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Population genetic analysis of Old Kladruber horse
Vostrá Vydrová, Hana ; Majzlík, Ivan (advisor) ; Karel, Karel (referee)
The Old Kladruber horse, along with the Lipizzaner horse, Andalusian horse and Lusitano horse, is of the original Italo-Spanish type. The Old Kladruber horse is kept in two colour varieties (grey and black). Because the population is closed, there is a concern about the loss of genetic variation. The genetic diversity and population structure were analysed in the Old Kladruber horse breed based on the pedigree information of animals that were registered in the Studbook to identify factors that may have affected the genetic variability of the breed. Pedigree records collected from 1729 to 2013 contained information on 7971 animals that were used in the analyses. The pedigree depth was up to 33 generations, with an average of 15.1 complete generations. The effective number of founders and ancestors contributing to the current genetic pool was 92.69 and 17.16, respectively. The average values of the inbreeding coefficient were as follows: 13% (with a maximum value of 29%) for the reference population (individuals that can currently take part in reproduction, n=612), 11% for the grey variety (with a maximum value of 25%) and 15% for the black variety (with a maximum value of 29%). The proportion of inbred animals was high (99%). The average rate of inbreeding in the reference population was 1%: 0.8% for the grey variety and 1.1% for the black variety, and the respective estimates of the effective population sizes were 52 for the reference population, 62 for the grey variety and 45 for the black variety. The estimated percentage of genetic diversity lost due to non-random mating within subpopulations and the reference population was 1.0, 1.0 and 1.2%, respectively. The total loss of genetic diversity in the reference population, in the grey variety and in the black variety was 11%, 13% and 17%, respectively.
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Information content in vocalization of guinea pigs (Cavia porcellus): individual distinction and recognition of predators
Baklová, Aneta ; Baranyiová, Eva (advisor) ; František, František (referee)
Guinea pigs represent domesticated precocious rodents which became common pets. From the first day after birth they are fully vocal. This thesis was devoted
to the vocalization of pups. The aim of the thesis was to 1) determine the age when the vocal individuality in whistle sound is demonstrable; 2) test possible ultrasonic signals emitted by young guinea pigs; 3) study the antipredator reactions and alarm calls to aerial (bird of prey) and terrestrial (dog) predators and human (control test).
A total of 16 guinea pig pups were tested for vocal individuality, 28 pups
for ultrasonic vocalization and 27 adolescents for predator recognition. When testing vocal ontogeny during the first 9 days after birth, I observed changes in temporal, frequency and parameter of intensity . When I test vocal individuality by cross-validated discriminant function analysis (DFA) based on ten acoustic parameters, calls were classified to correct animals with following success: day 1 = 71.9%, day 3 = 58.8%, day 5 = 53.10%, day 7 = 50.60% and day 9 = 63.10%. The highest frequency in whistle was 30.03 kHz. In predator discrimination reactions as freezing, fleeing and vigilance were observed. In the presence of dog, guinea pigs reacted for the longest time and most frequently by freezing. When confronted with a bird of prey, I observed for a longest time and most often fleeing and then freezing. When exposed to a human, guinea pigs showed mostly vigilance. Almost no vocalization was observed except for two events
of alarm calls - drrr as in the presence of dog and chirrup as reaction to bird of prey.
The following conclusions can be drawn from the presented results: 1) vocal individuality of guinea pigs is demonstrable immediately after birth and the rate
of individually different vocal parameters changes with age; 2) guinea pigs are able
to produce sound up to 30 kHz, i.e. within the ultrasound range, but signals of high frequencies are not crucial for their communication; 3) guinea pigs discriminate between terrestrial and aerial predators, but they emit alarm calls rather rarely.
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Antioxidant, anti-proliferative and immunomodulatory effect of fruits, vegetables and mushrooms in vitro
Doskočil, Ivo ; Havlík, Jaroslav (advisor) ; Orsák, Matyáš (referee)
Recently there has been an increasing interest in discovering of new species of plants and mushrooms which have antioxidant or anti proliferative activity. The interest is caused by the fact that these species have medicinal and food utilization. These properties of plants and mushrooms can be used when dealing with many diseases which may be connected with oxidative stress (inflammatory bowel disease, cardiovascular disease, hypertension, and tumour disease, etc.).
The thesis propounds characteristics of in vitro antioxidant and anti proliferative activity of 19 types of juices and 28 methanol extracts of fruits and vegetables, which are common parts of a diet. In the thesis there are also characteristics of 13 ethanol extracts of edible mushrooms of the order of Polypore (Popyporales). Antioxidant activity was quantifie by 2, 2 diphenyl 1 picrylhydrazyl (DPPH), oxygen radical absorbance capacity (ORAC), and inhibition of nitric oxide (NO) production. Cytotoxicity was measured by MTT (3 (4,5 dimethylthiazol 2 yl) 2,5 diphenyltetrazolium bromide. Immunomodulatory activity was determined by an assay of phagocytic activity of human neutrophil granulocytes. Further a total phenolic content (TPC) and total beta glucan content were investigated; these are considered to be the potentially active constituents participating in mentioned activities.
From the obtained results it is evident that juices (TPC = 1603.2 mg GAE/L; ORAC = 438.5 umol TE/g)
and a bilberry (Vaccinium myrtillus) fruit extract (ORAC 836.6 umol TE/g; DPPH = 404.6 umol TE/g) showed
the highest antioxidant activity of all tested samples of fruits and vegetables. Capsicum (Capsicum L.)
juices (TPC = 642.1 mg GAE/L; ORAC = 127.9 umol TE/g) and a radish (Raphanus sativus L.) extract
(ORAC 724.5 umol TE/g; DPPH = 52.2 umol TE/g) also proved to have the high values of antioxidant activity. From the tested fruits and vegetables the following inhibited to produce a nitric oxide: onion (Allium cepa L) juices (lowered the NO production by 57%), tangerine juices (Citrus reticulata Blanco)(by 52%), broccoli (Brassica oleracea var. botrytis italic) extract (by 21%), and orange (Citrus sinensis Pers.) extract (by 10%). Concerning edible
mushrooms, Lentinus tigrinus (Bull.) Fr. (TPC = 216.2 umol GAE/g of extract), Ganoderma lucidum (Curtis) P. Kras (TPC = 257.9 umol GAE/g of extract), and Royoporus badius (Pers.) A.B. De (TPC = 257.8 umol GAE/g of extract) presented the highest phenolic content. Sparassis crispa (Wulfen) Fr. (117.4 mg/g of extract) had the highest content of beta glucan. Substantial effect on phagocytic activity of granulocytes was noticed in connection with Neolentinus lepideus (Fr.) Redhead & Ginns, Polyporus squamosus (Huds.) Fr., and S. crispa. In connection with the latter of mentioned mushrooms, a moderate inhibitory effect towards HT 29 human colorectal adenocarcinoma cell line
(IC50 = 107 ug/ml of extract) was noticed.
The results indicate that the tested plants and mushrooms can be beneficial when reducing the negative effects of oxidative stress. The oxidative stress has been recognized as a contributing factor to a whole range of diseases and the reduction of the oxidative stress may lead to the decrease in the possibility of the diseases´ progression. The results show the possible favourable effects on the human health. When evaluating the results, the following fact should be taken into consideration; the in vitro tests and screenings are considered to be the first phase of systematic research of the effects and serve for the choice of respondents for further detailed studies.
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Frequency stabilized semiconductor laser source for high-resolution interferometry
Řeřucha, Šimon ; Hucl, Václav ; Holá, Miroslava ; Čížek, Martin ; Pham, Minh Tuan ; Pravdová, Lenka ; Lazar, Josef ; Číp, Ondřej
We have assembled an experimental iodine stabilized Distributed Bragg Reflector (DBR) diode based laser system lasing at a wavelength that is in a close proximity to the wavelength of a stabilized He-Ne lasers traditionally used for metrological applications (λ=632.9 nm in vacuum). The aim was to verify whether such a system could be used as an alternative to the He-Ne laser while yielding wider optical frequency tuning range, higher output power and high frequency modulation capability. We have measured the basic characteristics of the laser source and then we have compared the performance of the laser system with that of a traditional frequency stabilized He-Ne laser with a series of experimental arrangements similar to those usually found in laser interferometry and displacement metrology applications. The results indicate that DBR diode laser system provides a good laser source for applications in dimensional (nano)metrology since it provides more output power and advanced tunability options than stabilized He-Ne lasers while maintaining fundamental requirements such as the frequency stability, coherence length and also a defined traceability.\n\n
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Optical low dispersion rezonator as length sensor using optical frequency comb
Pravdová, Lenka ; Hucl, Václav ; Lešundák, Adam ; Lazar, Josef ; Číp, Ondřej
Ultra-high precis measurements are domain of lasers interferometers. An optical resonator measuring method using broad spectrum of radiation of an optical frequency comb was designed and experimentally verified at our workplace. The measuring of a quantity – a distance of resonator mirrors – is provided by its conversion to the value of repetition frequency of the pulse laser with mode-locked optical frequency comb. In this paper the comparison of the absolute scale of the optical resonator with an incremental interferometer scale is introduced. The incremental interferometer is implemented for verification of the optical resonator scale. The double beam incremental interferometer is operating at the wavelength of 633 nm and the measuring mirror with piezo actuator is used as one of its reflectors. It turns out that the major error signal is the reflection of the periodic nonlinearity of the incremental resonator scale. The relative resolution of our method reaches values up to 10-9 while maintaining measuring scale.
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Radio frequency resonator for feeding ion trap
Jedlička, Petr ; Pham, Minh Tuan ; Čížek, Martin ; Pavelka, Jan ; Lešundák, Adam ; Hucl, Václav ; Hrabina, Jan ; Řeřucha, Šimon ; Lazar, Josef ; Číp, Ondřej
Two versions of resonators were designed and manufactured - asymmetric and symmetric.\nThe resonator consists of a coil and capacity of ion trap which makes parallel resonant circuit.\nEnergy is supplied to the resonator through the coupling inductance. Resonator assembly was equipped with outputs for monitoring high-frequency voltage. Both versions have been tuned and tested.\n\n
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Optical frequency references
Hrabina, Jan
Optical frequency references based on absorption cells represent a traditional and essential tool for frequency locking of precise laser standards. One of the most often used absorption media is a molecular iodine 127I2, which offers a rich atlas of strong and narrow absorption lines across mostly whole visible part of optical spectrum. The main disadvatage of this media can be seen in its high corrosivity and sensitivity to presence of foreign substances. This contribution is oriented to comparison of possible measurement methods for bulk- and also optical fiber- based iodine absorption cells quality and chemical purity testing.\n\n
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Possibilities in monitoring of laser welding process
Horník, Petr ; Mrňa, Libor
With increasing demands on the quality of the welds, it is usual to apply automated machine welding with monitoring of the welding process. The resulting quality of the weld is largely affected by the behavior of keyhole. However, its direct observation during the welding process is practically impossible and it is necessary to use indirect methods. At ISI we develop optical methods of monitoring the process based on analysis of radiation of laser-induced plasma using Fourier and autocorrelation analysis. Observation of keyhole inlet opening is partially possible through a coaxial camera mounted on the welding head and the subsequent image processing. A high-speed rear camera to understand the dynamics of the plasma plume. Through optical spectroscopy of the plume, we can study the excitation of elements in a material. Shielding gas flow can be visualized using schlieren method.
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New Methods for Increasing Efficiency and Speed of Functional Verification
Zachariášová, Marcela ; Dohnal, Jan (referee) ; Steininger, Andreas (referee) ; Kotásek, Zdeněk (advisor)
Při vývoji současných číslicových systémů, např. vestavěných systému a počítačového hardware, je nutné hledat postupy, jak zvýšit jejich spolehlivost. Jednou z možností je zvyšování efektivity a rychlosti verifikačních procesů, které se provádějí v raných fázích návrhu. V této dizertační práci se pozornost věnuje verifikačnímu přístupu s názvem funkční verifikace. Je identifikováno několik výzev a problému týkajících se efektivity a rychlosti funkční verifikace a ty jsou následně řešeny v cílech dizertační práce. První cíl se zaměřuje na redukci simulačního času v průběhu verifikace komplexních systémů. Důvodem je, že simulace inherentně paralelního hardwarového systému trvá velmi dlouho v porovnání s během v skutečném hardware. Je proto navrhnuta optimalizační technika, která umisťuje verifikovaný systém do FPGA akcelerátoru, zatím co část verifikačního prostředí stále běží v simulaci. Tímto přemístěním je možné výrazně zredukovat simulační režii. Druhý cíl se zabývá ručně připravovanými verifikačními prostředími, která představují výrazné omezení ve verifikační produktivitě. Tato režie však není nutná, protože většina verifikačních prostředí má velice podobnou strukturu, jelikož využívají komponenty standardních verifikačních metodik. Tyto komponenty se jen upravují s ohledem na verifikovaný systém. Proto druhá optimalizační technika analyzuje popis systému na vyšší úrovni abstrakce a automatizuje tvorbu verifikačních prostředí tím, že je automaticky generuje z tohoto vysoko-úrovňového popisu. Třetí cíl zkoumá, jak je možné docílit úplnost verifikace pomocí inteligentní automatizace. Úplnost verifikace se typicky měří pomocí různých metrik pokrytí a verifikace je ukončena, když je dosažena právě vysoká úroveň pokrytí. Proto je navržena třetí optimalizační technika, která řídí generování vstupů pro verifikovaný systém tak, aby tyto vstupy aktivovali současně co nejvíc bodů pokrytí a aby byla rychlost konvergence k maximálnímu pokrytí co nejvyšší. Jako hlavní optimalizační prostředek se používá genetický algoritmus, který je přizpůsoben pro funkční verifikaci a jeho parametry jsou vyladěny pro tuto doménu. Běží na pozadí verifikačního procesu, analyzuje dosažené pokrytí a na základě toho dynamicky upravuje omezující podmínky pro generátor vstupů. Tyto podmínky jsou reprezentovány pravděpodobnostmi, které určují výběr vhodných hodnot ze vstupní domény. Čtvrtý cíl diskutuje, zda je možné znovu použít vstupy z funkční verifikace pro účely regresního testování a optimalizovat je tak, aby byla rychlost testování co nejvyšší. Ve funkční verifikaci je totiž běžné, že vstupy jsou značně redundantní, jelikož jsou produkovány generátorem. Pro regresní testy ale tato redundance není potřebná a proto může být eliminována. Zároveň je ale nutné dbát na to, aby úroveň pokrytí dosáhnutá optimalizovanou sadou byla stejná, jako u té původní. Čtvrtá optimalizační technika toto reflektuje a opět používá genetický algoritmus jako optimalizační prostředek. Tentokrát ale není integrován do procesu verifikace, ale je použit až po její ukončení. Velmi rychle odstraňuje redundanci z původní sady vstupů a výsledná doba simulace je tak značně optimalizována.
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