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Using wearables to monitor physical activity
Mádlová, Zdenka ; Větrovský, Tomáš (advisor) ; Omcirk, Dan (referee)
Title: Using wearables to monitor physical activity Objectives: The aim of this study is to assess the validity of the Fitbit Charge 5 compared to the ActiGraph wGT3x-BT for the assessment of physical activity (steps, time spent in moderate physical activity, vigorous physical activity and moderate to vigorous physical activity) in adults. Methods: The Fitbit Charge 5 commercial physical activity monitor was compared to the ActiGraph wGT3x-BT under daily living conditions. Healthy adults (n=32) wore both devices in a 7-day field study. Data were analyzed based on days for steps, minutes of moderate physical activity, minutes of vigorous physical activity and minutes of moderate to vigorous physical activity. Pearson's correlation coefficient and Bland-Altman plot were used to assess the correlation between the Fitbit Charge 5 device and the criterion. Mean percentage error (MPE) and mean absolute percentage error (MAPE) were calculated to assess differences. Results: The Fitbit Charge 5 had a very strong correlation (r = 0,94; 95% CI 0,92- 0,96) on the step measurement with criterion. The MAPE value was 23%. A weak correlation with respect to the criterion was demonstrated for the measured physical activity of moderate intensity (r = 0,33; 95% CI 0,27- 0,39). For vigorous physical activity a...
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Bioinformatics Tool for the Analysis of Gene Neighbourhoods
Hřebíček, Ondřej ; Kameník, Zdeněk (advisor) ; Větrovský, Tomáš (referee)
The discovery of novel biosynthetic gene clusters (BGCs), particularly in Actinobacteria, is key for the development of new antimicrobials and other bioactive compounds derived from bacterial specialized metabolites. BGC database-independent BGC-finding software represents a largely-unexplored avenue of research capable of finding BGCs missed by mainstream software due to its dependence on databases of published BGCs. In this work, a bioinformatics tool is presented, which seeks to unite the fragmented functions of database-independent BGC-finding software into a single comprehensive package and make it accessible to non-expert users through an easy-to-use graphical user interface. The software utilizes the output of NCBI BLAST containing user-selected marker proteins to identify points of co-localization, and then displays the results through a fully- interactive graphical interface which allows users to further analyse the data. The software's capabilities and limitations have been tested on L-tyrosine-derived and L-leucine-derived 4-alkyl-L- proline biosynthetic gene subclusters. The software was able to find 120 out of 121 manually-found biosynthetic gene subclusters, showcasing the reliability of the core algorithm. In addition, a further 131 putative L-leucine-derived 4-alkyl-L-proline...
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Physical and mental performance of morning and evening chronotypes in different times of day
Červená, Kateřina ; Bendová, Zdeňka (advisor) ; Jelínková, Dana (referee) ; Větrovský, Tomáš (referee)
Circadian rhythmicity, which evolved in accordance with the rhythmicity of the external environment tied to the earth's rotation, governs the regular rhythms of our physiology and behavior. The central circadian clock in the suprachiasmatic nuclei of the hypothalamus controls the roughly 24-hour rhythmicity of many peripheral clocks of most cells of the body, that can be observed from the molecular to the behavioral level. The intrinsic circadian period (τ) in humans is on average slightly longer than 24 h, but may also be slightly shorter. Individuals with a short τ are referred to as morning chronotypes, whereas individuals with a long τ are referred to as evening chronotypes. However, the majority of the population belongs to the so-called intermediate chronotype. The molecular mechanism of circadian oscillations controlled by the circadian clock has been shown to be closely linked to cellular metabolism. Many physiological processes important for physical and cognitive performance are also regulated by the circadian system. The main aim of both studies was to quantify the difference in performance during morning and evening testing in subjects of a pronounced evening and morning chronotype. While the motivation for conducting Study A was practical, with the aim of identifying potential biases...
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Tools for microbial community analysis using high-throughput amplicon sequencing data
Prášilová, Alžběta ; Větrovský, Tomáš (advisor) ; Novotný, Marian (referee)
Amplicon high-throughput sequencing is currently the most widely used technique to investigate complex microbial communities. In order to analyze amplicon sequencing data, specialized software and algorithms are required to turn raw sequencing data into biologically meaningful information. This thesis serves as an overview of the current pos- sibilities and an introduction to microbial community analysis. It provides a comparison of the most widely used bioinformatics pipelines as well as a newer pipeline SEED2 and a foundation for users to make a decision based on their preferences. 1
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The relationship between physical fitness and selected tests of cognitive functions in pupils of elementary schools
Šula, Marek ; Šteffl, Michal (advisor) ; Větrovský, Tomáš (referee)
Title: The relationship between physical fitness and selected tests of cognitive functions in pupils of elementary schools Objectives: The main aim of the thesis was to estimate the relationship between physical fitness and cognitive abilities among pupils of elementary schools Methods: The thesis was carried out as a cross-sectional study. Pupils aged 8 to 12 years (n = 66; age 9.8 ± 0.8) participated in the study. The cognitive abilities were determined using standardized online tests on the portal www.proskoly.cz, and the physical fitness levels was determined using the test battery Unifittest (6-60) Results: The girls did not differ from the boys in any of the tests. In the overall group, the relationships between cognitive abilities and physical fitness were very weak and statistically not significant. However, in girls, we found indirectly proportional statistically significant (p <0.05) relationships between the Visual Memory test and all the physical fitness tests as well as between the Perception test and Standing Long Jump test, Shuttle Run Agility test, Endurance test, and overall Unifittest (6-60) score. No statistically significant relationship was found in the boys; however, the correlation indicated that the relationships were directly proportional Key words: cognitive abilities,...
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Obesity monitoring in middle aged men in Hradec Králové
Senecký, Petr ; Bunc, Václav (advisor) ; Větrovský, Tomáš (referee)
Title: Obesity monitoring in middle aged men in Hradec Kralove Targets: The targets of thesis is to determine prevalence of the obesity in men at age 30 - 50 years in Hradec Kralove. The necessary data for this empirical research will be obtained on the basis of the questionnaires distributed among 30 active athletes and 30 pacients of prof. Martinik's diabetology office, who suffer from obesity and undergo treatment in his office. Subsequently, I will perform a deep analysis of all the data obtained from the questionnaries, in order to identify hazard factors for obesity, stress management, physical aktivity, fixed daily routine and life management or the prevalence of the genetic load in the group of surveyed athletes and surveyed obese patients of prof. Martiník's diabetology office. These data will be then compared in order to identifily the main differences between active athletes and obese patients. Methods: The empirical research was conducted at 30 randomly selected active athletes (at age 30 - 50 years), who live in Hradec Kralove and at 30 random patients (also at age 30 - 50 years) of prof. Martiník, who also live in Hradec Kralove and undergo medical treatment on the basis of the questionnaire, which I created myself and filled personally with the patients and athletes in order to...
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Pyrosequencing analysis of fungal assemblages and the effect of ITS rDNA intragenomic variation on diversity estimates
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Větrovský, Tomáš (referee)
The ITS region of nuclear ribosomal DNA has recently become a frequently studied region for its use as a barcode marker. It is employed in environmental metagenomic analyses, the determination of fungi and in studies of fungal phylogenetics. In genomes, rDNA occurs in the form of large multicopy tandem arrays. Thus common Sanger sequencing leads to a consensus of many copies which in fact conceals most of the potential intragenomic variation. However 454 pyrosequencing reveals the sequence of single copies. Although it is believed that most of the variation among copies is reduced during a process called concerted evolution, some variation might still be conserved, including variation of non-functional pseudogenes. As a consequence, when using 454 pyrosequencing, we are not able to discriminate between this variation and real diversity. This could have a huge impact on the estimation of real diversity as well as on the correct assessment of pyrosequence studies. This thesis reviews current knowledge of intragenomic variation among fungi and summarizes some papers applying pyrosequencing in the research of fungal diversity. At the same time it indicates intragenomic variation as a potential cause of untrue diversity in diversity studies. Up until now there hasn't existed any experimental survey covering...
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Soil microbial communities in agroecosystems and natural habitats contributing to resistance and resilience of the soil environment
Sarikhani, Ensyeh ; Kopecký, Jan (advisor) ; Demnerová, Kateřina (referee) ; Větrovský, Tomáš (referee)
Ensyeh Sarikhani Soil microbial communities in agroecosystems and natural habitats contributing to resistance and resilience of the soil environment. Summary The control of common scab of potatoes (CS) includes resistant varieties (cultivars), precise fertilization, increase of soil moisture, and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. A monitoring study was done in 32 sites to evaluate the relation between CS and biological/chemical soil parameters. Correlations were observed between scab severity and content of nutrients such as Fe, N, and Ca in soil and periderm, and between disease severity and abundance of actinobacteria and total bacteria, together with the pathogenicity determinant, txtB gene (biosynthetic gene of thaxtomin) in both soil and periderm of potatoes. The findings led to novel conclusions, which can help to understand relationships applicable in scab control. Peat and DTPA chelated iron were supplemented to pots filled with soil conducive for CS in order to determine the effects of soil organic matter, iron and pH on CS development. The results were compared with data obtained for a suppressive soil from a nearby field with naturally low CS severity. Both peat and iron supplements decreased CS and the combination...
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