Thesis deals with relationship between histomorphological and molecular-genetic findings of selected salivary gland tumors. Author, as a molecular-cytogeneticist mainly focused on detection of tumor-specific translocations of the salivary gland tumors which can serve as differential diagnostic markers. The thesis is composed as a commented files of authors own publications, and it is divided into four parts. First part deepens the knowledge of salivary adenoid cystic carcinoma. It was proved, that t(6;9)(q22-23;p23-24) resulting in fusion of transcription factors MYB-NFIB, or more rarely t(8;9) resulting in MYBL1-NFIB fusion represent robust differential diagnostic marker of adenoid cystic carcinoma. Further it was proved, that the 1p36 deletion can serve as an unfavorable prognostic indicator of adenoid cystic carcinoma, as the patients with 1p36 deletion had significantly lower survival. Second part summarizes new developments about mammary analogue secretory carcinoma (MASC), which was described by our group as a new salivary tumor entity characterized by translocation t(12;15)(p13;q25) resulting in ETV6-NTRK3 fusion. Another novel observation is a discovery of ETV6-RET fusion in a subset of MASC cases. Further, the first two MASCs of nasal mucosa origin have been described. Third part consists...

Marker assisted selection in hybrid breeding of oil seed rape

Esta pesquisa busca, tendo como eixo principal Chris Marker e o filme Le fond de lair est rouge, fazer uma retrospectiva histórica dos principais debates na experiência do cinema-militante francês. Com um caráter introdutório e a partir daí construir alguns apontamentos iniciais para uma interpretação crítica do filme. Através desta aventura político-cinematográfica comentar um fragmento do que se oculta atrás das barricadas da memória. / This research aims, having as an leit-motif Chris Marker and the film Le fond de l\'air est rouge, making a historical retrospective of the major debates on the experience of French militant cinema, introductory in nature and serving as first notes to a critical interpretation of the film. Through this cinematics and politics adventure it trys to make a comment on a fragment of what is hidden behind the barricades of memory.

Chris Marker é um cineasta que realizou documentários políticos pouco convencionais ao longo de quase sessenta anos de carreira. Depois de uma militância ativa e inserida no coração de acontecimentos cruciais na França e na Europa, e de uma carreira literária como editor, ensaísta e romancista, natural que seus filmes, vistos isoladamente, provoquem as mais equivocadas interpretações. Esta pesquisa procura, através de um levantamento de seus filmes e escritos, dos debates que foram se travando sobre a vida nacional francesa e mundial, sempre retomando os fios dos acontecimentos decisivos do período do Front Populaire (1936), da ocupação da França pelos nazistas e das lutas de Resistência buscar uma interpretação para muitos dos aspectos aparentemente desconcertantes de sua filmografia. Ao longo dos capítulos a pesquisa aborda, a partir de documentação esparsa em textos, declarações, debates, frases de filmes, os elementos biográficos \"enigmáticos\" de que se tem conhecimento, dada a discrição do cineasta sobre a sua pessoa. Em seguida o momento crucial da entrada de Marker, com 16 anos, no liceu em Paris e turbulências do ano de 1936, na França, discorre sobre o Front Populaire. Depois foca o nascimento de uma corrente, da qual Chris Marker participa, influenciada pela filosofia personalista de Emmanuel Mounier; e depois sua passagem pela revista Esprit e posteriormente a sua integração nas lutas da Resistência. Seguindo os passos do futuro cineasta, aborda o impacto da Resistência na vida militante e a formação dos cineclubes no meio operário com a Associação Peuple et Culture. Toda esta trajetória é permeada por comentários e análises de cenas dos futuros documentários. Por fim a pesquisa, aborda a problemática do cinema militante, analisando L\'ambassade (1973), filme de solidariedade com a Unidade Popular chilena e contra o golpe de Pinochet e o curta sobre o editor François Maspero. Os últimos percalços de nosso percurso busca construir um debate sobre A. Medvedkine e V. Maiakóvsky e a profanação da arte moderna, procurando investigar como na obra de Chris Marker coincidem cinema militante, cinema experimental, cinema ensaio e cinema documentário. / Chris Marker is an intriguing filmmaker who produced unconventional political documentaries over almost sixty years. After an active militancy, and inserted in the heart of crucial events in France and Europe, and working on a literary career as an editor, essayist and novelist, it is natural that his films, viewed in isolation, could cause the most equivocal interpretations. This research seeks, through a detailed analyses of his films and writings, to work with the debates that were important on the French national and global life of his time. Always thinking about the decisive events of the Front Populaire in the period (1936), the occupation of France by the German Nazis and the participation of Marker in the struggles of the Resistance. All of this puzzeled elements seek an interpretation for many of the seemingly confusing aspects of his filmography. Throughout the chapters of this research, we seek to approach, with this documentation, texts, statements, debates, films phrases, the enigmatic biographical elements of his uncanny formation. Marker is known by the discretion about himself. Working on his years of youth and formation, we see that when aged 16, in high school in Paris and the 1936 year in France, discussing at length the Front Populaire, we seek to work about Chris Marker influence by the personalist philosophy of Emmanuel Mounier and then by Esprit and later in it\'s integration in the struggles of resistance. Following in the footsteps of the filmmaker, this work discusses the impact of this years in his militant life, including the training of workers film clubs. All this history is permeated by scenes and debates of his future documentaries. Finally, the research addresses the issue of militant cinema, analyzing L\'ambassade (1973), the solidarity with the Chilean Popular Unity and the struggle against the totalitarian latin american dictatorships, and a short film-portrait of the editor Maspero. We end our research with a debate on A. Medvedkine and V. Mayakovsky and the profanation of modern art, trying to investigate how the work of Chris Marker coincide with militant cinema, experimental cinema, film essay and documentary cinema.

Chris Marker, (1921-2012) qui photographie et filme des lieux divers dans le monde entier, avait pour thème de prédilection la ville. En effet, ce lieu de circulation et de mobilité, dépassant toutes les clôtures, se prête particulièrement aux œuvres markériennes, caractérisées par l’entrecroisement de différents espace-temps, et par l’expérience de l’altérité. En étant à la fois cinéaste et voyageur, les images de la ville capturées par Marker se caractérisent par le déplacement, en particulier par l’expérience de la flânerie, qui constitue un élément essentiel de la réflexion philosophique sur la ville moderne de Walter Benjamin (1892-1940). Pour cette raison, cette thèse est consacrée à l’analyse des œuvres de Marker autour du thème de la flânerie. Ainsi, au cours de trois parties, nous travaillerons des concepts reliées à la flânerie : le seuil, l’allégorie, et le chiffonnier. Ces travaux thématiques nous aideront à comprendre la stratification complexe de l’espace-temps, le caractère transitoire, et l’art de l’assemblage dans les images markériennes. Ces recherches sont finalement élargies à la notion de la navigation comme version renouvelée de flânerie, pour analyser l’espace de L’Ouvroir, le monde virtuel crée sur Second Life par Marker dans sa dernière période. Par conséquence, à la lumière des problématiques abordées par la flânerie, on comprend que la création artistique de Marker est fondée sur la quête continuelle de nouvelles expérience visuelles qui remettent en question la modernité et la représentation cinématographique. / Chris Marker (1921-2012) is a filmmaker, who took photos and filmed various places by travelling all over the world. The city had been one of the important subjects for Marker’s works. Suppose every metropolis is essentially a limitless place, filled with flow and mobility, Marker’s works, described as intersection of different time and space and “otherness,” can be said that they inherit the nature of metropolis. Being filmmaker and traveler, Marker’s images of city are often characterized by “moving”, particularly by the experience of flânerie (stroll), which constitutes element of philosophical reflection of modern city by Walter Benjamin (1892-1940). In order to make this point clear, this dissertation deals with the films of Marker using Benjamin’s concept flânerie, as a major analyzing concept. Using four key concepts, threshold, allegory, and rag-and-bone man related to the experience of flânerie, this dissertation dissects the complex stratification of “space-time”, the “ephemeral character”, and the “art of collecting” in the images of Marker. Also, bringing the new concept “navigation”, as a renewed version of flânerie, the space of L’Ouvroir, the territorialities of Second Life, created in Marker’s last years of his life is analyzed. As a result, in the light of the issues raised by flânerie, we understand that Chris Marker problematizes the modernity and the system of cinematic representation based on the continual search for new visual experience.

The study of fungal diversity may lead to many fundamental discoveries and conclusions. Molecular genetics, and particularly high throughput sequencing methods using short DNA fragments as barcodes, has recently experienced a boom. The most frequently used marker for fungal research is the partial region of nuclear ribosomal DNA called ITS (Internal Transcribed Spacer). It occurs in the form of tandem repetitions of up to 200 copies. This fact greatly simplifies its amplification from the environment but also introduces some negatives. One of them can be an existence of intragenomic and intraspecific variability which confounds diversity estimates by exaggerating the real number of species. Using alternative low-copy markers can easily prevent these problems. In this study EF-1α and RPB2 protein- coding genes were compared with traditionally used ITS1 and ITS2 markers. An artificial mock community was created by blending genomic DNA of different fungal lineages. The community was sequenced for all markers and the data were processed according to guidelines commonly used in environmental studies. The results show that ITS2 is unequivocally a more suitable marker for environmental studies than other compared markers. The average coefficient of overestimation was deemed to be approximately two for ITS1, ITS2,...

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Supernumerary marker chromosomes (sSMCs) are a relatively rare cytogenetic phenomenon. Their laboratory examination is often difficult, and the clinical interpretation is even more challenging. The main reason is that most sSMC carriers have no clinical manifestations. The chromosome origin and exact range of the aberration are very important, as well as the fact that sSMCs are often found in mosaics that can strongly influence both the phenotype and the interpretation of result. Prenatal sSMC finding is one of the most challenging situations in both clinical and laboratory genetics. This work deals with the investigation process of sSMC carriers using molecular cytogenetic techniques, especially fluorescence in situ hybridization (FISH). We investigated a total of 67 families collected both prospectively and retrospectively, and we found 70 unique sSMCs in a total of 74 individuals. Six cases were familial and in three cases two sSMCs were found in one individual. According to the initial karyotype finding, the cases were divided into two groups, sSMCs supernumerary to a normal karyotype (group A) and sSMCT s supernumerary to the Turner karyotype (group B). The chromosomal origin was successfully determined in 88,6 % sSMCs. In group A the most common findings were sSMCs derived from chromosome 15,...

Augmented Reality är ett brett fält med många olika användningsområden. Det hargjorts flera studier om hur AR kan hjälpa oss att lösa olika arbetsuppgifter på ett effektivare sätt samt att det ingjuter självsäkerhet hos användaren som utför en uppgiftmed hjälp av AR. AR har även letat sig in i tillverkningsindustrin som gör det möjligtför ingenjörer att följa en arbetsprocess med hjälp av AR.Kretskort som är en del av ett system som gör det möjligt för oss att exempelvis ha tillgång till datorer och mobiltelefoner och behöver ibland felsökas. Elektronikingenjörerbehöver ibland identifiera testpunkter och komponenter i den krets på kretskortet somska felsökas. Detta kan underlättas med AR. I denna studie kommer ett experimentatt genomförs för att se om kretskort kan lämpa sig väl som ett Marker-based target.Marker-based target är en bild som möjliggör objektspårning för exempelvis en Head-mounted display, i detta fall en HoloLens. Här efter kommer Marker-based target attbenämnas som mönsterbaserad bild.Experimentet kommer att genomföras med en testgrupp om 10 personer där samtliga kommer att få testa att använda en HoloLens i syftet att lokalisera komponentereller testpunkter på ett kretskort. Detta kommer sedan att jämföras med en traditionell metod genom att identifiera samma komponenter eller testpunkter med en PDF.Testpersonerna kommer även att få svara på en enkät som tittar på om denna metodlämpar sig för att identifiera komponenter med hjälp av AR. En applikation kommeratt skapas som möjliggör att implementera metoden och att testpersonerna kommerkunna använda ett gränssnitt i lokaliseringsprocessen. Resultatet visar att med HoloLensen i jämförelse med traditionella metoden är nästan likvärdig tidsmässigt för attlokalisera komponenter men att vanan av användandet av HoloLensen hade inflytandepå resultatet. / Augmented Reality is an broad field with many different areas of applications. Therehave been several studies on how AR can help us solve various tasks in a more efficientway and that it instills self-confidence in the user who performs a task with the help of AR. AR has also found its way into the manufacturing industry, which enables engineers to follow a work process with the help of AR. For example circuit boards that arepart of a system that makes it possible for us to have access to computers and mobilephones, does sometimes need to undergo troubleshooting process by engineers duringmanufacture.Electronics engineers sometimes need to identify test points and components on thecircuit board that needs troubleshooting. AR can help in this process. In this study, anexperiment will be conducted to see if circuit boards can be well suited as a marker-based target. Marker-based target is an image that enables object tracking for examplewith a Head-mounted display, in this case a HoloLens.The experiment will be conducted with a test group of 10 people where all will beallowed to test a HoloLens in order to locate components or test points on a circuitboard. This method will then be compared to a traditional method by identifying thesame components or test points with a PDF. The test persons will also have to answer aquestionnaire that looks at whether this method is suitable for identifying componentsusing AR. An application will be created that implements the method and that the testpersons will be able to use in the localization process. The results show that the traditional method in comparison with the HoloLens is equivalent for locating components,but the habit of using HoloLens had an influence on the result.

Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.