Bioinformatics Tool for Prediction of Protein Solubility

Abychom dosáhli levnější a efektivnější výroby proteinů, musíme být schopni predikovat, zda budou proteiny rozpustné. V této práci se zabýváme vytvořením bioinformatických datových sad na základě databází Target Track a eSol, testováním příznaků používaných v existujících nástrojích zabývajících se rozpustností proteinů a tvorbou nového prediktoru. Přestože se nám nedaří vytvořit efektivní nástroj na predikci rozpustnosti proteinů, zjišťujeme, že ve většině případů staré příznaky na nové datové sadě nekorelují s rozpustností proteinů tak silně, jako tomu je u starších a menších datových sad.To achieve cheaper and more efficient protein production, we must be able to predict protein solubility. In this thesis, we describe creation of bioinformatic data sets based on Target Track and eSol databases, we test the features used in existing protein solubility prediction tools and create a new predictor. Even though we fail to create an effective prediction tool we find out that in most cases the old features tested on the new data do not correlate with protein solubility as strongly as others repot in older and smaller datasets.

Proposal of electrical equipment for soaking and drying cores for making castings

Tato diplomová práce řeší návrh zařízení na máčení a sušení jader pro tvorbu odlitků ve slévárně ve Velké Británii. Je zde ucelený náhled na systém technických norem ČSN a srovnání s britským systémem norem British standards. Ve druhé části práce je řešen podrobný návrh zařízení, včetně specifikace řídicího systému, specifikace jednotlivých napájecích a řídících kabelů a jednotlivých technologických celků. Celá projektová dokumentace je přiložena jako neoddělitelná příloha této diplomové práce.This diploma thesis deals with proposal of electrical equipment for soaking and drying cores for making castings at foundry in a Great Britain. It brings look at system of technical norms ČSN and it compares it with british system of technical norms British standards. The second part of this thesis contains detailed proposal of this equipment, including specification of control system, specification of power supply cables and control cables and particular technological units. The whole project documentation is enclosed as an inseparable attachment of this diploma thesis.

Excavator Wheel Drive Reconstruction.

Import 05/08/2014V této práci je popsán pomocný pohon kolesa rypadla a možnost jeho rozběhu softstartérem a frekvenčním měničem. V první části je probrán asynchronní motor s kotvou nakrátko, jeho popis a princip funkce. Další části se věnují softstartéru a frekvenčnímu měniči, jejich popisu, funkcím a možnostem řízení. Dále je zde provedeno měření jejich vlivu na síť. Poslední část je věnována návrhu rekonstrukce pohonu pro napájení s frekvenčním měničem.This thesis describes the auxiliary drive wheel excavators and the possibility of starting the softstarter and frequency converter. In the first part of the document the asynchronous motor with squirrel cage is discussed, its description and function. Other parts of the document are devoted to the soft starter and frequency converter, their description, function and management options. Furthermore, there is performed measurement of their effect on the network. The last section is devoted to the design of the reconstruction drive with the frequency converter.410 - Katedra elektroenergetikyvýborn

Arc optical diagnostics

Cílem bakalářské práce je rozdělení jednotlivých druhů elektrických výbojů, vysvětlení ionizace v plazmatu elektrického oblouku a objasnění energetické bilance uvnitř plazmatu. Elektrický oblouk představuje nežádoucí, těžko předvídatelný jev vyskytující se ve spínacích přístrojích při spínání a rozpínání obvodu. Dále jsou uvedeny starší metody vyhodnocování snímků pořízených vysokorychlostní kamerou. Na základě těchto snímků jsou vytvářeny ekvidenzity a ekvidenzitogramy sloužící k monitorování pohybu oblouku ve zhášecí komoře. Druhá část zahrnuje popis pokusu provedeného v laboratoři a popis vysokorychlostní kamery použité při pokusu. Dále je uvedena moderní metoda zpracování digitálního snímku pomocí výpočetního programu Matlab. Z pořízených snímků byl Matlabem vytvořen ekvidenzitogram znázorňující různé hladiny intenzity vyzařování.The aim of this bachelor thesis is to sort out the individual types of electric discharges, explain the ionization inside the plazma of the electric arc and the elucidation of the energetic balance inside the plazma. The electric arc is an undesirable and hardly predictable phenomenon occurring in switching devices during switching on and switching off the electric circuit. Some older methods of image processing obtained by a high-speed camera are also mentioned. Based on the images obtained from the camera, it is possible to make an equidensity or an equidensitogram that is used to monitor the arc in a quenching chamber. The second part includes the description of an experiment performed in a laboratory and the description of the high-speed camera used during this experiment. A modern method of the image processing using software Matlab is also described. An equidensitogram showing different levels of radioation was made in Matlab from the obtained images.

Plasma proteome changes associated with refractory cytopenia with multilineage dysplasia

<p>Abstract</p> <p>Background</p> <p>Refractory cytopenia with multilineage dysplasia (RCMD) is a subgroup of myelodysplastic syndrome (MDS), which belongs to oncohematological diseases, occurring particularly in elderly patients, and represents a heterogeneous group of bone marrow diseases. The goal of this study was to look for plasma proteins that changed quantitatively or qualitatively in RCMD patients.</p> <p>Results</p> <p>A total of 46 plasma samples were depleted, proteins were separated by 2D SDS-PAGE (pI 4-7), and proteomes were compared using Progenesis SameSpots statistical software. Proteins were identified by nanoLC-MS/MS. Sixty-one unique, significantly (p < 0.05, ANOVA) different spots were found; proteins in 59 spots were successfully identified and corresponded to 57 different proteins. Protein fragmentation was observed in several proteins: complement C4-A, complement C4-B, inter-alpha-trypsin inhibitor heavy chain H4, and endorepellin.</p> <p>Conclusions</p> <p>This study describes proteins, which change quantitatively or qualitatively in RCMD patients, and represents the first report on significant alterations in C4-A and C4-B complement proteins and ITIH4 fragments in patients with MDS-RCMD.</p

Computation of Stackelberg Equilibria of Finite Sequential Games

The Stackelberg equilibrium solution concept describes optimal strategies to commit to: Player 1 (termed the leader) publicly commits to a strategy and Player 2 (termed the follower) plays a best response to this strategy (ties are broken in favor of the leader). We study Stackelberg equilibria in finite sequential games (or extensive-form games) and provide new exact algorithms, approximate algorithms, and hardness results for several classes of these sequential games

GWAS in practical cattle breeding in Czech Republic, single step method, genetic progress

Development of genetic evaluation of animals is permanent process. It was going from estimated breeding value (EBV) calculated by CC-test, across a BLUP – animal model and RR-TDM, to the genomic enhanced breeding value (GEBV) using genetic markers. Methods of genetic evaluation become a part of marketing strategies of insemination companies. Therefore all countries and association of breeders seek to be compatible with others. Now we are in a period of massive global implementation of genomic evaluation, which combines traditional BLUP with huge quantity of genetic SNP markers. Multi-step procedures are now usual in practice, which work with deregressed proofs. Development of methods attained to the single-step procedure (ssGBLUP) which overcomes some difficulties of previous methods, improves reliabilities of evaluation and compares all animals, genotyped and ungenotyped, in entire nation-wide population. Genomic evaluation influence above all young genotyped animals. In Czech Republic single-step procedure is routinely used for national evaluation of milk, linear type traits, reproduction and longevity. GEBVs are accompanied by genomic reliabilities. Genetic trends over last 20 years are in some traits different for genomic evaluation compared to traditional BLUP evaluation, although input data and genetic parameters (heritability) are the same and genotyped animals were only small proportion from entire evaluated population. Differences in genetic trends increase mainly in new batches of animals. Reason of it could be in the changed variability of breeding values and “genomic correction” of relationship between animals, which is expanded from genotyped animals to others individuals in a population. Keywords: genomic breeding value, single-step, genomic relationship, genetic trend, SNP ReferencesBauer, J. et al. (2014) Approximation of the reliability of single-step genomic breeding values for dairy cattle in the Czech Republic. Anim. Sci. 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(2012) Comparison on genomic predictions using three GBLUP methods and two single step blending methods in the Nordic Holstein population. Genet. Sel.Evol. 44, pp. 8.Legarra A., Aguilar I. and Misztal, I. (2009) A relationship matrix including full pedigree and genomic information. J. Dairy Sci., 92, pp. 4656-4663.Masuda, Y. et al. (2016) Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals. J. Dairy Sci., 99, pp. 1968-1974.Mendel, G.J. (1866) Versuche über Pflanzen-Hybriden. Verh. Naturforsch. Ver. Brünn 4, pp. 3–47 (1901, J. R. Hortic. Soc. 26, pp. 1–32).Meuwissen, T.H.E., Hayes, B.J. and Goddard, M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, pp. 1819–1829.Misztal, I., Legarra A. and Aguilar, I. (2009) Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J. Dairy Sci., 92, pp. 4648–4655.Misztal, I. et al. (2013) Methods to approximate reliabilities in single-step genomic evaluation. J. Dairy Sci., 96, pp. 647-654.Pešek, P., Přibyl, J. and Vostrý, L. (2015) Genetic variances of SNP loci for milk yield in dairy cattle. J. Appl. Genet., 56, pp. 339-347.Přibyl, J. et al. (2014) Domestic and Interbull information in the single step genomic evaluation of Holstein milk production.  Czech J. Anim. Sci., 59, pp. 409-415.Přibyl, J. et al. (2015) Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values. Animal, 9, pp. 1635-1642.VanRaden, P.M. (2008) Efficient methods to compute genomic predictions. J. Dairy Sci., 91, pp. 4414–4423.VanRaden, P.M. et al. (2011) Genomic evaluations with many more genotypes. Genet. Sel.Evol. 43, pp. 10.Wright, S. (1921) Systems of mating. Genetics. 6, pp. 111-178.Zavadilová, L. et al. (2014) Single-step genomic evaluation for linear type traits of Holstein cows in Czech Republic. Anim. Sci. Papers and Reports vol. 32, pp. 201-208.

Synthesis, structure, and opto-electronic properties of organic-based nanoscale heterojunctions

Enormous research effort has been put into optimizing organic-based opto-electronic systems for efficient generation of free charge carriers. This optimization is mainly due to typically high dissociation energy (0.1-1 eV) and short diffusion length (10 nm) of excitons in organic materials. Inherently, interplay of microscopic structural, chemical, and opto-electronic properties plays crucial role. We show that employing and combining advanced scanning probe techniques can provide us significant insight into the correlation of these properties. By adjusting parameters of contact- and tapping-mode atomic force microscopy (AFM), we perform morphologic and mechanical characterizations (nanoshaving) of organic layers, measure their electrical conductivity by current-sensing AFM, and deduce work functions and surface photovoltage (SPV) effects by Kelvin force microscopy using high spatial resolution. These data are further correlated with local material composition detected using micro-Raman spectroscopy and with other electronic transport data. We demonstrate benefits of this multi-dimensional characterizations on (i) bulk heterojunction of fully organic composite films, indicating differences in blend quality and component segregation leading to local shunts of photovoltaic cell, and (ii) thin-film heterojunction of polypyrrole (PPy) electropolymerized on hydrogen-terminated diamond, indicating covalent bonding and transfer of charge carriers from PPy to diamond