Meiosis is a specialized cell division that produces haploid cells (gametes) from diploid progenitors. During meiosis parental chromosomes (homologs) need to pair, synapse and eventually segregate. Faithful chromosome segregation depends on chromosome recombination. In the beginning of prophase I programmed double strand breaks (DSBs) are introduced in meiotic cells by SPO11 enzyme. DSBs are positioned at hotspot sites that are specified by that action of DNA-binding histone methyltransferase PRDM9. Specific enzymes act at the site of breaks to create 5’ single stranded DNA ends. With the assistance of the strand exchange proteins DMC1 and RAD51 these ends invade homologous DNA sequence and DSB repair is initiated. DSB repair can be completed either as a crossover (reciprocal exchange of DNA) or as a non-crossover. Crossover events lead to the formation of chiasmata between homologs and ensure proper segregation during the first meiotic division. An interesting feature in male meiosis is the XY chromosomes. The shared region between sex chromosomes is short and is called pseudoautosomal region (PAR). Due to their large non synapsed region, XY chromosomes need to be transcriptionally silenced. Thus they are covered with the phosphorylated histone variant H2AX (γH2AX) forming the so called sex body. PAR region has higher density of DSBs than autosomes and it had been shown that sex chromosomes undergo delayed homologous pairing. Nevertheless little is known how meiotic recombination is regulated in PAR region of sex chromosomes. In close proximity with sex body it has been found a structure named dense body (DB). There are few reports suggesting that DB contains RNAs/proteins but no DNA. Its role in meiosis was unclear because no structural component had been described. In the present thesis the role of two meiotic expressed genes is described. In our group after performing RNA screens we identified several genes that are highly expressed during meiotic prophase I. Based on the expression profile we selected polycomb-related sex comb on midleg like 1 (Scml1) gene and the ankyrin repeat domain 31 (Ankrd31) to study their role in mammalian meiosis.:List of figures i List of abbreviations ii 1. Introduction 1 1.1 Gametogenesis 1 1.2 Meiotic prophase I 2 1.2.1 Meiotic recombination 4 1.2.2 Regulation of meiotic recombination 7 1.2.2.1 Meiotic recombination hotspots and PRDM9 activity 7 1.2.2.2 Meiotic surveillance mechanisms 8 1.3 Unique properties of XY recombination 9 1.4 Sex chromatin associated structure: The dense body 10 1.5 Aim of the thesis 11 2. Publications 12 3. Discussion 92 4. Summary 98 5. References 102 Acknowledgements 108 Declarations 109

Thesis deals with the study of palate morphology and variability of patients with UCLP, using modern methods of geometric morphometrics. Dental plaster casts of UCLP patients (average age 14,8) and the control group (average age 14,7) were used for evaluation. The models were scanned using a 3D scanner. For evaluation of total variability of patients with orofacial clefts, previously rated dental casts of BCLP patients (whose age ranged from 12,1 to 16,5) were also included. All patients were operated and treated at The Clinic of Plastic Surgery in Prague. The results are in accordance with literature, which describes the basic size and shape differences in the morphology of the palate in different types of clefts (e.g. narrowing of the palate in UCLP and BCLP and asymmetry of palatal vault in UCLP). Using "Dense correspondense models analysis" average surface models were computed and new informations about the shape and premaxila position were gained. Different location and slope of the palate in different types of clefts and within control group were detected by superimposition of average models and FESA. UCLP palate have typically asymetric palate vault with a maximum height in front of the cleft palate and at the back in the side without malformations. Variability of the shape of palate for each group...

Liquid waste discharged from industrial outfalls is categorized into two major classes based on their density. One type is the effluent that has a higher density than that of the ambient water body. In this case, the discharged effluent has a tendency to sink as a negatively buoyant jet. The second type is the effluent that has a lower density than that of the ambient water body and is hence defined as a (positively) buoyant jet that causes the effluent to rise. Negatively/Positively buoyant jets are found in various civil and environmental engineering projects: discharges of desalination plants, discharges of cooling water from nuclear power plants turbines, mixing chambers, etc. This thesis investigated the mixing and dispersion characteristics of such jets numerically. In this thesis, mixing behavior of these jets is studied using a finite volume model (OpenFOAM). Various turbulence models have been applied in the numerical model to assess the accuracy of turbulence models in predicting the effluent discharges in submerged outfalls. Four Linear Eddy Viscosity Models (LEVMs) are used in the positively buoyant wall jet model for discharging of heated waste including: standard k-ε, RNG k-ε, realizable k-ε and SST k-ω turbulence models. It was found that RNG k-ε, and realizable k-ε turbulence models performed better among the four models chosen. Then, in the next step, numerical simulations of 30˚ and 45˚ inclined dense turbulent jets in stationary ambient water have been conducted. These two angles are examined in this study due to lower terminal rise height for 30˚ and 45˚, which is very important for discharges of effluent in shallow waters compared to higher angles. Five Reynolds-Averaged Navier-Stokes (RANS) turbulence models are applied to evaluate the accuracy of CFD predictions. These models include two LEVMs: RNG k-ε, and realizable k-ε; one Nonlinear Eddy Viscosity Model (NLEVM): Nonlinear k-ε; and two Reynolds Stress Models (RSMs): LRR and Launder-Gibson. It has been observed that the LRR turbulence model as well as the realizable k-ε model predict the flow more accurately among the various turbulence models studied herein.

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Objective. Determine the relationship between dietary quality and body weight/composition in college women. Specific emphasis was made regarding adherence to current MyPyramid guidelines, fruit, vegetable and junk food consumption. Design/Participants. The study used a cross-sectional design. One hundred and sixty three women were recruited to participate in the study. All participants were university students (20.4 ± 1.6 y). Diet intake was measured using the Dietary History Questionnaire (DHQ) and the Healthy Eating Index (HEI) was calculated to assess diet quality. Body fat percentage was assessed using the Bod Pod and BMI was calculated using height and weight measurements. Physical activity was measured objectively using accelerometers over seven consecutive days. Results. There was no significant difference in BMI or body fat percentage across university year. There was no relationship between diet quality (as measured using the Healthy Eating Index) and percent body fat or BMI. The number of MyPyramid equivalents of fruit was negatively correlated to body fat percentage (r = -0.2, p ≤ 0,05) but not BMI (r = -0.093, p =0.26). The number of MyPyramid equivalents of dairy was also negatively related to both body fat percentage (r = -0.21, p ≤ 0.05) and BMI (r = -0.21, p ≤ 0.05). Percentage of calories from Non Nutrient Dense Foods (NNDF) was positively related to percent body fat ( r= 0.179, p = 0.029). For every 1-percentage increase in NNDF, there was a 0.12 percentage point increase in body fat. Conclusion. Increasing fruit, dairy, and vegetable intake, and reducing intake from Non Nutrient Dense Foods (NNDF) such as French fries, cookies, and candy, may have a beneficial influence on body composition in college women.

Warm dense matter (WDM) is an extreme state of matter induced by extreme conditions and characterized as an intermediary state between (high-pressure) condensed matter and plasma. It has sparked a lot of attention in recent years as a result of current innovations in experiments and theoretical methods for modeling such complex systems. Such conditions naturally occur in astrophysical objects such as the interiors of the planets, and in white and brown dwarfs. WDM can be created in the laboratory via various methods such as laser compression, Z-pinches and heated diamond anvil cells. This thesis describes the results obtained for many such systems across a range of conditions modeled using ab-initio simulation methods. The first testbed concerns the electronic structure and linear response of the carbon phases under high-pressure and warm dense matter conditions. The focus is on modeling inelastic x-ray scattering spectra across a range of conditions useful for the analysis and interpretation of x-ray Thomson scattering (XRTS) experiments. Another major goal is to improve the existing models to compute static properties such as the equation of state, density of states with the inclusion of highly accurate data from quantum Monte Carlo (QMC) simulations relevant at finite-temperatures. This approach improves the accuracy and is also computationally inexpensive compared to path integral Monte Carlo (PIMC) methods. Lastly, improvements in linear response theory relevant for XRTS are incorporated with the inclusion of local field corrections (LFC) and finite-temperature local field corrections (T-LFC) using data from QMC simulations.

Millimeter-wave (mmWave) is widely investigated for indoor communication scenarios thanks to the available rich spectrum. However, the shortened antenna size and the high frequency make mmWave extra sensitive to blockages. Indoor dense space (IDS) is a specific type of indoor environment, where the compact geometry together with a high number of blocking objects and users make it hard to fulfill the data rate required by all of the users in the mmWave network. With the capability of redirecting signals, the reconfigurable intelligent surface (RIS) has the potential to overcome the attenuation brought by the blockage. Aside from the promising improvement in data rate brought by the RIS, the power supply for RIS is also a major concern in IDS due to the cabling and the batteries. Dynamic RIS has the capability of reconfiguring its phase-shifts to offer a higher gain in data rate with the price of consuming power. In comparison, by sacrificing the reconfigurability, static RIS does not require any power, cabling, or batteries but is expected to provide lower data rates. To find the balance between the performance and cost trade-off, the concept of self-sustainable RIS in IDS is proposed. This approach involves the utilization of specific RIS elements to harvest energy, thereby providing support for the power requirements of the RIS operation, consequently reducing the reliance on traditional cabling infrastructure. In this work, we compare the coverage extension effect brought by deploying static, dynamic, and self-sustainable RISs in the aircraft cabin which is a typical example of an IDS. To capture the propagation characteristics of a RIS in IDS, we first provide guidelines for modeling the RIS in the ray tracing (RT) simulator, and then we select the best locations to deploy RISs among three candidates. For each type of RIS deployment, we propose an optimization algorithm, which jointly configures the RIS phase-shifts and the time resources to provide the maximum equal achievable data rate for all of the users. Additionally, for the self-sustainable RIS, the working mode of each RIS element is also jointly configured such that each element is used either to reflect the incoming signal or to use the signal for energy harvesting. Based on the results, the signal propagation of a single base station (BS) can be extended from 3 rows to 11 rows by deploying static or dynamic RISs. The minimal achievable data rate is 35.4 Mbps with the static RISs and 45.3 Mbps with the dynamic RISs. The results indicate that due to the limitation of self-sustainable constraints, RISs with 16 elements are hard to cover the whole 11 rows in the considered cabin. Nevertheless, with self-sustainable RIS, 10 more UEs are covered compared to the case where no RIS is deployed. The minimal data rate with the help of the self-sustainable RISs within the coverage is 0.75 Mbps. The feasibility study shows that this energy requirement has a greater likelihood of being fulfilled as the number of elements in RIS increases. / Millimetervåg (mmWave) är allmänt undersökt för inomhuskommunikationsscenarier tack vare det tillgängliga rika spektrumet. Den förkortade antennstorleken och den höga frekvensen gör dock mmWave extra känslig för blockeringar. Indoor dense space (IDS) är en specifik typ av inomhusmiljö, där den kompakta geometrin tillsammans med ett stort antal blockerande objekt och användare gör det svårt att uppfylla den datahastighet som krävs av alla användare i mmWave-nätverket. Med förmågan att omdirigera signaler har reconfigurable intelligent surface (RIS) potentialen att övervinna dämpningen av blockeringen. Bortsett från den lovande förbättringen av datahastigheten som RIS ger, är strömförsörjningen för RIS också ett stort problem inom IDS på grund av kablarna och batterierna. Dynamic RIS har förmågan att omkonfigurera sina fasförskjutningar för att erbjuda en högre förstärkning i datahastighet med priset för att förbruka energi. I jämförelse, genom att offra omkonfigurerbarheten, kräver statisk RIS ingen ström, kablar eller batterier utan förväntas ge lägre datahastigheter. För att hitta balansen mellan prestanda och kostnadsavvägning föreslås konceptet med självförsörjande RIS i IDS. Detta tillvägagångssätt involverar användningen av specifika RIS-element för att skörda energi, vilket ger stöd för strömkraven för RIS-driften, vilket minskar beroendet av traditionell kabelinfrastruktur. I det här arbetet jämför vi den täckningsförlängningseffekt som uppstår genom att installera statiska, dynamiska och självförsörjande RIS i flygplanskabinen, vilket är ett typiskt exempel på en IDS. För att fånga utbredningsegenskaperna för en RIS i IDS ger vi först riktlinjer för modellering av RIS i ray tracing (RT)-simulatorn, och sedan väljer vi de bästa platserna för att distribuera RIS bland tre kandidater. För varje typ av RIS-distribution föreslår vi en optimeringsalgoritm, som gemensamt konfigurerar RIS-fasförskjutningarna och tidsresurserna för att tillhandahålla den maximalt lika möjliga datahastigheten för alla användare. Dessutom, för den självförsörjande RIS, är arbetsläget för varje RIS-element också gemensamt konfigurerat så att varje element används antingen för att reflektera den inkommande signalen eller för att använda signalen för energiskörd. Baserat på resultaten kan signalutbredningen av en enda base station (BS) utökas från 3 rader till 11 rader genom att distribuera statiska eller dynamiska RIS:er. Den minsta möjliga datahastigheten är 35,4 Mbps med statiska RIS och 45,3 Mbps med dynamiska RIS. Resultaten indikerar att på grund av begränsningen av självförsörjande begränsningar är RIS med 16 element svåra att täcka hela 11 rader i den övervägda kabinen. Ändå, med självförsörjande RIS, täcks 10 fler UE jämfört med fallet där ingen RIS är utplacerad. Den minimala datahastigheten med hjälp av de självförsörjande RIS:erna inom täckningen är 0,75 Mbps. Förstudien visar att detta energibehov har större sannolikhet att uppfyllas i takt med att antalet element i RIS ökar.

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