Parallelization of the raytracing method I

Zkoumané implementace metod vykreslování scény pomocí sledování paprsků běží na paralelní architektuře GPU. Zanalyzoval jsem možné akcelerační struktury a otestoval implementaci různými scénami. Porovnal jsem CPU a GPU implementace a přehodnotil výběr programu MATLAB.Examined raytracing algorithms run on highly parallel GPU architecture. I implemented one acceleration structure after analyzing different options. I experimented on a few scenes with different complexity and compared CPU and GPU implementations. I reevaluated the choice of MATLAB

Evolutionary hypotheses of obesity origin

Obesity is a major social, ecological, economic and health problem of today's civilization. Humans evolved to adapt to a different environment than the one they live in today, had more exercise and consumed natural food sources. The imbalance in energy intake and expenditure that we observe in today's human populations is the most likely cause of obesity. However, this work will deal with a less discussed view of the origin of obesity, namely the possible explanation of the origin of obesity with evolutionary hypotheses. The work will also try to evaluate and discuss, based on a comparison of the available literature, whether these hypotheses could really clarify the origin of obesity at the global level. In the beginning of the thesis, we present the problem of obesity, its prevalence in the population and comorbidities associated with obesity. The next section describes the diagnosis of obesity, followed by a section on the history of obesity. The main part is devoted to the evolutionary hypotheses of obesity, namely the adaptation to frugality hypothesis, the genetic drift hypothesis and then other ecological- behavioral hypotheses and their evaluation. In conclusion, the work summarizes that the described hypotheses could be useful for clarifying the difference in obesity prevalence between...Obezita je velkým sociálním, ekologickým, ekonomickým a zdravotním problémem dnešní civilizace. Lidé se evolučně přizpůsobili na jiné prostředí, než ve kterém žijí dnes, měli více pohybu a konzumovali přirozené zdroje potravy. Nerovnováha v příjmu a výdeji energie, kterou pozorujeme u dnešních lidských populací je nejvíce skloňovanou příčinou obezity. Tato práce se však bude zabývat méně diskutovaným pohledem na vznik obezity, a to na možné vysvětlení vzniku obezity evolučními hypotézami. Práce se pokusí rovněž zhodnotit a diskutovat, na základě porovnání dostupné literatury, zdali by mohly tyto hypotézy skutečně objasnit původ obezity na globální úrovni. V úvodu práce představujeme problematiku obezity, její prevalenci v populaci a komorbidity s obezitou spojené. V další části je popsána diagnostika obezity, po které následuje část o historii obezity. Hlavní část je věnována evolučním hypotézám vzniku obezity, jmenovitě hypotézám adaptace na šetrnost, hypotéze genetického driftu a poté ostatním ekologicko-behaviorálním hypotézám a jejich zhodnocení. V závěru, práce shrnuje, že popsané hypotézy by mohli být užitečné pro objasnění rozdílu prevalence obezity mezi populacemi a studiu obezity v jednotlivých populací, nikoli však pro objasnění obezity v globálním měřítku.Katedra antropologie a genetiky člověkaDepartment of Anthropology and Human GeneticsFaculty of SciencePřírodovědecká fakult

Metformin treatment for diabetes mellitus correlates with progression and survival in colorectal carcinoma

BACKGROUND: Diabetes mellitus is unfavorably associated with cancer risk. The purpose of this multi-disciplinary project was to evaluate a possible association of diabetes mellitus and other comorbidities and their treatment with progression of colorectal cancer. PATIENTS AND METHODS: We investigated the correlation between pathological characteristics and clinical course, including comorbidities in 1004 Czech patients diagnosed and surgically treated for colorectal adenocarcinoma (CRC) between 1999 and 2016. RESULTS: In our data set, CRC patients treated with metformin due to coexisting diabetes mellitus type 2 (T2DM) developed fewer distant metastases which clinically correlates with slower CRC progression. Survival in metformin subgroup was longer, particularly in men with CRC. Osteoporosis may be a negative factor of survival in CRC patients. CONCLUSIONS: Our findings also indicate that aging, higher tumor grade and TNM stage, coexistence of selected endocrine disorders, and metabolic abnormalities may change the tumor microenvironment and impact survival in colorectal cancer, although mechanism of these observations yet to be explained. Patients with diabetes mellitus type 2 treated with metformin may represent the altered microenvironment with specifically tuned metabolic molecular responses and with various epigenetic characteristics. More awareness and increased understanding of the mechanisms underlying the positive effect of metformin on patients' survival could offer insight into new treatment methods and permit more individualized treatment plans.Web of Science13239238

CK20 Positive Large-cell Neuroendocrine Carcinoma Presenting with Skin Metastases

We present a case of cytokeratin (CK) 20-positive large cell neuroendocrine carcinoma (LCNEC) presenting with multiple skin metastases as the primary manifestation. The patient was a 55-year-old man who presented with a one- month history of subcutaneous skin colored nodules of various sizes on his trunk. Pathologic examination of the skin revealed a nested and solid proliferation of large undifferentiated cells with vesicular nuclei and prominent nucleoli. Tumor cells were found to be immunohistochemically positive for CK 20, chromogranin A, synaptophysin, and CD56. Based on these features, the tumor was diagnosed as a large cell neuroendocrine carcinoma with multiple skin metastases. Computed tomographic (CT) imaging found metastatic foci in the liver, pleura, bone, and lymph nodes. We were unable to identify the primary site of origin. To the best of our knowledge, this is the first case of a large cell neuroendocrine carcinoma with a primary manifestation of multiple skin metastases

Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins

During mitosis, chromosomes are highly condensed and transcription is silenced globally. One explanation for transcriptional repression is the reduced accessibility of transcription factors. To directly test this hypothesis and to investigate the dynamics of mitotic chromatin, we evaluate the exchange kinetics of several RNA polymerase I transcription factors and nucleosome components on mitotic chromatin in living cells. We demonstrate that these factors rapidly exchange on and off ribosomal DNA clusters and that the kinetics of exchange varies at different phases of mitosis. In addition, the nucleosome component H1c-GFP also shows phase-specific exchange rates with mitotic chromatin. Furthermore, core histone components exchange at detectable levels that are elevated during anaphase and telophase, temporally correlating with H3-K9 acetylation and recruitment of RNA polymerase II before the onset of bulk RNA synthesis at mitotic exit. Our findings indicate that mitotic chromosomes in general and ribosomal genes in particular, although highly condensed, are accessible to transcription factors and chromatin proteins. The phase-specific exchanges of nucleosome components during late mitotic phases are consistent with an emerging model of replication independent core histone replacement

Ki-67 is a PP1-interacting protein that organises the mitotic chromosome periphery

Copyright @ 2014 Booth et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.When the nucleolus disassembles during open mitosis, many nucleolar proteins and RNAs associate with chromosomes, establishing a perichromosomal compartment coating the chromosome periphery. At present nothing is known about the function of this poorly characterised compartment. In this study, we report that the nucleolar protein Ki-67 is required for the assembly of the perichromosomal compartment in human cells. Ki-67 is a cell-cycle regulated protein phosphatase 1-binding protein that is involved in phospho-regulation of the nucleolar protein B23/nucleophosmin. Following siRNA depletion of Ki-67, NIFK, B23, nucleolin, and four novel chromosome periphery proteins all fail to associate with the periphery of human chromosomes. Correlative light and electron microscopy (CLEM) images suggest a near-complete loss of the entire perichromosomal compartment. Mitotic chromosome condensation and intrinsic structure appear normal in the absence of the perichromosomal compartment but significant differences in nucleolar reassembly and nuclear organisation are observed in post-mitotic cells

A FRAP model to investigate reaction-diffusion of proteins within a bounded domain: a theoretical approach

Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been used over the past three decades to measure the mobility of macromolecules and protein transport and interaction with immobile structures inside the cell nucleus. A theoretical model is presented that aims to describe protein transport inside the nucleus, a process which is influenced by the presence of a boundary (i.e. membrane). A set of reaction-diffusion equations is employed to model both the diffusion of proteins and their interaction with immobile binding sites. The proposed model has been designed to be applied to biological samples with a Confocal Laser Scanning Microscope (CLSM) equipped with the feature to bleach regions characterised by a scanning beam that has a radially Gaussian distributed profile. The proposed model leads to FRAP curves that depend on the on- and off-rates. Semi-analytical expressions are used to define the boundaries of on- (off-) rate parameter space in simplified cases when molecules move within a bounded domain. The theoretical model can be used in conjunction to experimental data acquired by CLSM to investigate the biophysical properties of proteins in living cells.Comment: 25 pages. Abstracts Proceedings, The American Society for Cell Biology, 46th Annual Meeting, December 9-13, 2006, San Dieg