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Pokročilé výpočetní metody pro detekci CNV v bakteriálních genomech
Jugas, Robin; Bystrý, Vojtěch; Šafránek,, David; Vítková, Helena
2024 - English
The focus in the field of structural variations is mainly focused on human genomes. Thus, detecting copy number variation (CNV) in bacteria is a less developed field. Commonly used CNV detection methods do not consider the features of bacterial circular genomes and generally, there is a space to improve performance metrics. This thesis presents a CNV detection method called CNproScan focused on bacterial genomes. CNproScan implements a hybrid approach combining read depth and read pair signals. It considers all bacteria features and depends only on NGS data. Based on the benchmarking results, the CNproScan achieved very well in various conditions. Using the read pair information, the CNVs are classified into several categories. Also, compared with other methods, CNproScan can detect much shorter CNV events. Because of the necessity of merging not only the various feature signals but also the results of different algorithms, the thesis also introduces a pipeline called ProcaryaSV developed to easily employ five CNV detection tools and merge their results. ProcaryaSV handles the whole procedure from quality check, reads trimming, and alignment to the CNV calling. Hlavní pozornost v oblasti strukturálních variací je zaměřena na lidské genomy. Detekce změny variace počtu kopií (CNV) u bakterií je tedy méně rozvinutou oblastí. Běžně používané metody detekce CNV neberou v úvahu specifika bakteriálních kruhových genomů a obecně existuje prostor pro zlepšení metrik výkonnosti. Tato práce představuje metodu detekce CNV nazvanou CNproScan zaměřenou na bakteriální genomy. CNproScan implementuje hybridní přístup kombinující signály hloubky čtení a párů čtení. Bere v potaz všechny vlastnosti bakterií a využívá pouze sekvenační data. Na základě výsledků ze srovnání dosáhl CNproScan velmi dobrých výsledků v různých podmínkách. Pomocí informací z párových čtení jsou CNV klasifikovány do několika kategorií. Ve srovnání s jinými metodami může CNproScan také detekovat mnohem kratší CNV. Vzhledem k nutnosti slučovat nejen signály různých přístupů, ale také výsledky různých algoritmů, dizertační práce také představuje pipelinu nazvanou ProcaryaSV vyvinutou k detekci CNV s využitim pěti nástrojů a slučování jejich výsledků. ProcaryaSV se stará o celý postup od kontroly kvality čtení, ořezávání konců čtení, zarovnání čtení až k detekci CNV.
Keywords:
Next-generation sequencing; Structural variation; Copy number variation; Bacteria; sekvenování nové generace; strukturální variace; variace počtu kopií; bakterie
Available in a digital repository NRGL
Pokročilé výpočetní metody pro detekci CNV v bakteriálních genomech
The focus in the field of structural variations is mainly focused on human genomes. Thus, detecting copy number variation (CNV) in bacteria is a less developed field. Commonly used CNV detection ...
Computational and experimental assessment of natural frequencies in a bladed disk system
Mekhalfia, Mohammed Lamine; Procházka, Pavel; Maturkanič, Dušan; Voronova, Evgeniya; Hodboď, Robert
2024 - English
This paper examines the modal characteristics of a bladed disk in rotating machinery systems using a combination of analytical and experimental modal analysis methods. The analysis involves measuring natural frequencies and mode shapes under different operational conditions. A comparative analysis is conducted to assess modal properties obtained from both analytical and experimental approaches, while also considering the influence of rotation speed. Additionally, Finite Element Method (FEM) outputs are used to accurately position the strain gauge. Integrating these techniques provides a comprehensive understanding of the bladed disk's behaviour under varying rotational speeds, enhancing result accuracy and facilitating thorough investigation within rotating machinery systems.
Keywords:
natural frequencies; FEM; LDV; strain gauge
Available at various institutes of the ASCR
Computational and experimental assessment of natural frequencies in a bladed disk system
This paper examines the modal characteristics of a bladed disk in rotating machinery systems using a combination of analytical and experimental modal analysis methods. The analysis involves measuring ...
Flow simulations approach for flocculation tanks
Idžakovičová, Kristýna; Bílek, V.; Haidl, J.; Isoz, Martin; Pivokonský, M.
2024 - English
Flocculation in water treatment facilities plays a key role in the separation of colloidal inorganic and organic substances. Its optimization leads to a significant increase in its efficiency and savings of operational costs. However, it is currently based on trial-and-error experimental approaches. In this contribution, we focus on flow modeling in stirred flocculation tanks that would, after coupling with a calibrated model of particle aggregation, enable simulationbased flocculation optimization. Despite the abundance of literature on stirred tank modeling, there is no universal agreement on the methodology used to describe turbulence nor on the approach to the computational mesh creation. Consequently, there is no unified methodology for simulations and their validation. To address this, we present a best-practice methodology for economical, yet reliable flow simulations in the said device. This methodology includes the choice of the turbulence model, the approach to the design of a high quality mesh suitable for arbitrary geometries, and results evaluation. It is developed based on an extensive literature review, a multitude of flow simulations using several meshes of progressively higher quality and resolution, and various strategies to converge to steady-state flow conditions. The simulation quality indicators used here involve comparison with the experimental data on fluid velocity, stirrer power output, and flow rate through the impeller zone. Additionally, the resulting flow simulation models are compared using tracer transport simulations, hinting at their potential for coupling with particle aggregation models.
Keywords:
flocculation tank; stirring; MRF; CFD; OpenFOAM
Available at various institutes of the ASCR
Flow simulations approach for flocculation tanks
Flocculation in water treatment facilities plays a key role in the separation of colloidal inorganic and organic substances. Its optimization leads to a significant increase in its efficiency and ...
Studium metabolismu termofilní bakterie Caldimonas thermodepolymerans
Krempaská, Vladimíra; Sedlář, Karel; Buchtíková, Iva
2024 - English
Microbial polyesters such as polyhydroxyalkanoates (PHAs) can serve as intracellular carbon and energy reserves for cells. One of the main advantages of PHAs is their biodegradability and biocompatibility, making them a potential partial replacement for traditional petrochemical plastics. However, their biotechnological production remains costly, and alternative methods are being sought to reduce process costs. The use of extremophilic microorganisms, like the thermophilic bacterium Caldimonas thermodepolymerans, is a promising possibility. This bacterium can process carbohydrates, which are abundant in lignocellulosic waste. In this study, the metabolism of three lignocellulosic carbohydrates (xylose, glucose, and cellobiose) and their combinations were investigated for the DSM 15344 from the DSMZ-German Collection. The biomass PHA content was determined through CG-FID after cultivations on individual carbohydrate substrates. Finally, changes in carbohydrate substrates during cultivation were evaluated by RT-qPCR, focusing on selected xylF and gtsA genes. A preference for xylose and cellobiose as a substrate was observed in the studied DSM 15344 from the DSMZ-German Collection. Polyhydroxyalkanoáty (PHA) sa radia medzi mikrobiálne polyestery a bunkám dokážu poskytnúť vnútrobunkové zásoby uhlíka a energie. Hlavná výhoda PHA spočíva v tom, že ide o biodegradovateľné a biokompatibilné polyméry. Ich fyzikálne vlastnosti sú porovnateľné s petrochemickými plastami, ktoré by mohli v budúcnosti čiastočne nahradiť. Avšak, ich biotechnologická produkcia je stále veľmi nákladná. Preto sa hľadajú rôzne alternatívne metódy, ktoré by dokázali znížiť tieto procesné výdavky a ako jedna z možností sa javí využitie extrémofilných mikroorganizmov. Za jedného z vhodných kandidátov na priemyselnú produkciu PHA sa považuje termofilná baktéria Caldimonas thermodepolymerans. K jej ďalším výhodám okrem iného patrí aj to, že dokáže spracovávať sacharidy, ktoré sú vo veľkej miere obsiahnuté v lignocelulózových odpadoch. Táto práca bola konkrétne zameraná na štúdium metabolizmu troch lignocelulózových sacharidov (xylózy, glukózy a celobiózy) a ich vzájomných kombinácií u zbierkového kmeňa DSM 15344. V experimentálnej časti práce boli realizované kultivácie na jednotlivých sacharidových substrátoch, kde následne zo získanej biomasy bol stanovený celkový obsah PHA pomocou CG-FID. Na záver bola vyhodnotená expresia vybraných génov xylF a gtsA pri zmenách sacharidových substrátov v priebehu kultivácie za využitia RT-qPCR. U študovaného zbierkového kmeňa DSM 15344 bola pozorovaná preferencia xylózy a celobiózy ako substrátu.
Keywords:
Polyhydroxyalkanoates (PHAs); thermophilic bacteria; Caldimonas thermodepolymerans; Polyhydroxyalkanoáty (PHA); termofilné baktérie; Caldimonas thermodepolymerans
Available in a digital repository NRGL
Studium metabolismu termofilní bakterie Caldimonas thermodepolymerans
Microbial polyesters such as polyhydroxyalkanoates (PHAs) can serve as intracellular carbon and energy reserves for cells. One of the main advantages of PHAs is their biodegradability and ...
A New Hollow Fiber-Based Liquid-Phase Microextraction Method for the Determination of Antihypertensive Drug Lercanidipine in Biological Samples
Labzova, O.; Hrdlička, Vojtěch; Navrátil, Tomáš; Šelešovská, R.
2024 - English
A new hollow fiber-based liquid-phase microextraction (HF-LPME) method for the determination of antihypertensive drug lercandipine (LCN) in biological samples was developed. HF-LPME was\ncombined with optimized square wave voltammetry (SWV) on a cathodically pre-treated screenprinted boron-doped diamond electrode (SP-BDDE). Optimum HF-LPME conditions were:\nsupported liquid membrane (SLM) dodecane, 0.02 mol L-1 Britton-Robinson buffer (BRB, pH = 3) acceptor phase, BRB (pH = 7) donor phase, and time of extraction 30 min. Limits of quantification (LOQ) and detection (LOD) were 3.3 and 1.1 nmol L-1, respectively. The applicability of the developed method was verified on human urine, blood serum, and blood plasma with 20 and 100 nmol L-1 LCN addition.
Keywords:
Lercanidipine hydrochloride; Hollow fiber liquid-phase microextraction; Screenprinted boron-doped diamond electrode
Available on request at various institutes of the ASCR
A New Hollow Fiber-Based Liquid-Phase Microextraction Method for the Determination of Antihypertensive Drug Lercanidipine in Biological Samples
A new hollow fiber-based liquid-phase microextraction (HF-LPME) method for the determination of antihypertensive drug lercandipine (LCN) in biological samples was developed. HF-LPME was\ncombined with ...
Public spaces in fast-developing Wola district of Warsaw - adaptive reuse in search for a local center
Ramirez Venegas, Ana Paula; Wasilkowska, Alexandra; Kepiński, Kacper Ignacy
2024 - English
The Wola district, situated on the western fringe of downtown Warsaw, stands as an unmistakable testament to the city’s evolution. It embodies a vibrant blend of its industrial past and contemporary urbanism. Once a vibrant industrial hub spurred by railroad construction and postwar reconstruction, Wola has metamorphosed into a dynamic landscape marked by towering skyscrapers and high-end residential enclaves. Despite this, there are clear echoes of its industrial legacy in the repurposed facades of former factories, now buzzing hubs of commercial and cultural activity. The diploma project’s focus is on the rejuvenation of Kercelak, a once bustling marketplace and square that thrived from 1867 to 1947. Kercelak has a rich historical significance. However, it has succumbed to the tide of gentrification, and as a result, its communal spaces are neglected amidst the surge of modern investments. The project will breathe new life into these abandoned public realms through adaptive reuse and thoughtful design interventions. It will foster community engagement and connectivity. The project will create inclusive and accessible public spaces that transcend the dominance of vehicular traffic and gentrified enclaves. It will seamlessly integrate historical legacies, post-war housing, and contemporary developments to forge a cohesive, functional, and visually continuous spatial continuum. The project will not only revitalize Kercelak but also foster a sense of belonging and cohesion among its diverse inhabitants. The Wola district, situated on the western fringe of downtown Warsaw, stands as an unmistakable testament to the city’s evolution. It embodies a vibrant blend of its industrial past and contemporary urbanism. Once a vibrant industrial hub spurred by railroad construction and postwar reconstruction, Wola has metamorphosed into a dynamic landscape marked by towering skyscrapers and high-end residential enclaves. Despite this, there are clear echoes of its industrial legacy in the repurposed facades of former factories, now buzzing hubs of commercial and cultural activity. The diploma project’s focus is on the rejuvenation of Kercelak, a once bustling marketplace and square that thrived from 1867 to 1947. Kercelak has a rich historical significance. However, it has succumbed to the tide of gentrification, and as a result, its communal spaces are neglected amidst the surge of modern investments. The project will breathe new life into these abandoned public realms through adaptive reuse and thoughtful design interventions. It will foster community engagement and connectivity. The project will create inclusive and accessible public spaces that transcend the dominance of vehicular traffic and gentrified enclaves. It will seamlessly integrate historical legacies, post-war housing, and contemporary developments to forge a cohesive, functional, and visually continuous spatial continuum. The project will not only revitalize Kercelak but also foster a sense of belonging and cohesion among its diverse inhabitants.
Keywords:
Warsaw; Poland Wola district Development Historical market (Kercelak) Industrial backbone Gentrification Public transport Materiality and physical condition Public spaces Recreational spaces Mixed-use buildings Market installation Community development Cultural enrichment Historical context Transformation Gathering points Community sense of belonging Economic growth Sustainable development; Warsaw; Poland Wola district Development Historical market (Kercelak) Industrial backbone Gentrification Public transport Materiality and physical condition Public spaces Recreational spaces Mixed-use buildings Market installation Community development Cultural enrichment Historical context Transformation Gathering points Community sense of belonging Economic growth Sustainable development
Available in a digital repository NRGL
Public spaces in fast-developing Wola district of Warsaw - adaptive reuse in search for a local center
The Wola district, situated on the western fringe of downtown Warsaw, stands as an unmistakable testament to the city’s evolution. It embodies a vibrant blend of its industrial past and contemporary ...
Víceúrovňový měnič s aktivními hradlovými budiči pro Fault Ride-Through
Klement, Dominik; Holain, Martin; Götthans, Tomáš
2024 - English
This thesis explores multilevel converters, highlighting their benefits and current/potential future applications. It focuses on the Nested Neutral Point Piloted (NNPP) topology and develops a fault ride-through control algorithm with active capacitor voltage balancing and space vector modulation. The algorithm is validated through simulation. A prototype is designed for experimental validation. The thesis concludes by comparing the proposed fault-tolerant algorithm with existing methods. Tato práce se zabývá víceúrovňovými měniči, popisuje jejich výhody a současné/potenciální budoucí aplikace. Zaměřuje se na „Nested Neutral Point Piloted (NNPP)“ topologii a vývoj algoritmu řízení s aktivním vyrovnáváním napětí kondenzátoru a pokročilou vektorovou modulací pro tuto topologii. Tento algoritmus je ověřen pomocí simulací. Součástí práce je i návrh prototypu pro experimentální ověření. Práce je uzavřena porovnáním vyvinutého algoritmu s již existujícími metodami.
Keywords:
Nested Neutral Point Piloted Converter; Fault Ride-through; Active gate driver; Multilevel converters; SiC MOSFET; Power Electronics; Stacked Multicell Topology; High reliability; Nested Neutral Point Piloted měnič; Fault Ride-through; Aktivný hradlový budič; Víceúrovňový měnič; SiC MOSFET; Výkonová elektronika; Stacked Multicell topologie; Vysoká spolehlivost
Available in a digital repository NRGL
Víceúrovňový měnič s aktivními hradlovými budiči pro Fault Ride-Through
This thesis explores multilevel converters, highlighting their benefits and current/potential future applications. It focuses on the Nested Neutral Point Piloted (NNPP) topology and develops a fault ...
Energetická bilance UWC spoje
Bartoň, Jan; Látal,, Jan; Hudcová, Lucie
2024 - English
This semestral thesis is aimed at the description of the optical ray propagation through underwater environment, focusing mainly on the optical beam’s deflection by a turbulent space. In the first part of the thesis, the description of the properties of underwater environment and their impact on the optical beam is presented. In the second part, methods usable for the calculation of attenuation of an underwater environment are presented, focusing on the turbulent environment. In the third part, the software implementation of the algorithm presented in the second part is presented. The outcome of this thesis is a procedure for calculating the propagation of the optical beam through an underwater environment and its software implementation. Tato semestrální práce je zaměřená na popis šíření optického svazku podvodním prostředím se zaměřením na vliv turbulentního proudění na odsměrování svazku. V první části práce je poskytnut popis vlastností podvodního prostředí a jejich vliv na optický svazek. V druhé části jsou prezentovány metody použitelné pro výpočet útlumu podvodního prostředí, zaměřující se na popis turbulentního prostředí. Ve třetí části je představena softwarová implementace algoritmu popsaného ve druhé části. Výsledkem práce je postup výpočtu síření optického svazku podvodním prostředím a jeho softwarová implementace.
Keywords:
Turbulence; underwater environment; optical beam; attenuation; deflection; noise; chlorophyll; absorption; scattering; ABCD matrices; extinction coefficient.; Turbulence; podvodní prostředí; optický svazek; útlum; odsměrování; šum; chlorofyl; absorpce; rozptyl; ABCD matice; koeficient extinkce.
Available in a digital repository NRGL
Energetická bilance UWC spoje
This semestral thesis is aimed at the description of the optical ray propagation through underwater environment, focusing mainly on the optical beam’s deflection by a turbulent space. In the first ...
Softwarově definovaná anténní řada
Sedláček, David; Prokopec, Jan; Maršálek, Roman
2024 - English
The main objective of this thesis was to develop a demonstrator platform implementing signal processing algorithms for signal direction of arrival estimation. In total, six estimation techniques were described, and simulations of discussed beamforming and subspace-based methods were implemented in Python. A study was conducted on available hardware, comparing trade-offs between customised and off-the-shelf solutions. Specific hardware and software configurations were proposed for practical implementation of the estimation methods. Finally, a testbed was constructed to verify the performance of the implemented estimation methods. Tests were performed, and the results were critically evaluated. Hlavným cieľom tejto práce bolo vyvinúť demonštračnú platformu pre implementáciu algoritmov na odhad smeru príchodu signálu. Celkovo bolo opísaných šesť techník, ktoré boli následne implementované v Pythone spolu so simuláciami príchodu signálov. Bola vykonaná štúdia dostupného hardvéru, v ktorej boli porovnané rozdiely medzi na mieru prispôsobenými a voľne dostupnými riešeniami. Navrhli sa konkrétne hardvérové a softvérové konfigurácie pre praktickú implementáciu metód odhadu príchodu signálu. Na záver boli navrhnuté experimentálne merania na overenie účinnosti implementovaných metód. Vykonali sa testovacie merania a ich výsledky boli kriticky zhodnotené.
Keywords:
Antenna array; digital signal processing; direction-of-arrival estimation; MUSIC; software-defined radio; KrakenSDR; Python; Anténne pole; digitálne spracovanie signálov; odhad smeru príchodu; MUSIC; softvérovo definované rádio; KrakenSDR; Python
Available in a digital repository NRGL
Softwarově definovaná anténní řada
The main objective of this thesis was to develop a demonstrator platform implementing signal processing algorithms for signal direction of arrival estimation. In total, six estimation techniques were ...
Výpočty se zachováním důvěrnosti s využitím homomorfního šifrování
Rybár, Matej; Ricci, Sara; Člupek, Vlastimil
2024 - English
This master's thesis examines homomorphic encryption, focusing on theoretical foundations, security principles, and practical applications. The TFHE library's Rust variant (TFHE-rs) was selected for its performance and security. A military usage scenario involving the Military Grid Reference System (MGRS) was developed to demonstrate secure cloud computing. Homomorphic implementations of MGRS conversion, square root calculations, IEEE 754 floating-point representation, integer-based square root, floating-point square root, and SHA-256 hashing were created. Performance benchmarks showed the homomorphic floating-point square root required approximately 22 seconds and SHA-256 about 10 seconds. The thesis describes the process from receiving MGRS coordinates to returning the computed distance with its hash, detailing a secure client-server architecture. Docker Compose simulated the cloud environment, with Ansible automating deployment. The frontend, developed with React and Leaflet, provides an interactive interface. The successful implementation highlights the feasibility and significance of homomorphic encryption for enhancing data security. Táto diplomová práca skúma homomorfné šifrovanie, zameriavajúc sa na teoretické základy, bezpečnostné princípy a praktické aplikácie. Pre svoju výkonnosť a bezpečnosť bola vybraná knižnica TFHE vo svojej Rust variante (TFHE-rs). Bol vyvinutý scenár vojenského použitia zahŕňajúci systém Military Grid Reference System (MGRS) na demonštráciu bezpečného cloudového výpočtu. Implementovali sme homomorfné algoritmy pre konverziu MGRS, výpočet druhých odmocnín, reprezentáciu IEEE 754, algoritmus pre výpočet druhých odmocnín pomocou celých čísel, algoritmus pre výpočet druhých odmocnín pomocou desatinných čísel a SHA-256 hashing. Výkonnostné testy ukázali, že homomorfný algoritmus pre výpočet druhých odmocnín vyžadoval približne 22 sekúnd a SHA-256 približne 10 sekúnd. Práca opisuje celý proces od prijatia MGRS koordinátov po vrátenie vypočítanej vzdialenosti spolu s jej hashom, pričom podrobne opisuje bezpečnú klient-server architektúru. Docker Compose simuloval cloudové prostredie, pričom Ansible automatizoval nasadzovanie. Frontend, vyvinutý pomocou React a Leaflet, poskytuje interaktívne rozhranie. Úspešná implementácia zdôrazňuje uskutočniteľnosť a význam homomorfného šifrovania pri zvyšovaní bezpečnosti dát.
Keywords:
confidentiality-preserving computation; homomorphic encryption; military grid reference system; výpočty zachovávajúce dôvernosť; homomorfné šifrovanie; military grid reference system
Available in a digital repository NRGL
Výpočty se zachováním důvěrnosti s využitím homomorfního šifrování
This master's thesis examines homomorphic encryption, focusing on theoretical foundations, security principles, and practical applications. The TFHE library's Rust variant (TFHE-rs) was selected for ...
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