07 Fakultät Konstruktions-, Produktions- und Fahrzeugtechnik

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    Modeling of biocatalytic reactions: a workflow for model calibration, selection, and validation using Bayesian statistics
    (2019) Eisenkolb, Ina; Jensch, Antje; Eisenkolb, Kerstin; Kramer, Andrei; Buchholz, Patrick C. F.; Pleiss, Jürgen; Spiess, Antje; Radde, Nicole
    We present a workflow for kinetic modeling of biocatalytic reactions which combines methods from Bayesian learning and uncertainty quantification for model calibration, model selection, evaluation, and model reduction in a consistent statistical frame-work. Our workflow is particularly tailored to sparse data settings in which a considerable variability of the parameters remains after the models have been adapted to available data, a ubiquitous problem in many real-world applications. Our workflow is exemplified on an enzyme-catalyzed two-substrate reaction mechanism describing the symmetric carboligation of 3,5-dimethoxy-benzaldehyde to (R)-3,3',5,5'-tetramethoxybenzoin catalyzed by benzaldehyde lyase from Pseudomonas fluorescens. Results indicate a substrate-dependent inactivation of enzyme, which is in accordance with other recent studies.
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    Impact of repetitive, ultra-short soft X-ray pulses from processing of steel with ultrafast lasers on human cell cultures
    (2024) Holland, Julian; Lungu, Cristiana; Weber, Rudolf; Emperle, Max; Graf, Thomas
    Ultrafast lasers, with pulse durations below a few picoseconds, are of significant interest to the industry, offering a cutting-edge approach to enhancing manufacturing processes and enabling the fabrication of intricate components with unparalleled accuracy. When processing metals at irradiances exceeding the evaporation threshold of about 10 10 W/cm² these processes can generate ultra-short, soft X-ray pulses with photon energies above 5 keV. This has prompted extensive discussions and regulatory measures on radiation safety. However, the impact of these ultra-short X-ray pulses on molecular pathways in the context of living cells, has not been investigated so far. This paper presents the first molecular characterization of epithelial cell responses to ultra-short soft X-ray pulses, generated during processing of steel with an ultrafast laser. The laser provided pulses of 6.7 ps with a pulse repetition rate of 300 kHz and an average power of 500 W. The irradiance was 1.95 ×10 13 W/cm 2 . Ambient exposure of vitro human cell cultures, followed by imaging of the DNA damage response and fitting of the data to a calibrated model for the absorbed dose, revealed a linear increase in the DNA damage response relative to the exposure dose. This is in line with findings from work using continuous wave soft X-ray sources and suggests that the ultra-short X-ray pulses do not generate additional hazard. This research contributes valuable insights into the biological effects of ultrafast laser processes and their potential implications for user safety.
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    Bayesian estimation reveals that reproducible models in systems biology get more citations
    (2023) Höpfl, Sebastian; Pleiss, Jürgen; Radde, Nicole E.
    The Systems Biology community has taken numerous actions to develop data and modeling standards towards FAIR data and model handling. Nevertheless, the debate about incentives and rewards for individual researchers to make their results reproducible is ongoing. Here, we pose the specific question of whether reproducible models have a higher impact in terms of citations. Therefore, we statistically analyze 328 published models recently classified by Tiwari et al. based on their reproducibility. For hypothesis testing, we use a flexible Bayesian approach that provides complete distributional information for all quantities of interest and can handle outliers. The results show that in the period from 2013, i.e., 10 years after the introduction of SBML, to 2020, the group of reproducible models is significantly more cited than the non-reproducible group. We show that differences in journal impact factors do not explain this effect and that this effect increases with additional standardization of data and error model integration via PEtab. Overall, our statistical analysis demonstrates the long-term merits of reproducible modeling for the individual researcher in terms of citations. Moreover, it provides evidence for the increased use of reproducible models in the scientific community.