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Livestock animals, especially poultry, are a known reservoir for extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli). They may enter the pen either via positive day-old chicks or via the environment. We developed a mathematical model to illustrate the entry and dissemination of resistant bacteria in a broiler pen during one fattening period in order to investigate the effectiveness of intervention measures on this infection process. Different management measures, such as varying amounts of litter, a slow-growing breed or lower stocking densities, were tested for their effects on broiler colonization. We also calculated the impact of products that may influence the microbiota in the chicks’ digestive tract, such as pre- or probiotics, feed supplements or competitive exclusion products. Our model outcomes show that a contaminated pen or positive chicks at the beginning of the fattening period can infect the entire flock. Increasing the amount of litter and decreasing the stocking density were shown to be effective in our model. Differences in the route of entry were found: if the chicks are already positive, the litter quantity must be increased to at least six times the standard of 1000 g/m2, whereas, if the pen is contaminated on the first day, three times the litter quantity is sufficient. A reduced stocking density of 20 kg/m2 had a significant effect on the incidence of infection only in a previously contaminated pen. Combinations of two or three measures were effective in both scenarios; similarly, feed additives may be beneficial in reducing the growth rate of ESBL-producing E. coli. This model is a valuable tool for evaluating interventions to reduce the transmission and spread of resistant bacteria in broiler houses. However, data are still needed to optimize the model, such as growth rates or survival data of ESBL-producing E. coli in different environments.
Diese Arbeit beschäftigt sich mit der Analyse und Modellierung des Microarrayexperiments. Hierfür wird das gesamte Experiment in fünf Teilprozesse zerlegt, die Reverse Transkription, die Hybridisierung, das Waschen, die Fluoreszenz und die Detektion. Jeder Teilprozess wurde separat modelliert und analysiert. Anschließend wurde die Teilprozesse im Gesamtmodell vereint und dieses für verschiedene Parametersituationen simuliert. Diese Arbeit ermöglicht eine mathematische Handhabung des Microarrayexperiments und deckt seine Abhängigkeit von den einzelnen Schritten des Experiments auf. Dies kann benutzt werden, um Normalisierung und Analyse zu verbessern.
In this doctoral thesis, algorithms are presented that are designed for the investigation in the mesopause region between the upper Mesosphere and Lower Thermosphere (MLT). The photochemical models are proposed and applied to represent the oxygen airglow and the oxygen photochemistry in the MLT. Atomic oxygen, O, in the ground state, O(3P), is of special interest because it is a reactive trace gas actively contributing to the Earth’s airglow. The retrievals of O(3P) concentrations, [O(3P)], are based on the nightglow time series of the green line emission measured remotely as in the first part of this thesis and the individual profiles of multiple nightglow emissions of O and molecular oxygen (O2) measured in situ as in the second part of this thesis. To process the complete spectral time series measured by using the satellite-borne instrument SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY), an intricate set of algorithms is developed and applied with the regularized total least squares minimization approach to estimate a set of the optimal regularization parameters and to retrieve a corresponding set of vertical Volume Emission Rate (VER) profiles. Furthermore, these algorithms take emissions of another origin and the Earth's shape into account. Considering not identified states of O2, the established photochemical models are adjusted resulting in two model modifications. Both model modifications are employed to retrieve the [O(3P)] time series on the basis of the VER time series in the MLT. The model input parameters vary in the atmosphere that motivated to propose these two model modifications and to employ available sources of the input parameters. One semi-empirical model, one general circulation model and the satellite-borne instrument SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) are employed as sources of the reference [O(3P)] and input parameters time series. The SABER instrument employed as a source of the input parameters is preferred according to the comparison of the retrieved and reference [O(3P)] time series. Studying the impact of the 11-year solar cycle on O(3P) in the MLT, an algorithm is developed and applied with the Levenberg-Marquardt algorithm to estimate the optimal fit parameters step-wise. The results of the O(3P) sensitivity analysis obtained with respect to the solar activity forcing at the 11 year and 27 day time scales and the lunar gravitational forcing agree with the reference model simulations. The hypothesis regarding vertical shifts between different of Meinel bands at least partly caused by the hydroxyl radical (OH*) quenching with O(3P) is confirmed experimentally. Based on the conclusion drawn in the first part of this thesis that the data sets’ self-consistency is high as for the averaged SABER and SCIAMACHY measurements, a comprehensive set of available data with a higher level of the data sets’ self-consistency is employed in the second part of this thesis. Multiple airglow emissions measured in situ during four campaigns are employed to propose the Multiple Airglow Chemistry (MAC) model. Processed emissions are the Herzberg I, Chamberlain, Atmospheric and Infrared Atmospheric band emissions of O2 and the green line emission of O. Considering all widely known and additionally complemented reactions, the MAC model is proposed to represent the oxygen airglow and the oxygen photochemistry in the MLT. The presented MAC model is based on the hypothesis of Slanger et al. (2004) stating that higher excited states of O2 are coupled with each other through vibronic de-excitation caused by collisions among molecules of this group of O2 states in the MLT. This hypothesis is modified excluding the singlet Herzberg state of O2 from the group of O2 states considered by Slanger et al. (2004). The MAC calculations are carried out sequentially starting with higher excited O2 states to provide the retrieved output concentrations of these O2 states as the input concentrations to the next calculation steps. The final step is only based on concentrations of all species, whereas each of the earlier steps is based on a corresponding VER profile besides of the input concentrations. The oxygen photochemistry in the MLT is represented by all species considered at the final step that makes it possible to adopt the MAC reactions in a general circulation model. Four modifications of the MAC model, i.e. including or excluding the triplet Herzberg states of O2 and including or excluding ozone and odd hydrogen (hydrogen, OH* and hydroperoxy radical), lead to negligible differences in the retrieved [O(3P)] profiles. Based on the MAC calculations verified and validated on the basis of the four rocket campaigns, one of the effective modifications of the MAC model (excluding the triplet Herzberg states of O2, ozone and odd hydrogen) is further reduced to the most effective modification. This implies that for the [O(3P)] retrieval only the O2 Atmospheric band emission, temperature and concentrations of molecular nitrogen (N2) and O2 are sufficient to apply. Calculations carried out by using the most effective modification of the MAC model are verified and validated on the basis of self-consistent in situ measurements obtained simultaneously. The MAC model enables identifying precursors of (1) the three lowest O2 valence states and (2) the second excited O state responsible for (1) the Atmospheric and Infrared Atmospheric band emissions of O2 and (2) the green line emission of O, respectively. Particularly, the singlet Herzberg state of O2 is identified as the major precursor of the second excited O state resulting in the green line emission. In focus of potential further research is an extension of the MAC model with vibrationally excited states of O2 and ionized species.