Breast cancer is the most frequent malignant disease in the female population worldvide. About 10 % of all cases are of hereditary origin. The inactivation of tumor suppressor gene BRCA1 is the main genetic predisposing factor in breast cancer in the Czech Republic. Primarily, BRCA1 participates in DNA double strand break repair. Depending on cell cycle phase, the damage is repaired by homologous recombination or non-homologous end joining. Alternative splicing variants of BRCA1 are frequently detected during the genetic screening of high risk patients. The clinical significance of these variants is unknown. Understanding of the nature of breast cancer genetics is the critical factor for early diagnosis. Based on earlier studies from the Institute of Biochemistry and Experimental Oncology 1st Faculty of Medicine Charles University, two alternative splicing variants which were repeatedly detected in patients, were chosen for functional analysis. The aim of this work is to investigate the impact of alternative splicing variants BRCA1Δ5 and BRCA1Δ10 on DNA double strand breaks repair. Particular variants were over- expressed in the cells of model system. Activity of homologous recombination (HR) and non-homologous end joining (NHEJ) was scored by in vitro DNA repair assay. The cellular localization of...

Causes and consequences of alterations of municipal plans in Prague suburb Abstract The diploma thesis is concerned with town and country planning after the "Velvet revolution" in 1989. The surroundings of the capital are places where suburbanization takes place at present. Instruments, which can control the process of suburbanization, are very limited. Moreover there is a problem, that capital and its surroundings lay each in different administrative region. The municipal plan is currently key instrument by which can spatial development be influenced. Municipalities are therefore under pressure of private companies calling for extension of a built-up area. The aim of this thesis is to analyse causes and consequences of alterations of the municipal plans, which were procured in municipalities in the suburban territory of Prague, and to discover who are the main participants of these alterations. Keywords: town and country planning, alterations of municipal plans, suburbanization

In this project I have worked with strategies at regional level, as well as with alterations to an existing building, to strengthen and celebrate rural systems in a place called Naum, in Vara municipality in Västergötland. This I've donein order to challenge the dichotomy of urban and rural. I find that urbanity is very often celebrated in the architectural discipline, and in the public debate in general. There is a strong hierarchy of spaces in the national discourse of Sweden. By focusing on a rural space that I perceive have low status and connect it to networks that reach out to other spaces, cities, and regions, I treat the urban and rural as a continuous variation rather than a fixed binary. The binary is also challenged already by people constantly moving across this scale. Most of the residents of Naum, mapped out herecommute to Vara Town, or other adjacent towns or cities to work, to go school, to go the doctor, take part in cultural events etc. This project focus on the power of rural networks, on movement, and on rural systems of cooperation, and then I am making a number of alterations at a zoomed-in scale, to offer the inhabitants a more intimate relationship to this agricultural landscape. My project operate both at the intimate scale of an existing bygdegård, which is a specifically rural community space, in Naum, as well as on the larger scale of Vara municipality.To the bygdegård I propose three small scale alterations, a sauna called the 'Storytelling Sauna' (SECTION S S) an overnight stay shelter called the 'Please Stay',and an imaginative element of a 'Wisching-Well-Ditch”. In the larger scale I propose a strategic alteration to the treatment of roadsides, to increase biodiversity and human movement. I call this alteration the 'Thriving Passages'. The project also consist of this room-installation that we are all inside of, that aim to represent the different scales and allow us to move across them, and it consists of mappings of bygdegårds in Vara municipality and in Sweden and how they are connected by human movement, as well as mappings of historical and agricultural layers of this landscape.

Somatic Copy Number Alterations (CNAs) are common events in human cancers. Identifying CNAs and Significant Copy number Aberrations (SCAs) in cancer genomes is a critical task in searching for cancer-associated genes. Advanced genome profiling technologies, such as SNP array technology, facilitate copy number study at a genome-wide scale with high resolution. However, due to normal tissue contamination, the observed intensity signals are actually the mixture of copy number signals contributed from both tumor and normal cells. This genetic confounding factor would significantly affect the subsequent copy number analyses. In order to accurately identify significant aberrations in contaminated cancer genome, we develop a Java AISAIC package (Accurate Identification of Significant Aberrations in Cancer) that incorporates recent novel algorithms in the literature, BACOM (Bayesian Analysis of Copy number Mixtures) and SAIC (Significant Aberrations in Cancer). Specifically, BACOM is used to estimate the normal tissue contamination fraction and recover the "true" copy number profiles. And SAIC is used to detect SCAs using large recovered tumor samples. Considering the popularity of modern multi-core computers and clusters, we adopt concurrent computing using Java Fork/Join API to speed up the analysis. We evaluate the performance of the AISAIC package in both empirical family-wise type I error rate and detection power on a large number of simulation data, and get promising results. Finally, we use AISAIC to analyze real cancer data from TCGA portal and detect many SCAs that not only cover majority of reported cancer-associated genes, but also some novel genome regions that may worth further study. / Master of Science

Metabolic syndrome (MetS) is an association between obesity, dyslipidemia, hyperglycemia, hypertension, and insulin resistance. A relationship between MetS and vascular dementia was hypothesized. The purpose of this work is to investigate brain microanatomy alterations in obese Zucker rats (OZRs), as a model of MetS, compared to their counterparts lean Zucker rats (LZRs). 12-, 16-, and 20-weeks-old male OZRs and LZRs were studied. General physiological parameters and blood values were measured. Immunochemical and immunohistochemical techniques were applied to analyze the brain alterations. The morphology of nerve cells and axons, astrocytes and microglia were investigated. The blood–brain barrier (BBB) changes occurring in OZRs were assessed as well using aquaporin-4 (AQP4) and glucose transporter protein-1 (GLUT1) as markers. Body weight gain, hypertension, hyperglycemia, and hyperlipidemia were found in OZRs compared to LZRs. In the frontal cortex and hippocampus, a decrease of neurons was noticeable in the older obese rats in comparison to their age-matched lean counterparts. In OZRs, a reduction of neurofilament immunoreaction and gliosis was observed. The BBB of older OZRs revealed an increased expression of AQP4 likely related to the development of edema. A down-regulation of GLUT1 was found in OZRs of 12 weeks of age, whereas it increased in older OZRs. The behavioral analysis revealed cognitive alterations in 20-week-old OZRs. Based on these results, the OZRs may be useful for understanding the mechanisms through which obesity and related metabolic alterations induce neurodegeneration.

No description available.

Sleep is an essential component of optimal physiological and psychological functioning in humans. However, numerous studies have identified sleep deficits in patients within the critical care setting. Sleep deprivation has been shown to cause adverse effects including cardiovascular, respiratory, and endocrine variations, and altered psychological functioning such as cognitive dysfunction, decreased concentration, mood variability, and delirium. The critical care environment often contains stimuli that may be a causative factor in sleep alterations such as sleep deprivation, fragmentation or alterations in sleeping patterns. These environmental stimuli include noise, light, pain, discomfort, nursing care activities, medications, psychological stressors and underlying disease and have the capability to severely impact the quantity and quality of sleep in critically ill patients. The integrated research review identifies correlations between environmental stressors and sleep alterations in critically ill patients. Outcomes of interventions including earplugs and eye masks, behavior modification, complementary and alternative medicine and pharmacological considerations are examined. Additionally, implications for nursing education, research and practice are addressed. A current integrated research review incorporating nursing implications and alternative interventions could be significant to the provision of nursing care for the critically ill patient.

Cancer is a complex disease shaped by a heterogeneous landscape of inherited genetic variants and acquired somatic aberrations. Although specific patterns of somatic aberrations within key pathways are recognized as hallmarks of many cancers, and mounting evidence suggests a significant interplay between germline and somatic variants, the intricate relationship between germline predisposition and the disruption of these pathways remains poorly understood. Here, I present an integrative approach using multi-omics data to functionally characterize germline variants and explore the heterogeneous landscape of somatic mutations, with the aim of establish mechanistic links between functional variants and the disruption of cancer-related biological processes. To enable the identification of functional variants, I initially performed a comprehensive characterization of functionally annotated transcriptional regulatory elements, establishing a hierarchy of ‘consensus’ elements across multiple levels of abstraction. This analysis generated a vast collection of consensus promoters, enhancers, and active enhancers, spanning 198 cell lines and 38 tissue types, with aggregate data providing global consensus definitions for each element type. Additionally, ‘total binding affinity’ method was employed, integrating 1000 Genomes Project genotype data and thousands of transcription factor binding motifs, to further characterize and functionally annotate these regulatory elements. The results generated from this analysis can be interactively explored and visualized through the CONREL web application. To allow effective annotation of individual’s ancestry, I developed and successfully employed an improved version of EthSEQ (version 3), an R package that provides a rapid and reliable pipeline for ancestry annotation. Accurate stratification of individual ancestry is essential for correctly interpreting the impact of genomic variations in associations studies. EthSEQ version 3 was successfully utilized to determine the genetic ancestry of over 500 pediatric patients diagnosed with 11 different tumor types, enabling further investigation into the genetic landscape of patients confidently identified as of European ancestry.To further investigate into the interplay between germline and somatic variants, I conducted genome-wide association studies across 33 cancer types characterized by The Cancer Genome Atlas, using binary traits defined by somatic aberration profiles in ten oncogenic signaling pathways. Functional links between associated variants and somatic profiles were investigated through cis-eQTL data to identify regulatory interactions with pathway-related genes. Additionally, using GWAS summary statistics I employed polygenic scores to examine the contribution of germline genetic variation to somatic molecular profiles, tumor subtypes, and clinical outcomes such as patient survival and tumor aggressiveness. Polygenic scores were validated using external data from PCAWG and CCLE datasets. Lastly, to explore the heterogeneity of somatic mutational profiles, I employed a network-based approach to propagate somatic alterations through a molecular interaction network, aiming to reveal novel patterns of somatic alteration with potential significance in cancer. I then conducted a series of GWAS analyses, utilizing traits defined by combinations of these propagated somatic scores across genes involved in well-defined DNA repair pathways. Overall, I demonstrate that germline genetics can describe patients’ genetic liability to develop specific cancer molecular and clinical profiles. Understanding the functional roles of genetic variants can provide valuable insights into the biological mechanisms underlying a disease or trait.

Le carcinome médullaire de la thyroïde (CMT) est une tumeur neuroendocrine rare, se développant à partir des cellules sécrétant la calcitonine. Cette tumeur survient dans un contexte familial dans un tiers des cas. Toutes les formes germinales et près de 40% des formes sporadiques sont causées par une mutation ponctuelle activatrice de l’oncogène RET, codant pour un récepteur membranaire à activité tyrosine kinase. Les événements oncogéniques à l’origine des formes sporadiques non mutées RET restent mal définis, à l’exception de mutations activatrices des oncogènes RAS découvertes récemment.Le pronostic péjoratif du CMT est essentiellement lié à un envahissement ganglionnaire précoce. A ce titre, la chirurgie initiale est souvent insuffisante et les formes métastatiques ont longtemps été considérées en impasse thérapeutique. L’avènement récent des inhibiteurs séléctifs de tyrosine kinases (ITK) a apporté un nouvel élan à la prise en charge des tumeurs réfractaires, certains d’entre eux incluant dans leur spectre d’action le récepteur RET. Mais l’optimisation de ces traitements requiert une connaissance préalable des mécanismes moléculaires sous-jacents au développement tumoral.Dans ce contexte et en nous appuyant sur une collection importante de prélèvements humains, nous avons cherché à approfondir la decription du ‘paysage génomique’ du CMT.Dans un premier temps, nous avons évalué les anomalies structurales ponctuelles et chromosomiques présentées par les CMT. Nous avons montré, par optimisation de méthodes de séquençage, que les mutations des gènes RET et RAS interviennent dans plus de 96% des cas et que ces évènements sont mutuellement exclusifs. Ces mutations permettent de distinguer plusieurs groupes d’agressivité et de réponse aux traitements par ITK. Nous avons également observé - par technique d’hybridation génomique comparative - des anomalies de grande ampleur récurrentes dans cette pathologie : les délétions du bras court du chromosome 1 et des chromosomes entiers 4 et 22 apparaissent comme étant des évènements précoces et indépendants de la tumorigenèse du CMT.Dans un second temps, nous avons déterminé - par approche de type biopuce - les profils d’expression de microARN dans les CMT. Certains de ces régulateurs post-transcriptionnels majeurs semblent liés au caractère invasif de la tumeur, et notamment les miR-21, miR-199 et miR-129. Nous avons également démontré le potentiel d’utilisation des microARN miR-21 et miR-199 en tant que biomarqueurs circulants du CMT. L’impact fonctionnel des formes précurseurs mir-21 et mir-129 a ensuite été évalué par transfection dans les modèles cellulaires TT et MZ-CRC1.Les observations ainsi obtenues offrent de nombreuses perspectives d’études. Elles permettent la définition de marqueurs tissulaires distinguant a priori les tumeurs métastatiques et/ou réfractaires aux thérapies. Enfin, elles mettent en lumière de nouvelles pistes pour la découverte de cibles thérapeutiques additionnelles dans cette pathologie. / Medullary thyroid carcinoma (MTC) is a rare neuroendocrine tumor, arising from calcitonin-secreting cells. This cancer occurs in a family context in a third of cases. All inherited forms and nearly 40% of sporadic forms are caused by activating point-mutations in the RET oncogene, coding for a tyrosine-kinase receptor. Other oncogenic events causing sporadic cases remain unclear, but activating mutations of RAS oncogenes have been discovered recently.Prognosis of MTC is essentially linked to early lymph node occurrence. Initial surgery of metastatic forms is often insufficient and patients are considered in therapeutic dead-end. The recent advent of selective tyrosine-kinase inhibitors (TKIs) has brought a new impetus to the management of refractory tumors, some of them targeting the RET receptor. Optimization of these treatments require improving knowledge of the underlying molecular mechanisms of tumor development.In this context and helped by a large collection of human specimens, we have sought to deepen the description of genomic landscape of MTC.At first, we evaluated the structural and chromosomal abnormalities presented by MTC. We showed, by optimizing sequencing methods, that RET and RAS mutations are involved in over 96% of the cases, these events are mutually exclusives. These mutations can distinguish several groups of aggressiveness and of response to TKI treatments. We also observed, by comparative genomic hybridization techniques, recurrent abnormalities such as deletion of the short arm of chromosome 1 and loss of entire chromosomes 4 and 22. These losses appear to be early events of tumorigenesis MTC.In a second step, we determined - by a microarray approach – the microRNA expression profile of MTC. Some of these post-transcriptional regulators seem related to tumor invasiveness, such as miR-21, miR-199 and miR-129. We demonstrated the potential of microRNAs miR-21 and miR-199 as circulating diagnosis biomarkers of MTC. The functional impact of the precursor forms mir-21 and mir-129 was then evaluated by transfection in TT and MZ- CRC1 cellular models.Observations obtained pave the way for a lot of new potential studies. They allow the definition of tissue biomarkers distinguishing metastatic forms or refractory patients. Finally, they highlight new pathways for the discovery of additional therapeutic targets in this disease.

I have chosen this topic, because I am interested in building and related issues. Another reason for the selection of the work is that the construction industry is very promising, dynamic and lucrative field. The thesis is devided into five chapters with appendix. The work begins with a historical introduction to construction law and its major developmental milestones in the Czech Republic. The sources of public constructional law are discussed in detail in the following passage of the first chapter. Basic terms of construction law, relevant to the processing of the dissertation are defined in chapter 2. The issue of public administration that is related to the construction is described in chapter 3. Realization modes are described in chapter 4. First is called "free" mode, which is used in case of less technologically challenging projects and a minimum of intervening in the public and private interests (chapter 4.1). Second is the reporting regime and institute planning information given in section 4.2. And third, I consider the most important an authorization regime. In the authorization regime are carried out all constructions, if is not established that the reporting regime is sufficient or "free". To alternatives of authorization regime are dedicated separate subchapters. Public contracts (4....