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The Stateful Packet Processing in P4 Language
Kohout, Pavel ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
With the growing speed and complexity of computer networks, arise requirements for creating powerful devices that are capable of collecting statistics and changing their own functionality according to the demands of network administrators. These requirements can be described using specialized programming languages such as P4. In this bachelor thesis a design, implementation, testing and integration of register and counter stateful memory modules into P4 compiler system for FPGA technology was made. The created system supports the collection of statistics described in P4 language at speeds up to 100 Gbps.
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The Application of Variational Autoencoders for Ancestral Sequence Reconstruction
Kohout, Pavel ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
Protein engineering is an interdisciplinary science concerned with the design of improved proteins. A successful method used to design more stable and active proteins is ancestral sequence reconstruction. This method explores the evolutionary relationships between existing proteins and uses phylogenetic trees to generate their evolutionary ancestors, which often exhibit the desired improved properties. Therefore, new and more robust methods using mathematical models together with huge amounts of sequence data could become a powerful tool for protein engineering. This thesis explores the use of variational autoencoders as an alternative approach to ancestral sequence design compared to conventional methods using phylogenetic trees. Experiments were performed to optimize the architecture and statistical methods were proposed to evaluate the quality of the models and the sequences generated. At the same time, robustness tests of the whole method were performed and strategies for ancestral sequence generation were proposed and implemented.
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Changes of gut microbiome in patients with inflammatory bowel diseases
Schierová, Dagmar ; Jirásková Zákostelská, Zuzana (advisor) ; Hrdý, Jiří (referee) ; Kohout, Pavel (referee)
(EN) Microbes have coevolved with humans forming symbiotic communities that constantly challenge the immune system and, when imbalanced, could lead to diseases like inflammatory bowel disease (IBD). Patients with IBD suffer from microbial dysbiosis and chronic inflammation which could be potentiated by immune system reaction to the commensal microbiota. In the research presented here, firstly I have focused on the description of the gut and skin microbiome from patients with IBD and secondly, I investigated the process of antimicrobial defense. Patients with IBD on two different biological therapies targeting TNFα, IL-12 and IL-23 cytokines were tracked for changes in their gut and skin microbiome features. Although, neither differences in gut microbial diversity nor composition were linked with the progression of the therapies, an increased similarity to the healthy control group at week 38 of anti-TNFα therapy was found. This shift in microbiome could be considered beneficial and could be attributed to the inflammation reducing effect of the therapy. While analyzing the microbiome features, various patient characteristics were taken into account and the sources microbiome of variability were uncovered, out of which the interindividual variability stood out the most. Regarding the skin microbiome,...
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Current knowledge about the influence of the intestinal microbiome on the development, course and consequences of lactose intolerance
Černá, Pavlína ; Tomešová, Jitka (advisor) ; Kohout, Pavel (referee)
The bachelor thesis investigates the current knowledge about the influence of the gut microbiome on the development and severity of lactose intolerance, as well as whether and how it can be changed to influence the course of existing lactose intolerance and its immediate and long- term consequences. In the first part of this bachelor thesis I discuss lactose itself and its metabolism, which shows its direct link to the gastrointestinal tract. Lactose intolerance (LI) is also described, how it is diagnosed, what it manifests itself as, and what its degrees are. The next chapter discusses the relationship between LI, the gut, and the gut microbiome. First, I focus here on the possible adaptability of the gut, which is mainly determined by the presence of the microbiome. There is also a link between LI and other gastrointestinal disorders in which gut bacteria play a role. The microbiome is a very dynamic population of different types of bacteria, fungi and viruses that can influence the course of lactose intolerance. This can be exploated in the subsequent therapy of LI with probiotics, which are included in part three. The most commonly used probiotic bacteria are representatives of the genus Bifidobacterium and Lactobacillus. However, probiotics are not the only option for using the gut microbiome...
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Dietary habits of patients suffering from IBD
Metličková, Aneta ; Kohout, Pavel (advisor) ; Šimková, Simona (referee)
This diploma thesis titled "Dietary habits of patients suffering from IBD", deals with specifics of said diseases as well as nutrition of these patients. The theoretical part touches on Crohn's disease and ulcerative colitis, it lists characteristics, epidemiology, possible complications and treatments of these diseases. There is a detailed description of usage of medical nutrition therapy and various diets that use to be recommended to these patients. It also presents medical nutrition therapy as an indispensable element of the process of treating these diseases. The 4 main goals I set for my thesis were as follows: to map eating habits of respondents suffering from IBD; to compare eating habits of patients suffering from IBD with those of healthy respondents; to compare eating habits of patients suffering from CD with eating habits of patients suffering from UC and lastly - to find out where respondents get their information on their disease and nutrition from. The research consisted of 12 respondents in total of which half were patients suffering from IBD and the other half were healthy individuals. The group of respondents suffering from IBD consisted of 3 CD patients and 3 UC patients. To obtain the data I used a semi-structured interview as well as dietary recall. I chose to interview only...
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The Application of Variational Autoencoders for Ancestral Sequence Reconstruction
Kohout, Pavel ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
Protein engineering is an interdisciplinary science concerned with the design of improved proteins. A successful method used to design more stable and active proteins is ancestral sequence reconstruction. This method explores the evolutionary relationships between existing proteins and uses phylogenetic trees to generate their evolutionary ancestors, which often exhibit the desired improved properties. Therefore, new and more robust methods using mathematical models together with huge amounts of sequence data could become a powerful tool for protein engineering. This thesis explores the use of variational autoencoders as an alternative approach to ancestral sequence design compared to conventional methods using phylogenetic trees. Experiments were performed to optimize the architecture and statistical methods were proposed to evaluate the quality of the models and the sequences generated. At the same time, robustness tests of the whole method were performed and strategies for ancestral sequence generation were proposed and implemented.
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Impact of Immunonutrition on the Patients With Cystic Fibrosis
Hloch, Ondřej ; Charvát, Jiří (advisor) ; Kohout, Pavel (referee) ; Rušavý, Zdeněk (referee)
The impact of immunonutrition in patiens with cystic fibrosis Abstract The aim of the study was to evaluate the application of immunonutrition in adults with cystic fibrosis (CF) and malnutrition, who have been receiving enteral nutrition in the form of standard sipping for at least a year. In 30 adult patients, immunonutrice (Impact) was given for 8 weeks. After 8 weeks, patients returned to standard nutritional support. The application of immunonutrition led to a significant reduction in systolic blood pressure and heart rate, to an increase in glomerular filtration and significant changes in the plasma aminoacidogram. Serum amyloid-A (SAA) levels decreased significantly and increased again after the intervention. However, immunonutrition administration was associated with an increase in serum malonyldialdehyde, a decrease in serum glutathione peroxidase and selenium. Thus, administration of immunonutrition led to an increase in oxidative stress, but almost all values remained within physiological limits. At 6-year follow-up, the long- term prognosis in the multivariate analysis depended only on baseline FEV1 and the degree of pulmonary involvement, respectively. The frequency and duration of subsequent hospitalizations and long-term prognosis were significantly associated with plasma fibrinogen levels....
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New regulatory hormones of breast milk
Mitrová, Katarína ; Bronský, Jiří (advisor) ; Frühauf, Pavel (referee) ; Kohout, Pavel (referee)
Background: Breastfeeding is supposed to exert long-term protection of the infant from the development of civilisation diseases later in life. Adiponectin, leptin and AFABP are candidate proteins in nutritional programming of the infant. Aim: To determine intraindividual changes of breast milk levels of regulatory hormones (adiponectin, leptin, AFABP) and adipophilin in breast milk during 12 months of lactation. Methods: Proteins were measured using high sensitive ELISA method in 72 healthy mothers within 2 days of beginning of lactation (day 0) and 1, 3, 6 and 12 months following delivery. Results: Adiponectin levels in breast milk on day 0 (D0) were 22.8 ± 0.8 (mean ± S.E.M.), in 1 month (M1) 22.0 ± 0.6, in 3 months (M3) 20.5 ± 0.6, in 6 months (M6) 21.4 ± 0.8, and in 12 months (M12) 25.7±1.4 ng/ml. AFABP levels were 12.3 ± 2.0, 6.2 ± 1.3, 1.3 ± 0.2, 2.5 ± 1.0 and 4.6 ± 1.9 ng/ml, respectively. Leptin levels were 0.3 ± 0.04, 0.2 ± 0.03, 0.1 ± 0.01, 0.1 ± 0.02 and 0.2 ± 0.04 ng/ml, respectively. Adipophilin levels in D0 were 1.98 ± 0.12, in M1 2.83 ± 0.21, in M3 2.39 ± 0.17, in M6 2.57 ± 0.16, and in M12 3.25 ± 0.21 μg/ml. We found significantly higher levels of adiponectin in M12 in comparison to M3 and M6 (p = 0.0026), higher levels of AFABP in D0 and M1 when compared to M3, M6 and M12 (p < 0.0001) and...
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The Dietary System in Hospitals in the Czech Republic: Reality and Objective Needs
Pokorná, Daniela ; Kohout, Pavel (advisor) ; Humlová, Renata (referee)
Author: Pokorná Daniela Institution: Univerzita Karlova v Praze, 1. lékařská fakulta Title: The Dietary System in Hostitals in the Czech Republic: Reality and Objective Needs Tutor: Doc.MUDr.PavelKohout,PhD. Numberofpages: 88 Numberofsupplements: 6 Year: 2011 Keywords: diet, dietary system, dietology, dietotherapy, nutritional therapist, reality, objective needs This paper deals with the dietary system in the facilities in the Czech Republic, particularly in hospitals, with the focus on reality and objective needs. It is divided into two parts - theoretical and research part. The theoretical part explains the terms such as dietology, diet, nutritional therapist, and subsequently the history, present state and possible future of the dietary system in the Czech Republic. In the research part, the reality and objective needs in the given field are explored. The focus is on objective conclusions of the research exploration as well as on initiatives and comments from professionals in the particular facilities. Three hypotheses were set and subsequently examined. The above data was obtained from facilities such as hospital, spas and health resorts, and senior homes. The research was basic and quantitative in nature; data- collecting was done using a questionnaire. Basing on ideas and comments from the...
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The Education of Patients with Home Parenteral Nutrition
Kafková, Pavla ; Kulhavá, Miluše (advisor) ; Kohout, Pavel (referee)
This bachelor's dissertation tackles the problem of educational activities which are performed by a nurse taking care of a patient with planned home parenteral nutrition /HPN/. The theoretical part contains the outline of basic concepts and principles that are essential for the appropriate educational work. The substantial part of the dissertation deals with the parenteral nutrition and the tunnel catheter /Broviac's type/ as a vein access of the first choice concerning the majority of patients who depend on HPN. The empirical part concentrates on the creation of the manual for the patients with planned HPN and the documentation of educational process. The aim of the publication is to provide a patient with a comprehensive manual and hereby to try to reduce the percentage of complications /mainly infectious/ which have been caused by insufficient education. Not only patients and their families but also the medical personnel ought to benefit from the manual as there has not been any similar comprehensive manual until now. The absence of such publication might have caused great difficulties during the educational process. The systematic approach together with continuity should be ensured by the newly formed documentation.
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