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Generative Adversarial Networks and Applications in Bioinformatics
KOLESNICHENKO, Nikita
2021 - anglický
Generative Adversarial Networks (GAN) are currently considered a state-of-the-art method for image generation. Recently, Deep Convolutional Generative Adversarial Networks (DCGAN) yielded promising results in protein contact maps generation. The algorithm generated realistic protein structures, which were less erroneous than previously used generative methods. However, DCGAN is notorious for being hard to train due to the limitations of its loss function and complications in optimization. Wasserstein Generative Adversarial Networks (WGAN) was proposed, employing the Wasserstein loss function that stabilizes training and alleviates some of the DCGAN's training problems. In this thesis, a hyperparameter grid search for DCGAN and WGAN was conducted on the CIFAR-10 dataset. Runs with different hyperparameters were compared using Fréchet Inception Distance to determine whether WGAN is more stable than DCGAN. Generative Adversarial Networks (GAN) are currently considered a state-of-the-art method for image generation. Recently, Deep Convolutional Generative Adversarial Networks (DCGAN) yielded promising results in protein contact maps generation. The algorithm generated realistic protein structures, which were less erroneous than previously used generative methods. However, DCGAN is notorious for being hard to train due to the limitations of its loss function and complications in optimization. Wasserstein Generative Adversarial Networks (WGAN) was proposed, employing the Wasserstein loss function that stabilizes training and alleviates some of the DCGAN's training problems. In this thesis, a hyperparameter grid search for DCGAN and WGAN was conducted on the CIFAR-10 dataset. Runs with different hyperparameters were compared using Fréchet Inception Distance to determine whether WGAN is more stable than DCGAN.
Klíčová slova:
generative adversarial networks; WGAN; DCGAN; hyperparameter search; protein contact maps generation; protein design
Plné texty jsou dostupné v digitálním repozitáři JČU.
Generative Adversarial Networks and Applications in Bioinformatics
Generative Adversarial Networks (GAN) are currently considered a state-of-the-art method for image generation. Recently, Deep Convolutional Generative Adversarial Networks (DCGAN) yielded promising ...
Lung Data Analysis With Deep Learning
KESAVAN VIJAYAKUMAR, Harikrishnan
2021 - anglický
Medical images can have extremely high resolutions which cannot be handled properly by typical stateofart machine learning models. In this thesis, I compared the performance of two approaches of multiple instance learning models where the high resolution images are downscaled into smaller patches and low dimensional embedding are calculated using Resnet. Then low dimensional embedding are aggregated using multiple instance learning to attain class labels. The data set for this thesis consisted of high resolution histological slides of human lung which were classified to contain cancer or not. Medical images can have extremely high resolutions which cannot be handled properly by typical stateofart machine learning models. In this thesis, I compared the performance of two approaches of multiple instance learning models where the high resolution images are downscaled into smaller patches and low dimensional embedding are calculated using Resnet. Then low dimensional embedding are aggregated using multiple instance learning to attain class labels. The data set for this thesis consisted of high resolution histological slides of human lung which were classified to contain cancer or not.
Klíčová slova:
CLAM; Multiple instance learning; Lung data analysis
Plné texty jsou dostupné v digitálním repozitáři JČU.
Lung Data Analysis With Deep Learning
Medical images can have extremely high resolutions which cannot be handled properly by typical stateofart machine learning models. In this thesis, I compared the performance of two approaches of ...
Counteracting constitutive activity of Orai1 with an H171Y mutation
MARKO, Ricarda
2021 - anglický
The functions and structures of the Orai1-ANSGA mutation are still not completely known. To further investigate possible changes in pore structure, Orai1 ANSGA and H171Y in combination with different amino acids were used in cysteine-crosslinking studies, to see if the ANSGA and H171Y mutations affect the orientation of pore-lining residues.
Klíčová slova:
Ion channels; Ca2+ channels; Orai1; ANSGA; cysteine-crosslinking; H171Y
Plné texty jsou dostupné v digitálním repozitáři JČU.
Counteracting constitutive activity of Orai1 with an H171Y mutation
The functions and structures of the Orai1-ANSGA mutation are still not completely known. To further investigate possible changes in pore structure, Orai1 ANSGA and H171Y in combination with ...
Characterisation of PolydimethylSiloxane(PDMS) by liquid-state NMR spectroscopy
HADDADY KHELEJAN, Solmaz
2021 - anglický
This work analyzes how two liquid /viscose base materials (Base and Curing Agent by Ecoflex ?), after putting together and polymerization, will produce silicones. We want to show how vinyl groups are consumed and how methyl attached groups increase during this process. And how Base and Curing Agent are different. This work analyzes how two liquid /viscose base materials (Base and Curing Agent by Ecoflex ?), after putting together and polymerization, will produce silicones. We want to show how vinyl groups are consumed and how methyl attached groups increase during this process. And how Base and Curing Agent are different.
Klíčová slova:
silicone elastomer; polydimethylsiloxane; PDMS; polymerization; NMR spectrometry-
Plné texty jsou dostupné v digitálním repozitáři JČU.
Characterisation of PolydimethylSiloxane(PDMS) by liquid-state NMR spectroscopy
This work analyzes how two liquid /viscose base materials (Base and Curing Agent by Ecoflex ?), after putting together and polymerization, will produce silicones. We want to show how vinyl groups are ...
Occurrence of the cALAs gene in the BCCO Actinomycetes collection and cultivation improvements for the overproduction of secondary metabolites in soil associated Actinomycetes
PULFERER, Lisa
2021 - anglický
Metabolites produced by Bacteria are known to have a wide range of biological activities, which are applied in various fields, like medicine. Most of them are synthesized by members of the group Actinomycetes, in particular from the genus Streptomyces. This thesis deals with the screening process of various Streptomyces strains for a specific gene which is involved in the synthesis of a manumycin-like secondary metabolite. Another aspect discussed here is how the addition of agar to the fermentation media and the pH value can influence the synthesis of bioactive metabolites. To determine the effectiveness of the metabolites various experiments were conducted. Metabolites produced by Bacteria are known to have a wide range of biological activities, which are applied in various fields, like medicine. Most of them are synthesized by members of the group Actinomycetes, in particular from the genus Streptomyces. This thesis deals with the screening process of various Streptomyces strains for a specific gene which is involved in the synthesis of a manumycin-like secondary metabolite. Another aspect discussed here is how the addition of agar to the fermentation media and the pH value can influence the synthesis of bioactive metabolites. To determine the effectiveness of the metabolites various experiments were conducted.
Klíčová slova:
Actinomycetes; Streptomyces; Kutzneria; secondary metabolites; cyclizing 5-aminolevulinate synthase; antibacterial activity
Plné texty jsou dostupné v digitálním repozitáři JČU.
Occurrence of the cALAs gene in the BCCO Actinomycetes collection and cultivation improvements for the overproduction of secondary metabolites in soil associated Actinomycetes
Metabolites produced by Bacteria are known to have a wide range of biological activities, which are applied in various fields, like medicine. Most of them are synthesized by members of the group ...
Expression, purification and crystallization of the putative transcriptional regulator MSMEG_6227 from Mycobacteria
HALAS, Simon
2021 - anglický
MSMEG_6227, a putative transcriptional regulator from Mycobacterium smegmatis, was cloned and expressed in E. coli BL21 cells. The expressed protein was purified by chromatographic methods and an optimized protocol for the expression and purification of MSMEG_6227 was established. With the purified protein initial crystallization trials were set up, which need to be further optimized and scaled up in the future to resolve the X-ray structure of MSMEG_6227. MSMEG_6227, a putative transcriptional regulator from Mycobacterium smegmatis, was cloned and expressed in E. coli BL21 cells. The expressed protein was purified by chromatographic methods and an optimized protocol for the expression and purification of MSMEG_6227 was established. With the purified protein initial crystallization trials were set up, which need to be further optimized and scaled up in the future to resolve the X-ray structure of MSMEG_6227.
Klíčová slova:
Mycobacteria; MSMEG_6227; Mycobacterium smegmatis; putative transcriptional regulator
Plné texty jsou dostupné v digitálním repozitáři JČU.
Expression, purification and crystallization of the putative transcriptional regulator MSMEG_6227 from Mycobacteria
MSMEG_6227, a putative transcriptional regulator from Mycobacterium smegmatis, was cloned and expressed in E. coli BL21 cells. The expressed protein was purified by chromatographic methods and an ...
Characterization of Bartonella species infecting North American Triatominae (kissing bugs)
KOGLER, Alexandra
2021 - anglický
The aim of this thesis was to characterize Bartonella spp. within T. rubida gut microbiomes, using multilocus sequence typing (MLST), and to determine its incidence at different sampling localities. The aim of this thesis was to characterize Bartonella spp. within T. rubida gut microbiomes, using multilocus sequence typing (MLST), and to determine its incidence at different sampling localities.
Klíčová slova:
kissing bugs; T. rubida; Bartonella
Plné texty jsou dostupné v digitálním repozitáři JČU.
Characterization of Bartonella species infecting North American Triatominae (kissing bugs)
The aim of this thesis was to characterize Bartonella spp. within T. rubida gut microbiomes, using multilocus sequence typing (MLST), and to determine its incidence at different sampling ...
Characterization of Trypanosoma brucei MICOS subunit Mic20.
DEISENHAMMER, Sebastian
2021 - anglický
This study focuses on the trypanosome MICOS complex related membrane protein Tb927.10.11900 (TbMic20) in Trypanosoma brucei. This research aimed to express TbMic20 in E. coli cells under soluble conditions and further determine its standard redox potential. This study focuses on the trypanosome MICOS complex related membrane protein Tb927.10.11900 (TbMic20) in Trypanosoma brucei. This research aimed to express TbMic20 in E. coli cells under soluble conditions and further determine its standard redox potential.
Klíčová slova:
trypanosoma brucei; recombinant protein; mitochondria; redox potential
Plné texty jsou dostupné v digitálním repozitáři JČU.
Characterization of Trypanosoma brucei MICOS subunit Mic20.
This study focuses on the trypanosome MICOS complex related membrane protein Tb927.10.11900 (TbMic20) in Trypanosoma brucei. This research aimed to express TbMic20 in E. coli cells under soluble ...
The Portrayal of the Roaring Twenties in Francis Scott Fitzgerald's Novel The Great Gatsby
BAULA, Dariia
2021 - anglický
Cílem této bakalářské práce je prozkoumat dopad dvacátých let minulého století amerických dějin, známých také jako The Roaring Twenties, v jedinečné knize Francise Scotta Fitzgeralda Velký Gatsby. Tato práce užívá historických akademických textů za účelem usazení zmíněné knihy do jejího literárního kontextu a k analýze vlivů událostí, které inspirovaly autora k jejich zobrazení v uměleckém díle. Bakalářská práce se skládá ze čtyř kapitol, každá se soustředí na určitou problematiku. První popisuje téma, metodologii, okrajově nastiňuje děj a soustředí se na autorovu biografii s ohledem na Velkého Gatsbyho. Druhá kapitola se soustřeďuje na knižní líčení post-válečných Spojených států. Následující kapitola je zaměřena na popisy americké společnosti a jejích mnohých úskalí. Nakonec čtvrtá vyzdvihuje Fitzgeraldovu reprezentaci dobové kultury spojené s Roaring Twenties. The aim of this bachelor thesis is to examine the reflection of the Roaring Twenties in Francis Scott Fitzgerald's outstanding novel The Great Gatsby. The study uses historical academic texts to place the book in its literary context and analyse what particular characteristics of the period influenced the author and how he portrays them in his work of literary art. This thesis consists of four parts, each of which concentrates on a specific subject. The first chapter introduces the topic and methodology, briefly describes the plot and pays attention to the author's biography regarding its influence on The Great Gatsby. The second part deals with the portrayal of the post-war United States in the novel. The following section analyses how the writer describes American society and its issues, while the fourth chapter studies Fitzgerald's depiction of the culture of the Roaring Twenties.
Klíčová slova:
Velký Gatsby; Francis Scott Fitzgerald; historický kontext; Spojené státy americké; společnost; kultura.
Plné texty jsou dostupné v digitálním repozitáři JČU.
The Portrayal of the Roaring Twenties in Francis Scott Fitzgerald's Novel The Great Gatsby
Cílem této bakalářské práce je prozkoumat dopad dvacátých let minulého století amerických dějin, známých také jako The Roaring Twenties, v jedinečné knize Francise Scotta Fitzgeralda Velký Gatsby. ...
A comparative analysis of linguistic devices used in English-written menus
DYTRICH, Jiří
2021 - anglický
Tato bakalářská práce analyzuje a interpretuje užití jazyka v současných anglicky psaných menu. Analýza se zabývá obecnými způsoby využití jazyka v menu restaurací různých cenových kategorií. Analýza rovněž zkoumá, jak se tyto způsoby užití jazyka uplatňují v praxi. Pro účely práce byl vytvořen soubor analytických deskriptorů, které reprezentují rozličné úhly pohledu, jimiž lze na lexikum a jazykový styl jednotlivých menu nahlížet. Následná analýza vzorku 90 restauračních menu staví na využití korpusového nástroje KWords k poskytnutí komplexního vhledu do podstaty menu. Práce dále pojednává o tom, co zjištění nalezená v průběhu analýzy menu znamenají pro zákazníky a jak je lze využít v případě začínajících podniků. Při provádění výzkumu čerpám z výzkumu zmíněného v Jurafsky (2014), který doplňuji o nově vypozorované trendy. Výsledná data kvantifikuji a interpretuji. This thesis explores how language is negotiated in the present-day English written menus. The analysis deals with various strategies of using language in menus of different price range establishments and examines how these strategies are applied. In conducting the research, I draw on the study reported in Jurafsky (2014) but have developed a set of analytical descriptors to explore and evaluate different perspectives from which the menus and their lexis may be analysed. The analysis is data driven; it employs a Czech National Corpus tool KWords to provide a complex insight into the nature of menus. The resulting data are quantified and interpreted. The discussion part of the thesis reviews the implication of the findings, identifies newly observed trends by comparing the findings to Jurafsky's (2014) original study, and proposes how the learning can be of use to both customers and up and coming start-ups.
Klíčová slova:
aplikovaná lingvistika; jazyková analýza; menu; použití jazyka; KWords
Plné texty jsou dostupné v digitálním repozitáři JČU.
A comparative analysis of linguistic devices used in English-written menus
Tato bakalářská práce analyzuje a interpretuje užití jazyka v současných anglicky psaných menu. Analýza se zabývá obecnými způsoby využití jazyka v menu restaurací různých cenových kategorií. Analýza ...
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