07 Fakultät Konstruktions-, Produktions- und Fahrzeugtechnik
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/8
Browse
10 results
Search Results
Item Open Access Process evaluation for smart concrete road construction : road surface and thickness evaluation using high-speed LiDAR technology(2021) Skalecki, Patric; Sesselmann, Maximilian; Rechkemmer, Sabrina; Britz, Thorsten; Großmann, Andreas; Garrecht, Harald; Sawodny, OliverThe enhancement of new quality criteria in highway construction is a key aspect to improving the construction process and lifetime of road. In particular, mobile laser scanning systems are nowadays able to provide realistic 3D elevation profiles of a road to detect anomalies. In this context, this study utilizes a high-accuracy high-speed mobile mapping vehicle and evaluates a weighted longitudinal profile as an improved measure for evenness analysis. For comparison a classical method with a rolling straight edge was evaluated on the same road section and observed effects are discussed. The second focus is the areal reconstruction of the road thickness. For this purpose, a modern method was developed to spatially synchronize two high-speed laser scans using reference boxes next to the road, to transfer the point clouds into a surface model and to calculate the layer thickness. This procedure was conceptually validated by some pointwise measurements of the layer thickness. With this information, imperfections in the base layer could be detected automatically over a wide area at an early stage and countermeasures might be initiated before constructing the highway.Item Open Access Rapid sampling of Escherichia coli after changing oxygen conditions reveals transcriptional dynamics(2017) Wulffen, Joachim von; Ulmer, Andreas; Jäger, Günter; Sawodny, Oliver; Feuer, RonnyEscherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.Item Open Access Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions(2014) Henkel, Sebastian; Beek, Alexander ter; Steinsiek, Sonja; Stagge, Stefan; Bettenbrock, Katja; Teixeira de Mattos, M. Joost; Sauter, Thomas; Sawodny, Oliver; Ederer, MichaelFor adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions.Item Open Access A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria(2013) Bóna-Lovász, Judit; Bóna, Aron; Ederer, Michael; Sawodny, Oliver; Ghosh, RobinA simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%-100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.Item Open Access Model-based characterization of inflammatory gene expression patterns of activated macrophages(2016) Rex, Julia; Albrecht, Ute; Ehlting, Christian; Thomas, Maria; Zanger, Ulrich M.; Sawodny, Oliver; Häussinger, Dieter; Ederer, Michael; Feuer, Ronny; Bode, Johannes G.Macrophages are cells with remarkable plasticity. They integrate signals from their microenvironment leading to context-dependent polarization into classically (M1) or alternatively (M2) activated macrophages, representing two extremes of a broad spectrum of divergent phenotypes. Thereby, macrophages deliver protective and pro-regenerative signals towards injured tissue but, depending on the eliciting damage, may also be responsible for the generation and aggravation of tissue injury. Although incompletely understood, there is emerging evidence that macrophage polarization is critical for these antagonistic roles. To identify activation-specific expression patterns of chemokines and cytokines that may confer these distinct effects a systems biology approach was applied. A comprehensive literature-based Boolean model was developed to describe the M1 (LPS-activated) and M2 (IL-4/13-activated) polarization types. The model was validated using high-throughput transcript expression data from murine bone marrow derived macrophages. By dynamic modeling of gene expression, the chronology of pathway activation and autocrine signaling was estimated. Our results provide a deepened understanding of the physiological balance leading to M1/M2 activation, indicating the relevance of co-regulatory signals at the level of Akt1 or Akt2 that may be important for directing macrophage polarization.Item Open Access A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen(2014) Ederer, Michael; Steinsiek, Sonja; Stagge, Stefan; Rolfe, Matthew D.; Beek, Alexander tek; Knies, David; Teixeira de Mattos, M. Joost; Sauter, Thomas; Green, Jeffrey; Poole, Robert K.; Bettenbrock, Katja; Sawodny, OliverThe efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of energy supply, carbon and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.Item Open Access Transition of an anaerobic Escherichia coli culture to aerobiosis: balancing mRNA and protein levels in a demand-directed dynamic flux balance analysis(2016) Wulffen, Joachim von; Sawodny, Oliver; Feuer, RonnyThe facultative anaerobic bacterium Escherichia coli is frequently forced to adapt to changing environmental conditions. One important determinant for metabolism is the availability of oxygen allowing a more efficient metabolism. Especially in large scale bioreactors, the distribution of oxygen is inhomogeneous and individual cells encounter frequent changes. This might contribute to observed yield losses during process upscaling. Short-term gene expression data exist of an anaerobic E. coli batch culture shifting to aerobic conditions. The data reveal temporary upregulation of genes that are less efficient in terms of energy conservation than the genes predicted by conventional flux balance analyses. In this study, we provide evidence for a positive correlation between metabolic fluxes and gene expression. We then hypothesize that the more efficient enzymes are limited by their low expression, restricting flux through their reactions. We define a demand that triggers expression of the demanded enzymes that we explicitly include in our model. With these features we propose a method, demand-directed dynamic flux balance analysis, dddFBA, bringing together elements of several previously published methods. The introduction of additional flux constraints proportional to gene expression provoke a temporary demand for less efficient enzymes, which is in agreement with the transient upregulation of these genes observed in the data. In the proposed approach, the applied objective function of growth rate maximization together with the introduced constraints triggers expression of metabolically less efficient genes. This finding is one possible explanation for the yield losses observed in large scale bacterial cultivations where steady oxygen supply cannot be warranted.Item Open Access IL-1β and TNFα differentially influence NF-κB activity and FasL-induced apoptosis in primary murine hepatocytes during LPS-induced inflammation(2019) Rex, Julia; Lutz, Anna; Faletti, Laura E.; Albrecht, Ute; Thomas, Maria; Bode, Johannes G.; Borner, Christoph; Sawodny, Oliver; Merfort, IrmgardMacrophage-derived cytokines largely influence the behavior of hepatocytes during an inflammatory response. We previously reported that both TNFα and IL-1β, which are released by macrophages upon LPS stimulation, affect Fas ligand (FasL)-induced apoptotic signaling. Whereas TNFα preincubation leads to elevated levels of caspase-3 activity and cell death, pretreatment with IL-1β induces increased caspase-3 activity but keeps cells alive. We now report that IL-1β and TNFα differentially influence NF-κB activity resulting in a differential upregulation of target genes, which may contribute to the distinct effects on cell viability. A reduced NF-κB activation model was established to further investigate the molecular mechanisms which determine the distinct cell fate decisions after IL-1β and TNFα stimulation. To study this aspect in a more physiological setting, we used supernatants from LPS-stimulated bone marrow-derived macrophages (BMDMs). The treatment of hepatocytes with the BMDM supernatant, which contains both IL-1β and TNFα, sensitized to FasL-induced caspase-3 activation and cell death. However, when TNFα action was blocked by neutralizing antibodies, cell viability after stimulation with the BMDM supernatant and FasL increased as compared to single FasL stimulation. This indicates the important role of TNFα in the sensitization of apoptosis in hepatocytes. These results give first insights into the complex interplay between macrophages and hepatocytes which may influence life/death decisions of hepatocytes during an inflammatory reaction of the liver in response to a bacterial infection.Item Open Access Path planning for graded concrete element fabrication(2023) Blagojevic, Boris; Sawodny, OliverThe technology of functionally graded concrete (FGC) is a new methodology in the field of concrete construction, striving for mass savings by adjusting the elements interior design. A promising approach herein is meso-gradation, where concrete hollow spheres are placed inside the formwork before casting the element; this allows up to 50% mass savings without a loss in load-bearing capacity, whilst also ensuring recyclability compared to e.g. bubble decks. In order to prevent damage/displacement of the spheres during automated fabrication, the extruded concrete flow must avoid the spheres, whilst neatly covering the elements area in order to prevent cavities. Both requirements formulate a complex path planning problem that must be solved in order to achieve automated fabrication. In this paper, we propose a method for solving this problem, which is based on theoretical findings on Hamiltonian triangulations. Our approach is based on the idea that the elements area is triangulated, such that all sphere centers are corners of triangles. For each triangle, a smooth path can be planned straightforwardly on a consideration of the geometry, such that the global path is made of a sequence of local ones. This necessitates finding a triangulation that is hamiltonian, i.e. a sequence where all triangles are visited exactly once. To this end, we first present a new class of triangulations and proof their hamiltonicity, followed by an algorithm that generates such triangulations on certain FGC element geometries. This is followed by the local path planning problem, whose special structure with start/end tangential and curvature constraints facilitates the use of a polar coordinate approach.Item Open Access Cystoscopic depth estimation using gated adversarial domain adaptation(2023) Somers, Peter; Holdenried-Krafft, Simon; Zahn, Johannes; Schüle, Johannes; Veil, Carina; Harland, Niklas; Walz, Simon; Stenzl, Arnulf; Sawodny, Oliver; Tarín, Cristina; Lensch, Hendrik P. A.Monocular depth estimation from camera images is very important for surrounding scene evaluation in many technical fields from automotive to medicine. However, traditional triangulation methods using stereo cameras or multiple views with the assumption of a rigid environment are not applicable for endoscopic domains. Particularly in cystoscopies it is not possible to produce ground truth depth information to directly train machine learning algorithms for using a monocular image directly for depth prediction. This work considers first creating a synthetic cystoscopic environment for initial encoding of depth information from synthetically rendered images. Next, the task of predicting pixel-wise depth values for real images is constrained to a domain adaption between the synthetic and real image domains. This adaptation is done through added gated residual blocks in order to simplify the network task and maintain training stability during adversarial training. Training is done on an internally collected cystoscopy dataset from human patients. The results after training demonstrate the ability to predict reasonable depth estimations from actual cystoscopic videos and added stability from using gated residual blocks is shown to prevent mode collapse during adversarial training.