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Optimizations and applications of non-linear spectral unmixing in flow cytometry
Nemec, Matěj ; Musil, Jan (advisor) ; Stuchlý, Jan (referee)
Recent advances in flow cytometry techniques enable high-throughput single-cell experiments with extensive marker sets. In order to leverage this technology the measured signal must be unmixed to recover interpretable re- sults. Current approaches to unmixing typically leverage linear deconvolution algorithms such as fitting by ordinary least squares method, that tend have issues dealing with various noise sources inherit to the data collection pro- cess. This thesis evaluates the performance of a novel non-linear approach of unmixing called nougad. For the evaluation, we have generated realistic arti- ficial data with known ground truth for testing, implemented multi-threaded version of nougad and tuned its hyperparameters using Bayesian optimiza- tion, and collected several performance metrics of nougad and the other algorithms on the testing datasets. The results show that nougad is able to outperform the tested linear algorithms making this non-linear method more suitable for practical applications and a good candidate for further refinement and optimization efforts. 1
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Characterization of biological and functional features of a new type of CD27- memory B lymphocytes.
Bajzíková, Martina ; Růžičková, Šárka (advisor) ; Šinkora, Marek (referee)
The increased frequencies of two novel B cell populations defined as IgM+ CD19+ CD27- CD21low CD38low CD24+ and IgM+ CD19+ CD27- CD21low CD38low CD24- in peripheral blood of patients with common variable immunodeficiency (CVID) compared to healthy donors were found. The aim was to search for such B cells in patients with rheumatoid arthritis (RA) and their further characterization. The production of immunoglobulin (Ig) mRNA in single B cells was analyzed using flow cytometry, single cell sorting and RT-PCR, IgVH-specific PCR, cycle sequencing and statistical analysis. The study was focused on analysis of variable regions of the heavy chains of Igs and significant differences in the usage of VH, DH and JH gene segments, mutational frequencies, distribution of silent and replacement mutations, length and composition of CDR3 regions, clonal relation and RAG gene expression in above mentioned B cell populations were found. Because of lack of the surface CD27 molecule being regarded as marker of B cells that have undergone antigen-driven germinal reactions, analyzed populations were considered as naive. However, the pattern and type of mutations suggested that these cells could represent a new type of differentiated memory/antigen- experienced B lymphocytes (in CVID less maturated) with the likely role in...
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Characterization of biological and functional features of a new type of CD27- memory B lymphocytes.
Bajzíková, Martina ; Růžičková, Šárka (advisor) ; Šinkora, Marek (referee)
The increased frequencies of two novel B cell populations defined as IgM+ CD19+ CD27- CD21low CD38low CD24+ and IgM+ CD19+ CD27- CD21low CD38low CD24- in peripheral blood of patients with common variable immunodeficiency (CVID) compared to healthy donors were found. The aim was to search for such B cells in patients with rheumatoid arthritis (RA) and their further characterization. The production of immunoglobulin (Ig) mRNA in single B cells was analyzed using flow cytometry, single cell sorting and RT-PCR, IgVH-specific PCR, cycle sequencing and statistical analysis. The study was focused on analysis of variable regions of the heavy chains of Igs and significant differences in the usage of VH, DH and JH gene segments, mutational frequencies, distribution of silent and replacement mutations, length and composition of CDR3 regions, clonal relation and RAG gene expression in above mentioned B cell populations were found. Because of lack of the surface CD27 molecule being regarded as marker of B cells that have undergone antigen-driven germinal reactions, analyzed populations were considered as naive. However, the pattern and type of mutations suggested that these cells could represent a new type of differentiated memory/antigen- experienced B lymphocytes (in CVID less maturated) with the likely role in...
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