|
|
High-performance exploration and querying of selected multi-dimensional spaces in life sciences
Kratochvíl, Miroslav ; Bednárek, David (advisor) ; Glaab, Enrico (referee) ; Svozil, Daniel (referee)
This thesis studies, implements and experiments with specific application-oriented approaches for exploring and querying multi-dimensional datasets. The first part of the thesis scrutinizes indexing of the complex space of chemical compounds, and details a design of high-performance retrieval system for small molecules. The resulting system is then utilized within a wider context of federated search in heterogeneous data and metadata related to the chemical datasets. In the second part, the thesis focuses on fast visualization and exploration of many-dimensional data that originate from single- cell cytometry. Self-organizing maps are used to derive fast methods for analysis of the datasets, and used as a base for a novel data visualization algorithm. Finally, a similar approach is utilized for highly interactive exploration of multimedia datasets. The main contributions of the thesis comprise the advancement in optimization and methods for querying the chemical data implemented in the Sachem database cartridge, the federated, SPARQL-based interface to Sachem that provides the heterogeneous search support, dimensionality reduction algorithm EmbedSOM, design and implementation of the specific EmbedSOM-backed analysis tool for flow and mass cytometry, and design and implementation of the multimedia...
|
|
|
High-performance exploration and querying of selected multi-dimensional spaces in life sciences
Kratochvíl, Miroslav ; Bednárek, David (advisor) ; Glaab, Enrico (referee) ; Svozil, Daniel (referee)
This thesis studies, implements and experiments with specific application-oriented approaches for exploring and querying multi-dimensional datasets. The first part of the thesis scrutinizes indexing of the complex space of chemical compounds, and details a design of high-performance retrieval system for small molecules. The resulting system is then utilized within a wider context of federated search in heterogeneous data and metadata related to the chemical datasets. In the second part, the thesis focuses on fast visualization and exploration of many-dimensional data that originate from single- cell cytometry. Self-organizing maps are used to derive fast methods for analysis of the datasets, and used as a base for a novel data visualization algorithm. Finally, a similar approach is utilized for highly interactive exploration of multimedia datasets. The main contributions of the thesis comprise the advancement in optimization and methods for querying the chemical data implemented in the Sachem database cartridge, the federated, SPARQL-based interface to Sachem that provides the heterogeneous search support, dimensionality reduction algorithm EmbedSOM, design and implementation of the specific EmbedSOM-backed analysis tool for flow and mass cytometry, and design and implementation of the multimedia...
|
|
|
Hematopoiesis in the models of zebrafish and medaka as a recipient for human HSC xenograft
Pravcová, Naďa ; Drbal, Karel (advisor) ; Svoboda, Ondřej (referee)
Danio rerio (zebrafish) and Oryzias latipes (medaka) have recently become popular model organisms to study hematopoiesis. These model organisms present several advantages in comparison to other commonly used models, the most common being Mus musculus (mouse). The advantages are shorter generation time, large offspring production, frequent spawning, external fertilization and development, the optical transparency of embryos amenable to genetic manipulation on the background of vast numbers of transgenic lines (mainly in zebrafish) and inbred strains (in medaka). Moreover, most of the mechanisms behind zebrafish and medaka hematopoiesis are conserved in higher vertebrates. Most importantly, the optical transparency in early development and in adult mutant transparent strains allows for observation of hematopoietic stem cell (HSC) development in vivo. Therefore, it is possible to generate humanized fish using xenotransplanted human HSCs for studies of the engraftment, differentiation, and trafficking of human HSC in vivo. Currently, the most popular organism for human HSC xenotransplantation is mice. This model system is not suitable for in vivo imaging of HSC engraftment. Moreover, a prior immunodepletion step is necessary. The process of immunodepletion includes genetic manipulation or irradiation...
|
|
|
Morphological variability of birch genus (Betula L.) in chosen regions of the Czech Republic with a focus on tetraploid taxa
Linda, Rostislav ; Kuneš, Ivan (advisor) ; Jana, Jana (referee)
The aim of this work is to propose reliable method for distinguishing between diploid (2n) and tetraploid (4n) taxa of the genus Betula L., based on leaf measurements. These measurements are realized by common tools, such as ruler or protractor. Main advantage of these methods is that they can be applied even in the field. The further aim of work is to describe and evaluate genetic variability within tetraploid taxa, whose taxonomic relationships are still unclear and under discussions.
For statistical analysis, 97 individuals from 6 localities within Šumava region were selected and 4 leaves from every individual were analysed. In total, 20 parameters were measured on every leaf (16 quantitative and 4 qualitative). Each individual was also analysed by flow cytometry method to determine real genome size (ploidy).
Differences in selected parameters between individuals with different ploidy were statistically tested. Significant results were observed in 12 of 16 quantitative and 2 of 4 qualitative parameters. For real ploidy prediction, the classification function was designed, whose reliability was 96 % for the primary data.
The reliability of classification function was verified on samples from three different regions within the Czech Republic and compared with functions suggested by other authors. Function designed in this work was able to correctly determine real ploidy in 89 %, which is the most of all compared functions.
Genetic variability, especially within tetraploid taxa is mentioned in relation to other author's previous studies. Distinguishing between B. pubescens and B. carpatica was not possible using selected genetic markers. Genetic conformity of these taxa is also mentioned in publications of foreign authors, as contrasted to Czech literature, which generally distinguishes B. pubescens and B. carpatica as separated species.
|
|
| |
guest ::
