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Bioinformatic analysis of protein/DNA interactions
Božíková, Paulína ; Schneider, Bohdan (advisor) ; Hašek, Jindřich (referee)
In this thesis, we focused on local structural features of the DNA backbone in protein-complexed DNA and non-complexed (naked) DNA, and its dependence on types of a base pairing in DNA, and on the base sequence. To reach this goal we analyzed about 1,400 crystal structures of DNA in complexes with proteins and more than 400 crystal structures of naked DNA. DNA local conformations were structurally classified into 38 dinucleotide conformers ntCs, which were described previously (Svozil et al. Nucleic Acids Res. 2008). The ntC were further clustered into 16 structural alphabet classes ntA to reduce the number of analyzed variables. We assembled base-paired dinucleotides from double helical DNA structures accord- ing to their assigned structural alphabet classes into so called Association matrices. Three basic Association matrices were analyzed; two compare ntA/ntA associations between dinucleotides forming only Watson-Crick base pairs in protein/DNA com- plexes and in naked DNA, respectively; the third one ntA/ntA associations between dinucleotides base-paired also by non-Watson-Crick pairs. We also analyzed As- sociation matrices of dinucleotides as a function of their sequences. The analyzes revealed differences in structural behavior of various ntA and their dependence on dinucleotide sequences.
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Atrial fibrillation detection using time-domain methods
Sámel, Maroš ; Ronzhina, Marina (referee) ; Janoušek, Oto (advisor)
The purpose of this work is to get better understanding of the problems of atrial fibrillation followed by the processing methods for detection of atrial fibrillation based on an analysis of the ventricular rhythm. Methods that are described: method of medians, methods based on histograms (using coefficient of variation and density histograms of RR and RR intervals), method using RdR map, method using complexity of RR intervals and methods based on a statistical framework by Gaussian distribution and Laplace function The practical part of this work is focused on comparing these methods and selecting the best one – method of medians is the chosen one. This is followed by implementation of this method in the Matlab and testing it on the real data from a selected database. In the end, the detection ability of our method is evaluated and compared with the thoeretical detection abilities of the other methods. Our algorithm for detection of atrial fibrillations, based on the median method, achieved excellent results with the highest value of specificity obtained at 93,976%, sensitivity at 89,182% and AUC (area under the curve) at 0,973.
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The use of quantification of nursing care in psychiatric hospitals
STUCHLÍKOVÁ, Jindřiška
Theme of the bachelor thesis is a utilization of quantification of nursing care in psychiatric hospitals. Psychiatry provides a treatment to persons with mental disorder. In most cases there is nobody to help the patient with his problems. So he searches some specialiste, in this case a psychologist or a psychiatrist. The doctor determines hospitalization of the sick man if the patient is not able to visit an ambulant treatment. For these patients there is performed a basic and a special nursing care. The basic nursing care is composed of feeding, hygiene, etc. The special nursing care provides diagnostic, terapeutic and monitoring operations. The thesis has theoretical and scientific parts. The theoretical part deals with discipline of psychiatry, with form and methodes of care, with legislative definition and with education and competences of nurses. The scientific research was realized by methode of quantification of nursing care by Pochylá and Pochylý (2008), it is a qualitative and quantitative methode. The first part deals with collecting of datas and subsequent recording datas to a record sheet. Next step was to determine activities of special nursing care. There were determined averages and standard deviations for operations thereby we gained average periods of all operations. The purpose of the thesis was to determine average time difficulty of all operations and to determine time values of nursing care of selected groups of patients. The research finds that the nursing care is the most used operation for sick men. Nursing care changes in patients according to the current state of health. Other specifics of nursing care include monitoring patients who may endanger themselves or their surroundings. The most often performed operation in psychiatric hospital in medication is per os. We chose 3 goals for the job. The first objective was to inventory special nursing care in psychiatric hospitals. Another objective is to determine the average time values for individual nursing activities of special nursing care in a psychiatric hospital. The final goal was to determine the time values of special nursing care in selected patient groups. Based on the first goal, a research question has been identified: What is the most common performance in a psychiatric hospital? Based on the second objective, the research question was determined: What are the average time values for individual nursing activities of special nursing care in a psychiatric hospital? Based on the third objective, the hypothesis was chosen: The time values of special nursing care are different for selected patient groups.
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Bioinformatic analysis of protein/DNA interactions
Božíková, Paulína ; Schneider, Bohdan (advisor) ; Hašek, Jindřich (referee)
In this thesis, we focused on local structural features of the DNA backbone in protein-complexed DNA and non-complexed (naked) DNA, and its dependence on types of a base pairing in DNA, and on the base sequence. To reach this goal we analyzed about 1,400 crystal structures of DNA in complexes with proteins and more than 400 crystal structures of naked DNA. DNA local conformations were structurally classified into 38 dinucleotide conformers ntCs, which were described previously (Svozil et al. Nucleic Acids Res. 2008). The ntC were further clustered into 16 structural alphabet classes ntA to reduce the number of analyzed variables. We assembled base-paired dinucleotides from double helical DNA structures accord- ing to their assigned structural alphabet classes into so called Association matrices. Three basic Association matrices were analyzed; two compare ntA/ntA associations between dinucleotides forming only Watson-Crick base pairs in protein/DNA com- plexes and in naked DNA, respectively; the third one ntA/ntA associations between dinucleotides base-paired also by non-Watson-Crick pairs. We also analyzed As- sociation matrices of dinucleotides as a function of their sequences. The analyzes revealed differences in structural behavior of various ntA and their dependence on dinucleotide sequences.
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The efect of environmental variables on diversity of lichen photobionts
Červenková, Tereza ; Škaloud, Pavel (advisor) ; Peksa, Ondřej (referee)
Lichens represent a synergistic combination of at least two organisms, a heterotrophic fungus and a photosynthetic alga or a cyanobacterium. This association has resulted in a symbiotic organism, which is well tolerant to environmental influences. In fact, symbiotic relationship provides mutual benefit for both organisms. It is generally well known that the fungal partners of lichens are far less sensitive to environmental conditions, such as the temperature, altitude, rainfall or the type and composition of the substrate, in comparison to their algal partners. Therefore, lichen forming fungi have much wider ecological valences than the photobionts interacting with them. Indeed, most of the photosyntetic genera and species are adapted only to certain environmental conditions. For this reason, the symbiotic algae and cyanobacteria probably play a major role during the initial lichen formation on the site. This thesis focuses on the adaptability of photoautotrophic symbionts of lichens, coccoid green algae and cyanobacteria, to environmental conditions. Ecological diversification of photobionts has a direct impact on their genetic differentiation and thus to differentiate lichen species themselves. Unfortunately, in many studies the authors mostly dealt with the diversity of macroscopic symbiotic...
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Stratification risk of disease progression in patients with abnormal cervical cytologic finding by means of molecular genetic analysis of selected biological factors
Gomolčáková, Barbora ; Kašpírková, Jana (advisor) ; Španielová, Hana (referee)
The aim of this thesis was to track the impact of selected herpesviruses, polyomaviruses, Chlamydia trachomatis and methylation of tumor supressor genes at the development and progression of high grade- lesion in HPV - positive patients by means of molecular-genetic techniques. Confirmation of these markers presence in women with severe lesions of cervix would help to raise necessary specificity of molecular genetics HPV testing and recommend it as a primary screening test for cervical carcinoma prevention. HPV testing could thus replace currently prevailing cytology which has relatively low sensitivity and therefore the number of false negative results. The analyzed samples consisted of cytological cervical smears of 51 HPV positive women, with histologically confirmed presence of severe lesions, collected in liquid medium. Samplings from 51 women without infection were used as a control. The possible effect on disease progress was confirmed only in the case of gene promoters' methylation whose presence was detected in up to 26 patients. It is, however, very unlikely that cancer would develop in all these women. This marker could thus help to stratify patients at risk but only to some extent. Although the individual effect of remaining markers has not been established in the carcinogenesis of cervical...
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Automatic sleep scoring using polysomnographic data
Kříženecká, Tereza ; Potočňák, Tomáš (referee) ; Ronzhina, Marina (advisor)
The thesis is focused on automatic classification of polysomnographic signals based on various parameters in time and frequency domain. The parameters are acquired from 30 seconds long segments of EEG, EMG and EOG signals recorded during different sleep stages. The parameters used for automatic classification of sleep stages are selected according to statistical analysis. Classification is performed using the SVM method and evaluation of the success of the classification is done using sensitivity, specificity and percentage success. Classification method was implemented using Matlab.
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Fingerprint biometry
Smékal, Ondřej ; Drahanský, Martin (referee) ; Fedra, Petr (advisor)
Algorithms designed for identification and verification persons by fingerprints recognition are spread and used as in forensics aplications as in private sector for a long time. The aim of this thesis is to make us aquainted with various aplicated mathematic models of fingerprint processing in digital way. Second task is the presentation algorithmic solution of chosen subject identification procedure by force of Fingerprint matching. Algorithm is solid in the development environment platform Matlab.
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Quality measures of classification models and their conversion
Hanusek, Lubomír ; Hebák, Petr (advisor) ; Řezanková, Hana (referee) ; Skalská, Hana (referee)
Predictive power of classification models can be evaluated by various measures. The most popular measures in data mining (DM) are Gini coefficient, Kolmogorov-Smirnov statistic and lift. These measures are each based on a completely different way of calculation. If an analyst is used to one of these measures it can be difficult for him to asses the predictive power of a model evaluated by another measure. The aim of this thesis is to develop a method how to convert one performance measure into another. Even though this thesis focuses mainly on the above-mentioned measures, it deals also with other measures like sensitivity, specificity, total accuracy and area under ROC curve. During development of DM models you may need to work with a sample that is stratified by values of the target variable Y instead of working with the whole population containing millions of observations. If you evaluate a model developed on a stratified data you may need to convert these measures to the whole population. This thesis describes a way, how to carry out this conversion. A software application (CPM) enabling all these conversions makes part of this thesis. With this application you can not only convert one performance measure to another, but you can also convert measures calculated on a stratified sample to the whole population. Besides the above mentioned performance measures (sensitivity, specificity, total accuracy, Gini coefficient, Kolmogorov-Smirnov statistic), CPM will also generate confusion matrix and performance charts (lift chart, gains chart, ROC chart and KS chart). This thesis comprises the user manual to this application as well as the web address where the application can be downloaded. The theory described in this thesis was verified on the real data.
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Nursing specifics in patients with leukemia
KAFKOVÁ, Zuzana
The topic of the essay was {\clq},Specific features of nursing patiens suffering from leukemia``. In the past the non-medical public understood the term onco-hematology to include one thing {--} leukemia. Qualitative research was used to prepare this essay; interviews and monitoring of processes in the internal medicine ward intermediary treatment in České Budějovice Hospital were applied in the process of data collection.
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