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Application, analysis and evaluation of a novel medical image annotation and segmentation tools
Sucháček, Jan ; Paštěka, Richard (oponent) ; Dr.Benjamin Ramberger, MSc. BSc. BSc. (vedoucí práce)
Tato práce se zabývá vytvářením 3D modelů horních cest dýchacích člověka na základě CT snímků, aby se zlepšilo porozumění složitým anatomickým detailům horních cest dýchacích, pomohlo odhalit patologické změny a usnadnilo terapeutické rozhodování. Tyto modely rovněž umožňují simulaci a hodnocení charakteristik proudění vzduchu v horních cestách dýchacích člověka. K vytvoření těchto 3D modelů byly použity dvě anotační a tři segmentační metody na souboru dat šesti CT snímků pacientů. Pro všechny výsledné 3D modely byly vypočteny různé metriky, jako je počet trojúhelníků, plocha povrchu, objem, objem průsečíku modelů, Diceův koeficient a vzdálenost mezi modely, aby bylo možné modely charakterizovat a metody porovnat. Byla provedena podrobná analýza zaměřená na čtyři anatomické části: nosní dutinu s dutinami, hltan, hrtan a průdušnici. Kromě toho byla na jednom modelu provedena simulace výpočetní dynamiky tekutin (CFD) pro analýzu proudění vzduchu v horních cestách dýchacích během dýchání. Tato simulace umožnila nahlédnout do dynamiky proudění vzduchu v horních cestách dýchacích a potenciálně snížit potřebu invazivních vyšetření. Výsledky této práce ukazují potenciál 3D modelů horních cest dýchacích pro zlepšení přesnosti diagnostiky, plánování léčby a výsledků léčby pacientů v respiračním lékařství.
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Experimental evaluation of medical nebulizers
Zajacová, Lucia ; MSc, Lara Alina Schöllbauer (oponent) ; Paštěka, Richard (vedoucí práce)
With the worsening of global atmospheric conditions, the occurrence of respiratory diseases is on the rise, necessitating the development of more efficient devices. Among these devices, medical nebulizers are frequently used for inhalation therapy. While their usability has been repeatedly tested and confirmed, ongoing improvements are desired. This thesis aims to explore existing studies and information to design an experimental setup for evaluating medical nebulizers. The thesis incorporates the utilization of an idealized mechanical upper-airway Alberta model, a breathing simulator xPULM, and an optical aerosol spectrometer PALAS Promo 2000 in combination with the Wellas sensor 2200. Subsequently, it outlines the design of connections between the utilized components and the planning of measurement methods for accurate evaluation. The employed methods provide valuable insights into the characteristics of aerosols produced by the tested nebulizers. Starting from characterization parameters such as nebulizer aerosol output and output rate, residual volume, particle size, and particle size distribution, the evaluation progresses to assessing deposition and establishing the nebulizer efficiency in delivering aerosol particles to different regions of the respiratory tract.
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Evaluation of perfusate solution after ex vivo lung perfusion
Dobrovolná, Terezie ; Enghuber, Florian (oponent) ; Paštěka, Richard (vedoucí práce)
The aim of this master’s thesis is to introduce lung perfusion procedures and determine the parameters that are connected to the state of the lungs after perfusion and during preservation. In the perfusion process and for storing the lung, the phosphate-buffered saline (PBS) solution is used. The work focuses mainly on the parameters that can be measured and evaluated in the perfusate solution during the perfusion and preservation of the lungs such as pH, total dissolved solids, and proteins. These factors can be measured according to several procedures that are based on different principles. The mentioned process has been selected and implemented with regard to availability, feasibility, and appropriateness given. The pH and TDS parameters have been acquired by electrodes. Therefore, sensor calibration is an integral part of the measure ment. The concentration of the proteins was measured with the Bradford assay where it is important to follow the established protocol. Materials for that were present and provided in the Tissue engineering laboratory. Another intention is to assess the state of the lung tissue, meaning how the lungs gradually change their appearance, weight, and mechanical properties over time. The weight is obtained with the calibrated load cell sensor. For this sensor, a platform had to be assembled in order to function correctly and with great accuracy. From the field of mechanical properties of the lungs, the compliance and PV loops have been selected and presented. Five lungs were used for measurement. The appearance of the lungs changed over time and the necrosis was progressing. The lung viability was preserved with the PBS solution with balanced pH. The value of pH was maintained around pH 7. The concentration of the total dis solved solids (TDS) was determined and similar values were obtained in all lungs because the same solution was used. The TDS fluctuated slowly same as pH because they are correlated. The weight of the lungs decreased with passage of the time as expected. Protein concentration increased over time. That can indicate the inflammatory processes in the lung tissue or lung injury. The surface temperature was also obtained with a laser thermometer and decreasing values were noted with increasing storage time. Static compliance had unexpected charac teristics in some of the lungs. This was probably influenced by leakage due to an unsecured trachea. The last parameter was PV loops. The shape of the PV loops looked good until 48h in the majority of the loops. Then, the shape flatted and the shortage of curves appeared due to shortness of breath.
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Modelling of flow and pressure characteristics in the model of the human upper respiratory tract under varying conditions
Karlíková, Adéla ; Forjan,, Mathias (oponent) ; Paštěka, Richard (vedoucí práce)
The aim of this master’s thesis is to create 3D model of upper respiratory tract (URT) according to the original model segmented from CT data, apply different conditions to the air flow inside the model, and afterwards, evaluate the change of characteristics of velocity and pressure. The model of URT was realized in the interface of Computational Fluid Dynamics software ANSYS and the Navier-Stokes equations were used for modeling the air flow inside the model. Firstly, simple 2D model was created for familiarization with the ANSYS interface. Furthermore, the 3D model of URT was constructed, and velocity and pressure characteristics were modeled under varying conditions. These conditions include different placement and quantity of sampling gaps within the model and choice of different combinations of inlets. Finally, the results are presented and evaluated along with the illustrations of the models modeled under varying conditions. The 3D model of URT means a compromise between computational load and model complexity and can be used as a basis for further research.
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Exploring the Population Characteristics of Direction-Selective Ganglion Cells Across the Retinal Space
Svatoň, Jan ; Paštěka, Richard (oponent) ; Jösch, Maximilian (vedoucí práce)
In the last century, substantial research has been dedicated to gaining an understanding of how visual information is encoded by neural populations and circuits. The overall picture that emerged from these efforts shows that visual information is first processed by intricate circuitries in the retina and subsequently relayed to higher brain structures. Both stages appear to have developed remarkably sophisticated computations. The functional study of these neuronal transformations has been examined either using electrophysiological or imaging techniques. In the retina, these techniques have limited the analysis of spatial specializations across the retina, either by the number of available electrodes (in electrophysiology) or the size of the field-of-view (FOV) (in imaging experiments). For example, simultaneous recordings of retinal ganglion cells (RGC) have been confined to an area (~ 200 x 200 um2) using state-of-the-art imaging techniques. In my thesis, I have explored a newly developed method that uses a FOV, which is 40-times larger in comparison with conventional optical methods, allowing me to overcome this technical limitation. This thesis uses this novel method to explore population characteristics of direction-selective ganglion cells (DSGCs) across the retinal space of mouse retinas. By recreating already known population patterns, we confirmed that our novel imaging method works. In addition, this thesis investigates the effects of adjuvants for enhanced global RGC infection rates that may potentially facilitate the unbiased recording of RGCs and introduces a novel stimulus for inspecting receptive fields (RFs) of RGCs. This novel stimulus outperforms conventional stimuli used in current studies in both the resolution of the yielded RF and the necessary time of stimulus presentation. It opens the door for following studies to describe for the first time the distribution patterns of RFs across the retinal space and to improve the clustering of cell classes.
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Development of an ex vivo lung perfusion system focusing on the preservation of fresh animal lungs for experiments and storage
Mesíková, Klaudia ; Forjan, Mathias (oponent) ; Paštěka, Richard (vedoucí práce)
A mechanical combined lung model is a type of model used in human breathing simulation. The biggest currency of the model is a high similarity with the human lungs. In order to work with the animal lungs for a longer time and so follow the principles of the 3Rs, a perfusion system is involved in the procedure. The perfusion system filled with a chosen perfusate solution is responsible to prolong the period in which the animal lungs are viable for experiments and storage in the ex-vivo environment. The development of the properly functioning perfusion system is based on the several components included in the process. Choosing the right solution for the perfusion of the inner environment of the lungs is one of the most important things that need to be taken into account. The roller pump is considered the drive motor of the system. Pressure and flow sensors are responsible for monitoring the process parameters that could describe the functionality and the ability to preserve the animal lungs in the ex-vivo environment. The validation of the developed system by using the fresh animal lungs is a part of the thesis as well as the checking procedure of the solution’s influence with the time of the storage. The perfusion system was successfully created and tested. The pressure and flow parameters gained during the measurement were compared while using the saline solution, the Ringer’s solution, and Histofix in the system. The compliance parameter of the lungs were been monitored during the perfusion as well as during the storage with the aim to determine the behaviour of the preserved lungs with the time and the impact of the chosen solution on it. Compliance initially decreased and then stabilized at a certain value throughout the storage period. For the perfusion with the saline and Ringer’s solution, it dropped by one-third. For Histofix preservation, the drop was by half of the initial compliance. The preservation time without the presence of the tissue necrosis was 120 hours using the Saline solution, 240 hours using the Ringer’s solution, and at least 268 hours using Histofix. The perfusion system could further be used in medical research and make a positive aspect in terms of less consumption of the animal organs for experimental purposes in various fields of the research. For future research, the improvement of the perfusion system and solution composition to ensure even longer preservation is welcomed.
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Osciloskop v systému Android
Paštěka, Richard ; Balogh, Jaroslav (oponent) ; Sekora, Jiří (vedoucí práce)
Bakalářská práce se zabývá návrhem digitálního osciloskopu pomocí vývojové platformy Arduino Mega ADK. V teoretické části práce jsou rozebrány základní parametry digitálních osciloskopů, typy vzorkování a obecné vlastnosti A/D převodníků. Práce se dále zabývá popisem vývojové platformy Arduino Mega ADK. Praktická část práce popisuje jednotlivé kroky realizace osciloskopu. Od obecného návrhu přechází v konkrétní popis řešení softwaru a hardwaru. Software se skládá ze dvou navzájem komunikujících programů. První, program mikrokontroléru, obstarává akvizici dat. Druhý slouží k vykreslení měřených průběhů na obrazovku počítače. Hardware přeřazený platformě Arduino Mega ADK vhodně upravuje vstupní měřený signál pro účely měření. Ve výsledcích jsou zhodnoceny průběhy a parametry vytvořeného osciloskopu, které byly otestovány pomocí funkčního generátoru.
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Integration and testing of a real time processing unit for lung simulation
Paštěka, Richard ; Drauschke, Andreas (oponent) ; Sekora, Jiří (vedoucí práce)
An active mechanical lung simulator (iLung) provides the possibility of simulating human breathing patterns. The aim of this thesis is to implement and test an real time embedded control and acquisition system cRIO as iLung control unit. Resulting connections are documented in tables and also by labelling assembly drawings with corresponding pin functions. One of the major improvements was made by tuning the motor and modifying the proportional-integral controller in the software. Those modifications resulted in significantly reduced motor oscillations around zero value. In order to increase usability and accessibility of the simulator a user manual and corresponding laboratory experiment were additionally created. The Validation of cRIO implementation was not limited to simple testing routines, but also extended on testing the simulator as a whole functioning unit. The results of simulator based measurements were compared and discussed to the spirometry measurements, taken from 20 subjects. Measurements showed a high degree of similarity between breathing patterns simulated by iLung and normal human breathing supporting the possibility for further research applications.
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Evaluation of selected thermophysiological model for the isolated, confined mission in Antarctica
Bečička, Martin ; Dobrovolná,, Julie (oponent) ; Paštěka, Richard (vedoucí práce)
Over the past few decades, numerous models have been created to estimate human thermal responses. These models rely on energy balance equations that consider the heat exchange between the human body and its environment. These models have substantially progressed from one-node models into complex structures organized in multiple layers and connected by a circulatory blood flow. Although there is literature available comparing the possible utility of the thermophysiological models in different scenarios, little is known about the utility of these mod els in specific conditions. This work investigates and compares selected thermophysiological models, focusing on selecting a suitable model for the use case scenario of Antarctica. The data was collected during a longitudinal study located at Johann Gregor Mendel Czech Antarctic station. The local skin temperature of participants (n = 16) was measured 6 times over the period of the study. The first of each measurement set consisted of orthostatic tests in addition to psychomotor vigilance task and Iowa gambling test present which were present in each of the subsequent measurements. After examining specific experimental conditions, four thermophysiological models were com pared, and the JOS-3 model was determined to be the most appropriate for the thermal data obtained during the experiment. The results revealed that the selected JOS-3 model can accurately predict mean skin temper atures for both experiment designs (RMSD 0.72 and 0.75 C for experiment design 1 and 2 respectively). Furthermore, the JOS-3 model was able to reliably predict head (RMSD 0.82 and 1.13 C), neck (RMSD 0.61 and 1 C), and chest (RMSD 1.01 and 1.22 C) skin temperatures. However, deviations observed for back, hand, and foot segments were significant (RMSD 2.08 - 2.25 and 2.55 - 2.68 C). Possible explanations include uncertainty in clothing insulation of the worn clothing, uncertainty in measurement circumstances (contact with surfaces - floor, table), and the placement of the thermal sensors. The highest deviation was observed in the pelvis (RMSD 2.25 and 3.72 C) and is possibly a result of the JOS-3 model overestimation of heat production in the segment. The study has underscored the significance of obtaining compre hensive data on clothing type and sensor placement for enhancing the accuracy of simulation outcomes.
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Evaluation of perfusate solution after ex vivo lung perfusion
Dobrovolná, Terezie ; Enghuber, Florian (oponent) ; Paštěka, Richard (vedoucí práce)
The aim of this master’s thesis is to introduce lung perfusion procedures and determine the parameters that are connected to the state of the lungs after perfusion and during preservation. In the perfusion process and for storing the lung, the phosphate-buffered saline (PBS) solution is used. The work focuses mainly on the parameters that can be measured and evaluated in the perfusate solution during the perfusion and preservation of the lungs such as pH, total dissolved solids, and proteins. These factors can be measured according to several procedures that are based on different principles. The mentioned process has been selected and implemented with regard to availability, feasibility, and appropriateness given. The pH and TDS parameters have been acquired by electrodes. Therefore, sensor calibration is an integral part of the measure ment. The concentration of the proteins was measured with the Bradford assay where it is important to follow the established protocol. Materials for that were present and provided in the Tissue engineering laboratory. Another intention is to assess the state of the lung tissue, meaning how the lungs gradually change their appearance, weight, and mechanical properties over time. The weight is obtained with the calibrated load cell sensor. For this sensor, a platform had to be assembled in order to function correctly and with great accuracy. From the field of mechanical properties of the lungs, the compliance and PV loops have been selected and presented. Five lungs were used for measurement. The appearance of the lungs changed over time and the necrosis was progressing. The lung viability was preserved with the PBS solution with balanced pH. The value of pH was maintained around pH 7. The concentration of the total dis solved solids (TDS) was determined and similar values were obtained in all lungs because the same solution was used. The TDS fluctuated slowly same as pH because they are correlated. The weight of the lungs decreased with passage of the time as expected. Protein concentration increased over time. That can indicate the inflammatory processes in the lung tissue or lung injury. The surface temperature was also obtained with a laser thermometer and decreasing values were noted with increasing storage time. Static compliance had unexpected charac teristics in some of the lungs. This was probably influenced by leakage due to an unsecured trachea. The last parameter was PV loops. The shape of the PV loops looked good until 48h in the majority of the loops. Then, the shape flatted and the shortage of curves appeared due to shortness of breath.
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