abstract: The discovery that mechanical forces regulate microbial virulence, stress responses and gene expression was made using log phase cultures of Salmonella Typhimurium (S. Typhimurium) grown under low fluid shear (LFS) conditions relevant to those encountered in the intestine. However, there has been limited characterization of LFS on other growth phases. To advance the growth-phase dependent understanding of the effect of LFS on S. Typhimurium pathogenicity, this dissertation characterized the effect of LFS on the transcriptomic and phenotypic responses in both stationary and lag phase cultures. In response to LFS, stationary phase cultures exhibited alterations in gene expression associated with metabolism, transport, secretion and stress responses (acid, bile salts, oxidative, and thermal stressors), motility, and colonization of intestinal epithelium (adherence, invasion and intracellular survival). Many of these characteristics are known to be regulated by the stationary phase general stress response regulator, RNA polymerase sigma factor S (RpoS), when S. Typhimurium is grown under conventional conditions. Surprisingly, the stationary phase phenotypic LFS stress response to acid and bile salts, colonization of human intestinal epithelial cells, and swimming motility was not dependent on RpoS. Lag phase cultures exhibited intriguing differences in their LFS regulated transcriptomic and phenotypic profiles as compared to stationary phase cultures, including LFS-dependent regulation of gene expression, adherence to intestinal epithelial cells, and high thermal stress. Furthermore, the addition of cell-free conditioned supernatants derived from either stationary phase LFS or Control cultures modulated the gene expression of lag phase cultures in a manner that differed from either growth phase, however, these supernatants did not modulate the phenotypic responses of lag phase cultures. Collectively, these results demonstrated that S. Typhimurium can sense and respond to LFS as early as lag phase, albeit in a limited fashion, and that the lag phase transcriptomic and phenotypic responses differ from those in stationary phase, which hold important implications for the lifecycle of this pathogen during the infection process. / Dissertation/Thesis / Transcriptomic Data / Doctoral Dissertation Microbiology 2020

In the thesis, we discuss the existence and numerical approximations of solutions of a regularized mean-field game with a low-order regularization. In the first part, we prove a priori estimates and use the continuation method to obtain the existence of a solution with a positive density. Finally, we introduce the monotone flow method and solve the system numerically.

The master's thesis focuses on creating a numerical model of a polymeric heat sink with emphasis on its significant thermal conductivity anisotropy. This anisotropy is caused by highly thermally conductive graphite filler. Its final orientation is given by the melt flow inside the mould cavity during injection molding. The numerical model is created on the basis of a heat sink prototype subjected to experimental measurements, whose physical conditions are reliably replicated by the model. The determination of anisotropy is divided into two parts. The qualitative part is based on the fracture analysis of the heat sink prototype and determines the principal directions of the conductivity tensor in individual sections of the geometry. The computation of principal conductivities falls into the quantitative part, in which this task is formulated as an inverse heat conduction problem. The input data for the proposed task are experimentally obtained temperatures at different places of the geometry. The values of principal conductivities are optimized to minimize the difference between the measured and simulated temperatures.

Subject master´s thesis is design of a measuring device for the study of sliding contact. It including description sliding contact, its importance and application possibilities. Specification of examination possibilities of sliding contact, indicate the possibilities of evaluating the measured results. Design a stationary measuring device for long-term tests of the sliding contact and verify its the basic system concept. Master´s thesis including too elektronic make graphes with courses quantity on real machine.

This diploma thesis discusses methods of dictionary learning to inpaint missing sections in the audio signal. There was theoretically analyzed and practically used algorithms K-SVD and INK-SVD for dictionary learning. These dictionaries have been applied to the reconstruction of audio signals using OMP (Orthogonal Matching Pursuit). Furthermore, there was proposed an algorithm for selecting the stationary segments and their subsequent use as training data for K-SVD and INK-SVD. In the practical part of thesis have been observed efficiency with training set selection from whole signal compared with algorithm for stationary segmentation used. The influence of mutual coherence on the quality of reconstruction with incoherent dictionary was also studied. With created scripts for multiple testing in Matlab, there was performed comparison of these methods on genre distinct songs.

Cette thèse traite de l'approximation de fonctions coûteuses à évaluer et présentant un comportement hétérogène selon les régions du domaine d'entrées. Dans beaucoup d’applications industrielles comme celles issues de la sûreté nucléaire et menées à l’IRSN, les codes de calcul de simulation physique ont des coûts numériques importants et leurs réponses sont alors approchées par un modèle. Les modèles par processus gaussien (PG) sont répandus pour construire des plans d'expériences au budget d'évaluations limité. Alors que les méthodes de planifications standard explorent le domaine en partant souvent d'une hypothèse de stationnarité et en utilisant des critères d'échantillonnages basés sur la variance, nous abordons sous deux aspects le problème d'adapter la planification d'expériences par PG aux fonctions à variations hétérogènes : d'une part sur la modélisation, en proposant une nouvelle famille de covariances (WaMI-GP) qui généralise deux noyaux existants (noyaux à indice multiple et noyaux à déformation tensorielle), et d'autre part sur la planification, en définissant et calculant de nouveaux critères d'échantillonnage à partir des dérivées du PG et dédiés à l'exploration de régions à grandes variations. Une analyse théorique de la nouvelle famille de PG ainsi que des expériences numériques montrent à la fois une certaine souplesse de modélisation et un nombre modéré de paramètres de modèle à estimer. Par ailleurs, un travail sur le couplage entre ondelettes et PG a conduit au développement d'un modèle non stationnaire, appelé ici wav-GP, qui utilise l'échelle locale pour approcher la dérivées de la déformation de manière itérative et non paramétrique. Les applications de wav-GP sur deux cas d'étude mécaniques fournissent des résultats prometteurs pour la prédiction de fonctions ayant un comportement hétérogène. D'autres part, nous formulons et calculons de nouveaux critères de variance qui reposent sur le champs de la norme du gradient du PG, et cela quelques soient les propriétés de (non) stationnarité du modèle. Les critères et les modèles sont comparés avec des méthodes de références sur des cas d'étude en ingénierie. Il en résulte que certains des critères par gradient proposés sont plus efficaces que les critères de variance plus conventionnels, mais qu'il est encore mieux de combiner le modèle WaMI-GP avec ces critères de variance. Ce modèle est souvent le plus compétitif dans des situations où les évaluations sont séquentielles et à nombre réduit. D'autres contributions s'inscrivant dans le thème de l'optimisation globale concernent en particulier le critère d'échantillonnage d'amélioration espérée (connu en anglais comme le critère d'expected improvement) et sa version multipoint pour l'évaluation en parallèle par paquet. Des formules analytiques et des approximations rapides sont établies pour une version généralisée du critère et pour son gradient. / This work deals with approximating expensive-to-evaluatefunctions exhibiting heterogeneous sensitivity to input perturbationsdepending on regions of the input space. Motivated by real test caseswith high computational costs coming mainly from IRSN nuclear safetystudies, we resort to surrogate models of the numerical simulatorsusing Gaussian processes (GP). GP models are popular for sequentialevaluation strategies in design of experiments under limited evaluationbudget. While it is common to make stationarity assumptions for theprocesses and use sampling criteria based on its variance forexploration, we tackle the problem of accommodating the GP-based designto the heterogeneous behaviour of the function from two angles: firstvia a novel class of covariances (WaMI-GP) that simultaneouslygeneralises existing kernels of Multiple Index and of tensorised warpedGP and second, by introducing derivative-based sampling criteriadedicated to the exploration of high variation regions. The novel GPclass is investigated both through mathematical analysis and numericalexperiments, and it is shown that it allows encoding muchexpressiveness while remaining with a moderate number of parameters tobe inferred. Moreover, exploiting methodological links between waveletsanalysis and non-stationary GP modelling, we propose a new non-stationary GP (Wav-GP) with non-parametric warping. The key point is aniterated estimation of the so-called local scale that approximates thederivative of the warping. Wav-GP is applied to two mechanical casestudies highlighting promising prediction performance. Independently ofnon-stationarity assumptions, we conduct derivations for new variance-based criteria relying on the norm of the GP gradient field. Criteriaand models are compared with state-of-the-art methods on engineeringtest cases. It is found on these applications that some of the proposedgradient-based criteria outperform usual variance-based criteria in thecase of a stationary GP model, but that it is even better to usevariance-based criteria with WaMI-GP, which dominates mostly for smalldesigns and in sequential set up. Other contributions in samplingcriteria address the problem of global optimisation, focusing on theexpected improvement criterion and its multipoint version for parallelbatch evaluations. Closed form formulas and fast approximations areestablished for a generalised version of the criterion and its gradient. Numerical experiments illustrate that the proposed approachesenable substantial computational savings.

The aim of this work was finding suitable conditions for separation of enantiomers of citalopram and citadiol, optimization of chromatographic system and validation of the analytical method for determination of selected enantiomers in drugs. Drugs are often chiral compounds. In many cases, only enantiomer has required pharmacological effects. Advanced chemical technologies associated with the synthesis, separation and analysis of the individual enantiomers caused an increase of the number of new chiral drugs in the form of single pure enantiomers, the chiral switch. Citalopram is one of the widely used antidepressants of selective serotonin reuptake inhibitors (SSRI). Citalopram is used for treatment of depression, panic anxienty or obsessive compulsive disorder of pathological laughing and crying. The pharmacological activity is associated with the S-citalopram, while R-enantiomer is essentially inactive and even counteracts the activity of escitalopram. Citadiol is a chiral syntetic precursor of citalopram. This thesis was focused on monitoring enantioseparation "behaviour" of selected enantiomers. HPLC method with chiral stationary phases based on macrocyclic antibiotics, cyclofructans and cellulose was applied for enantioseparation of the above-mentioned compounds. The optimized chromatographic...

The aim of this work was to develop and to optimize HPLC method for enantioseparation of newly synthesized derivatives of amino acids. The set of these analytes contained four N- blocked derivatives of D,L-Phenylalanine, three N-unblocked derivatives of D,L- Phenylalanine, , one methylated derivative of D,L-Tyrosine and D,L-Tyrosine. Two separation modes i.e. reversed phase and polar-organic modes and two columns i.e. Chirobiotic® T and Chirobiotic® T2 were used. Chiral stationary phases of these columns were composed of macrocyclic antibiotic teicoplanin coated on silica gel support. As mobile phases in revesed phase mode, methanol and acetate buffer were used with Chirobiotic® T column. The most suitable concentration were 20 mM and the most suitable pH value were 4.00. Under the above mentioned conditions eight analytes of ten were separated and the optimal conditions were found. Polar-organic mode and Chirobiotic® T column were suitable only for enantioseparation of three N-blocked derivatives of D,L- Phenylalanine. Mobile phases were composed of methanol with small additions of triethylamine and acetic acid. Chirobiotic® T2 column in reversed phase mode was not suitable for tested set of analytes. Only partial separation of D,L-Tyrosine derivative and one N-unblocked D,L-Phenylalanine...

This diploma thesis is focused on the comparison of enantioselective potential of chiral stationary phases based on derivatized cellulose by high performance liquid chromatography (HPLC). Polysaccharide - based chiral stationary phases are suitable choice for enantioseparation of various chiral compounds. In this work Chiralpak IB column containing cellulose tris(3,5-dimethylphenylcarbamate) selector immobilized onto silica gel and Chiralpak IC column containing cellulose tris(3,5- dichlorophenylcarbamate) selector immobilized onto silica gel were used. Their ability of enantioseparation was tested on 28 structurally different chiral analytes. Reversed- phase separation mode was used for enantioseparation. Mobile phases were composed of organic modifiers acetonitrile or methanol and the aqueous part was selected according to the nature of analytes. Acidic analytes were separated in mobile phases containing aqueous solution of formic acid (pH 2.1). Analytes of bifunctional nature were separated in the presence of aqueous solution of formic acid (pH 2.1), 10 mM ammonium acetate buffer (pH 8.8) or 100 mM solution of KPF6. Mobile phases containing 10 mM ammonium acetate buffer (pH 8.8) or 100 mM solution of KPF6 were used for enantioseparation of alkaline chiral analytes. Twelve chiral analytes were...

The aim of this diploma thesis was to prepare two new chiral stationary phases by dynamic coating of sulphobutylether-β-cyclodextrin (SBE-β-CD) with varying degrees of substitution onto strong anion-exchange stationary phases. The enantioselective potential and stability of the newly prepared chiral stationary phases were tested using a set of chiral analytes. The set contained structurally diverse analytes, i.e. benzodiazepines (oxazepam, lorazepam), phenothiazines (thioridazine, promethazine), β-blockers (labetalol, pindolol, propranolol, alprenolol), profens (carprofen, fenoprofen, flurbiprofen, indoprofen), flavanones (6-hydroxyflavanone, 7-hydroxyflavanone), DL-tryptophan and its derivatives (5-OH-DL-tryptophan, 5-F-DL-tryptophan, DL-tryptophan butylester and blocked aminoacid (t-Boc-DL-tryptophan)), dipeptides (glycyl-DL-phenylalanine, glycyl-DL-tryptophan) and Troger's base. Measurements were carried out in reversed-phase high-performance liquid chromatography. Mobile phases consisted of methanol/formic acid (pH 2.10) and methanol/10mmol l-1 ammonium acetate buffer (pH 4.00) in various volume ratios. The chiral stationary phase containing hexasubstituted SBE-β-CD was suitable for enantioseparation of eleven analytes. Four of them were baseline enantioresolved and seven partially. The chiral...