under myoblastdifferentiering och identifierar PKCξ som en uppströms regulator av Cdk5 aktivitet och myoblast differentiering.

Cultural distance and negotiation behavior : Perception of entrepreneurs operating in Turku

This thesis investigates the influence of cultural distance on entrepreneurs’ negotiation behaviour. For this purpose, Turku was chosen as the unit of analysis due to the exponential demographic change experienced during the last two decades that has derived in a more diversified local environment. The research aim set for this study was to identify to what extent entrepreneurs face cultural distance, how cultural distance influences the entrepreneur’s negotiation behaviour and how can it be addressed in order to turn dissimilarities into opportunities. This study presented the relation and apparent dichotomy of cultural distance and global culture, including the component of diversity. The impact of cultural distance in the entrepreneurial mindset and its consequent effect in negotiation behaviour was presented too. Addressing questions about the way individuals perceive, behave and interact allowed the use of interviews for this qualitative research study. In the empirical part of this study it was found that negotiation behaviour differed in terms of how congenial entrepreneurs felt when managing cultural distance, encompassing their performance. It was also acknowledged that after time and effort, some of the personal traits were enhanced while others reduced, allowing for more flexibility and adaptation. Furthermore, depending on the level of trust and shared interests, entrepreneurs determined their attitudinal approach, being adaptive or reactive subject to situational aspects. Additionally, it was found that the acquisition of cultural savvy not necessarily conveyed to more creativity. This experiential learning capability led to the proposition of new ways of behaviour. Likewise, it was proposed that growing cultural intelligence bridge distances, reducing mistrusts and misunderstandings. The capability of building more collaborative relationships allows entrepreneurs to see cultural distance as a cultural perspective instead of as a threat. Therefore it was recommended to focus on proximity rather than distance to better identify and exploit untapped opportunities and better perform when negotiating in whichever cultural conditions.

Nanoclustering augmentation : a novel mechanism of Ras activation in cancer

Proteins of the Ras family are central regulators of crucial cellular processes, such as proliferation, differentiation and apoptosis. Their importance is emphasized in cancer, in which the isoforms H-ras, N-ras and K-ras are misregulated by mutations in approximately 20 – 30 % of cases. Thus, they represent major cancer oncogenes and one of the most important targets for cancer drug development. Ras proteins are small GTPases, which cycle between the GTP-bound active and GDP-bound inactive state. Despite the tremendous research conducted in the last three decades, many fundamental properties of Ras proteins remain poorly understood. For instance, although new concepts have recently emerged, the understanding of Ras behavior in its native environment, the membrane, is still largely missing. On the membrane Ras organizes into nanoscale clusters, also called nanoclusters. They differ between isoforms, but also between activation states of Ras. It is considered that nanoclusters represent the basic Ras signaling units. Recently, it was demonstrated that on the membrane Ras adopts distinct conformations, the so-called orientations, which are dependent on the Ras activations state. The membrane-orientation of H-ras is stabilized by the helix α4 and the C-terminal hypervariable region (hvr). The novel switch III region was proposed to be involved in mediating the change between different H-ras orientations. When the regions involved in this mechanism are mutated, H-ras activity is changed by an unknown mechanism. This thesis has explained the connection between the change of Ras orientation on the membrane and Ras activity. We demonstrated that H-ras orientation mutants exhibit altered diffusion properties on the membrane, which reflect the changes in their nanoclustering. The altered nanoclustering consequently rules the activity of the mutants. Moreover, we demonstrated that specific cancer-related mutations, affecting the switch III region of different Ras isoforms, exhibit increased nanoclustering, which consequently leads to stronger Ras signaling and tumorigenicity. Thus, we have discovered nanoclustering increase as a novel mechanism of Ras activity modulation in cancer. The molecular architecture of complexes formed on the membrane upon Ras activation is another poorly understood property of Ras. The following work has provided novel details on the regulation of Ras nanoclustering by a known H-ras-GTP nanoclustering stabilizer galectin-1 (Gal-1). Our study demonstrated that Gal-1 is not able to bind Ras directly, as it was previously proposed. Instead, its effect on H-ras-GTP nanoclustering is indirect, through binding of the effector proteins. Collectively, our findings represent valuable novel insights in the behavior of Ras, which will help the future research to eventually develop new strategies to successfully target Ras in cancer.

Optimal distance of the light-curing tip for light transmission through the resin composite

Hammaslääketieteessä käytetettävien komposiittien valonläpäisevyys vaihtelee. Samoin LED-valokovettimet eroavat toisistaan valotehonsa ja muotoilunsa perusteella. On yleisesti tiedossa, että valokovettimesta tulevan valon intensiteetti pinta-alayksikköä kohden heikkenee, kun kovettimen etäisyys kasvaa. Toisaalta ei ole tiedossa, miten valokovetettavan kohteen ja valokovettimen kärjen väliin sijoitettu materiaali tarkalleenottaen vaikuttaa valon intensiteettiin eri etäisyyksiä käytettäessä. Tämän tutkimuksen tarkoituksena on selvittää, miten valokovetettavan kohteen ja valokovettimen kärjen väliin asetettava etukäteen polymerisoitu materiaali vaikuttaa valon intensiteettiin eri etäisyyksillä. Tutkimus suoritettiin käyttämällä kahta eri valokovetinta. Jotta etäisyyden vaikutusta valotustehoon voitiin demonstroida, vaihdettiin kovettimen etäisyyttä sensorista 0,2,4,6,8,10mm välillä. Valotehot rekisteröitiin MARC resin calibrator -laitteella. Sensorin ja valokovettimen kärjen väliin asetettavat erilaiset komposiittilevyt olivat valmiiksi kovetettuja,1mm paksuisia, filleripitoisuuksiltaan neljää erilaista muovia. Valotehot rekisteröitiin jokaiselta etäisyydeltä komposiitin ollessa sensorin päällä. Rinnakkaisesti verrattiin myös etäisyyden vaikutusta valotehoon ilman esikovetettua materiaalia kovettimen kärjen ja valoa mittaavan sensorin välissä. Vertailun suorittamiseksi laskettiin intensiteettisuhdeluku muovillisen ja muovittoman arvon välillä aina tietyllä etäisyydellä Valokovettimen kärjen etäisyyden kasvattaminen sensorista (eli valokovetettavasta kohteesta) odotusten mukaisesti pienensi valotehoa. Laittamalla sensorin ja kovettimen väliin komposiittilevy, valoteho pieneni odotetusti vielä enemmän. Tutkittaessa intensiteettisuhdetta (valoteho muovin kanssa : valoteho ilman muovia) kuitenkin huomattiin, että 4-6mm:n kohdalla suhdeluku oli suurempi kuin 0,2,8 ja 10mm kohdalla. Johtopäätöksenä oli, että suurin mahdollinen valokovetusteho saavutetan laittamalla kovetuskärki mahdollisimman lähelle kohdetta. Jos valokovetettavan kohteen ja valokovettimen kärjen välissä oli kiinteä komposiittipalanen, suurin mahdollinen valokovetusteho kohteeseen saavutetaan edelleen laittamalla kovetuskärki kiinni muoviin. Jos etäisyyttä muovin pinnasta sen sijaan kasvatettiin, valokovetusteho ei laskenutkaan niin nopeasti kuin oli odotettu. Tämä voi liittyä siihen, että tehokkaan valokeilan halkaisijan koko on suurempi verrattuna komposiitin sekä sensorin halkaisian kokoon. Toiseksi on arvioitu, että resiinikomposiitin täyteaineet voisivat fokusoida läpi kulkevaa valoa sensoriin. Se, pitääkö tämä ilmiö paikkansa, vaatii kuitenkin enemmän tutkimusta

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.