Probabilistic topic models are a versatile class of models for discovering latent themes in document collections through unsupervised learning. Conventional inferential methods lack the scaling capabilities necessary for extensions to large-scale applications. In recent years Stochastic Expectation Maximization has proven scalable for the simplest topic model: Latent Dirichlet Allocation. Performing analytical maximization is unfortunately not possible for many more complex topic models. With the rise of probabilistic programming languages, the ability to infer flexibly specified probabilistic models using sophisticated numerical optimization procedures has become widely available. These frameworks have however mainly been developed for optimization of continuous parameters, often prohibiting direct optimization of discrete parameters. This thesis explores the potential of utilizing probabilistic programming for generic topic modeling using Stochastic Expectation Maximization with numerical maximization of discrete parameters reparameterized to unconstrained space. The method achieves results of similar quality as other methods for Latent Dirichlet Allocation in simulated experiments. Further application is made to infer a Dirichlet-multinomial Regression model with metadata covariates. A real dataset is used and the method produces interpretable topics.

Title: Excitation of molecules by cold electrons Author: Miroslav Šulc Department / Institute: Institute of Theoretical Physics, Charles University in Prague Supervisor of the doctoral thesis: prof. RNDr. Jiří Horáček, DrSc., Institute of Theoretical Physics, Charles University Abstract: Several methods for low energy collisional processes are investigated. In the first part, attention is especially devoted to examination of applicability of the R-matrix method combined with the Schwinger-Lanczos (SL) variational principle for potential scattering with long-range forces. Next sections deal with the development of the interaction correlation-polarization (CP) potential in the framework of the Dis- crete Momentum Representation (DMR) method on the grounds of the Local Density Approximation in the Density Functional Theory (DFT) context. Obtained results are then utilized in body-frame (BF), static exchange + polarization (SEP), calcula- tions within an analysis of experimental data for e−-N2 scattering comprising a part of a larger project addressing theoretical examination of rotational excitations of small molecules in the gas phase induced by electron impact. For N2, a new phenomenon consisting in suppression of backward cross-section below 95 meV is observed and con- sequently attributed to...

Erosion processes cause serious ecologic and economic problems because of their negative consequences in terms of soil and water deterioration as well as for the environment as a whole. Water erosion implicates that the fine soil particles, nutrients and organic components are washed out. This thesis adresses the size of water erosion and erosion control measures in the region Huánuco (Carpsih) in Peru. Size of erosion was determined using an universal equation - Revised Universal Soil Loss Equation (RUSLE). The main results of the work is the determination of the extent of soil erosion in the are of interest, its displeving in the map bases and the suggestion of soil protection in the most endangered areas.

Soil and terrain changes as a result of increased erosion and accumulation processes in selected locations Abstract Colluvial soils are formed in areas with increased intensity of soil erosion. Colluvial soils originate as a result of their position in terrain, they are usually found in places where has accumulated erosion material. Very often they are to be found at the around of slopes. Their accumulation horizon is deeper than 25 cm with a great amount of organic carbon buried in it. In my diploma thesis I will attempt to take a closer look at three locations, each having different types of dominant soils. The aim of this diploma thesis is to rebuild the original shape of the terrain before the beginning of the soil erosion process. Keywords: colluvial soil, soil erosion, soil accumulation, land use, digital terrain model (DTM)

This study is focused on characterization of the hardrock environment in surroundings of Sazava river. It is based on the archival data of groundwater table in boreholes, results of pumping tests from Geofond database and topographic data (DMR , watercourse, etc.). ArcMap 10.1 and Excel were used for data processing. The relations between the groundwater table depth, water table gradient, specific yield, transmissivity and variety of topographic parameters (distance from a watercourse, elevation, relative elevation above the nearest watercourse, the terrain gradient, etc.) were studied. Close linear relationship exists between the gradient of the terrain and groundwater table (rxy 0.96) in the study area. Groundwater table gradient is on average 88 % of terrain gradient. Mean groundwater table gradient is 10 % (6). The average transmissivity in the area is 1.27 x 10-4 m2 /s, specific yield is usually between 0.01 and 0.1 l/s m. This corresponds to the low and very low transmissivity class. Variability of transmisivity values is high. The difference between transmisivity in discharge and recharge zone, assumed by previous authors, was not confirmed in the study area. Specific base flow calculated from mean transmissivity, terrain/ water table gradient and river network density based on Krásný and...

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Face à la rapidité des changements climatiques, les arbres doivent faire preuve de plasticité phénotypique. Les mécanismes épigénétiques font partie des pistes de recherche actuelles pour expliquer la plasticité phénotypique. Cette thèse visait à évaluer le rôle de la méthylation de l’ADN dans la plasticité phénotypique d’un organisme pérenne séquencé, le peuplier, en réponse à des variations de disponibilité en eau du sol. Les travaux, combinant écophysiologie et épigénomique, se sont focalisés sur le méristème apical caulinaire, centre de la morphogenèse de la tige feuillée. Trois résultats majeurs sont issus de cette thèse : i) Chaque état hydrique est associé à un méthylome et un transcriptome spécifiques, ii) Certaines régions différentiellement méthylées sont conservées dans le temps et entre contextes environnementaux, iii) Des lignées RNAi hypométhylées soumises à différents contextes hydriques présentent une réponse modifiée. Les résultats acquis lors de cette thèse appuient une contribution de la méthylation de l’ADN à la plasticité phénotypique et suggèrent un rôle des mécanismes épigénétiques dans la mémoire d’un stress chez les arbres. / Due to rapid climate changes, trees must exhibit phenotypic plasticity. Epigenetic mechanisms are part of current research to explain phenotypic plasticity. This thesis aimed to evaluate the role of DNA methylation in phenotypic plasticity of a perennial sequenced organism, poplar, in response to variations in soil water availability. The work, combining ecophysiology and epigenomics, focused on the shoot apical meristem, the center of morphogenesis of the leafy stem. Three major results emerge from this thesis: (i) Each hydric state is associated with a specific methylome and transcriptome, (ii) Some differentially methylated regions are conserved in time and between environmental contexts, (iii) Hypomethylated RNAi lines subjected to different contexts show a modified response. The results obtained during this thesis support a contribution of DNA methylation to phenotypic plasticity and suggest a role of epigenetic mechanisms in stress memory in trees.

L’hypothyroïdie congénitale par dysgénésie thyroïdienne (HCDT) est la condition endocrinienne néonatale la plus fréquemment rencontrée, avec une incidence d’un cas sur 4000 naissances vivantes. L’HCDT comprend toutes les anomalies du développement de la thyroïde. Parmi ces anomalies, le diagnostic le plus fréquent est l’ectopie thyroïdienne (~ 50% des cas). L’HCDT est fréquemment associée à un déficit sévère en hormones thyroïdiennes (hypothyroïdisme) pouvant conduire à un retard mental sévère si non traitée. Le programme de dépistage néonatal assure un diagnostic et un traitement précoce par hormones thyroïdiennes. Cependant, même avec un traitement précoce (en moyenne à 9 jours de vie), un retard de développement est toujours observé, surtout dans les cas les plus sévères (c.-à-d., perte de 10 points de QI). Bien que des cas familiaux soient rapportés (2% des cas), l’HCTD est essentiellement considérée comme une entité sporadique. De plus, plus de 92% des jumeaux monozygotiques sont discordants pour les dysgénésies thyroïdiennes et une prédominance féminine est rapportée (spécialement dans le cas d’ectopies thyroïdiennes), ces deux observations étant clairement incompatible avec un mode de transmission héréditaire mendélien. Il est donc cohérent de constater que des mutations germinales dans les facteurs de transcription thyroïdiens connus (NKX2.1, PAX8, FOXE1, and NKX2.5) ont été identifiées dans seulement 3% des cas sporadiques testés et furent, de plus, exclues lors d’analyse d’association dans certaines familles multiplex. Collectivement, ces données suggèrent que des mécanismes non mendéliens sont à l’origine de la majorité des cas de dysgénésie thyroïdienne. Parmi ces mécanismes, nous devons considérer des modifications épigénétiques, des mutations somatiques précoces (au stade du bourgeon thyroïdien lors des premiers stades de l’embryogenèse) ou des défauts développementaux stochastiques (c.-à-d., accumulation aléatoire de mutations germinales ou somatiques). Voilà pourquoi nous proposons un modèle «2 hits » combinant des mutations (épi)génétiques germinales et somatiques; ce modèle étant compatible avec le manque de transmission familial observé dans la majorité des cas d’HCDT. Dans cette thèse, nous avons déterminé si des variations somatiques (épi)génétiques sont associées à l’HCTD via une approche génomique et une approche gène candidat. Notre approche génomique a révélé que les thyroïdes ectopiques ont un profil d’expression différent des thyroïdes eutopiques (contrôles) et que ce profil d’expression est enrichi en gènes de la voie de signalisation Wnt. La voie des Wnt est cruciale pour la migration cellulaire et pour le développement de plusieurs organes dérivés de l’endoderme (p.ex. le pancréas). De plus, le rôle de la voie des Wnt dans la morphogénèse thyroïdienne est supporté par de récentes études sur le poisson-zèbre qui montrent des anomalies du développement thyroïdien lors de la perturbation de la voie des Wnt durant différentes étapes de l’organogénèse. Par conséquent, l’implication de la voie des Wnt dans l’étiologie de la dysgénésie thyroïdienne est biologiquement plausible. Une trouvaille inattendue de notre approche génomique fut de constater que la calcitonine était exprimée autant dans les thyroïdes ectopiques que dans les thyroïdes eutopiques (contrôles). Cette trouvaille remet en doute un dogme de l’embryologie de la thyroïde voulant que les cellules sécrétant la calcitonine (cellules C) proviennent exclusivement d’une structure extrathyroïdienne (les corps ultimobranchiaux) fusionnant seulement avec la thyroïde en fin de développement, lorsque la thyroïde a atteint son emplacement anatomique définitif. Notre approche gène candidat ne démontra aucune différence épigénétique (c.-à-d. de profil de méthylation) entre thyroïdes ectopiques et eutopiques, mais elle révéla la présence d’une région différentiellement méthylée (RDM) entre thyroïdes et leucocytes dans le promoteur de FOXE1. Le rôle crucial de FOXE1 dans la migration thyroïdienne lors du développement est connu et démontré dans le modèle murin. Nous avons démontré in vivo et in vitro que le statut de méthylation de cette RDM est corrélé avec l’expression de FOXE1 dans les tissus non tumoraux (c.-à-d., thyroïdes et leucocytes). Fort de ces résultats et sachant que les RDMs sont de potentiels points chauds de variations (épi)génétiques, nous avons lancé une étude cas-contrôles afin de déterminer si des variants génétiques rares localisés dans cette RDM sont associés à la dysgénésie thyroïdienne. Tous ces résultats générés lors de mes études doctorales ont dévoilé de nouveaux mécanismes pouvant expliquer la pathogenèse de la dysgénésie thyroïdienne, condition dont l’étiologie reste toujours une énigme. Ces résultats ouvrent aussi plusieurs champs de recherche prometteurs et vont aider à mieux comprendre tant les causes des dysgénésies thyroïdiennes que le développement embryonnaire normal de la thyroïde chez l’homme. / Congenital hypothyroidism from thyroid dysgenesis (CHTD) is the most common congenital endocrine disorder with an incidence of 1 in 4,000 live births. CHTD includes multiple abnormalities in thyroid gland development. Among them, the most common diagnostic category is thyroid ectopy (~ 50 % of cases). CHTD is frequently associated with a severe deficiency in thyroid hormones (hypothyroidism), which can lead to severe mental retardation if left untreated. The newborn biochemical screening program insures the rapid institution of thyroid hormone replacement therapy. Even with early treatment (on average at 9 d), subtle developmental delay is still be observed in severe cases (i.e., IQ loss of 10 points). Although there have been some reports of familial occurrence (in 2% of the cases), CHTD is mainly considered as a sporadic entity. Furthermore, monozygotic (MZ) twins show a high discordance rate (92%) for thyroid dysgenesis and female predominance is observed in thyroid dysgenesis (especially thyroid ectopy), these two observations being incompatible with simple Mendelian inheritance. In addition, germline mutations in the thyroid related transcription factors NKX2.1, PAX8, FOXE1, and NKX2.5 have been identified in only 3% of sporadic cases and linkage analysis has excluded these genes in some multiplex families with CHTD. Collectively, these data point to the involvement of non-Mendelian mechanisms in the etiology of the majority of cases of thyroid dysgenesis. Among the plausible mechanisms are epigenetic modifications, somatic mutations occurring in the thyroid bud early during embryogenesis, or stochastic developmental events. Hence, we proposed a two-hit model combining germline and somatic (epi)genetic variations that can explain the lack of clear familial transmission of CTHD. In this present thesis, we assessed the role of somatic (epi)genetic variations in the pathogenesis of thyroid dysgenesis via a genome-wide as well as a candidate gene approach. Our genome wide approach revealed that ectopic thyroids show a differential gene expression compared to that of normal thyroids, with enrichment for the Wnt signalling pathway. The Wnt signalling pathway is crucial for cell migration and for the development of several endoderm-derived organs (e.g., pancreas). Moreover, a role of Wnt signalling in thyroid organogenesis was further supported by recent zebrafish studies which showed thyroid abnormalities resulting from the disruption of the Wnt pathway during different steps of organogenesis. Thus, Wnt pathway involvement in the etiology of thyroid ectopy is biologically plausible. An unexpected finding of our genome-wide gene expression analysis of ectopic thyroids was that they express calcitonin similar to normally located (orthotopic) thyroids. Such a finding, although in contradiction with our current knowledge of the embryological development of the thyroid attributes C cell origins to extrathyroidal structures (ultimobrachial bodies) upon fusion with a fully-formed, normally situated gland. Using a candidate gene approach, we were unable to demonstrate any differences in the methylation profile between ectopic and eutopic thyroids, but nevertheless we documented the presence of a differentially methylated region (DMR) between thyroids and leukocytes in the promoter of FOXE1, a gene encoding the only thyroid related transcription factor known to play a crucial role in regulating the migration of the thyroid precursors during development as shown by animal studies. We demonstrated by in vivo and in vitro studies that the methylation status of this DMR is correlated with differential expression of FOXE1 in non-tumoral tissues (thyroids and leukocytes). Knowing that DMRs are hotspots for epi(genetic) variations, its screening among CTHD patients is justifiable in our search for a molecular basis of thyroid dysgenesis, currently underway in a case-control study. The results generated during my graduate studies represent unique and novel mechanisms underlying the pathogenesis of CHTD, the etiology of which is still an enigma. They also paved the way for many future studies that will aid in better understanding both the normal and pathogenic development of the thyroid gland.

Breast cancer presents serious epidemiological problem, in result of which die more than 2 000 czech women every year. Screening mammography is one of the most expanded and most effective examinations for early detection of this desease but one has to take into account an inconsiderable risk connected with the procedure based on X-ray ionizing radiation. This diploma thesis deals with evaluation of the dose absorbed by the tissue. It contains the description of evaluation of the average dose in glandular tissue on PMMA phantom, as well as results of the measurements on conventional and digital mammograph. A data file with exposure parameters from mammography screening is included and interpreted. Also the Monte Carlo method was used for the dose evaluation, the thesis contains the brief description of the method, concept of analysis model in mammography and results of simulations.