@phdthesis{Arend2024,
  author    = {Arend, Marius},
  title     = {Comparing genome-scale models of protein-constrained metabolism in heterotrophic and photosynthetic microorganisms},
  doi       = {10.25932/publishup-65147},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651470},
  school      = {Universit{\"a}t Potsdam},
  pages     = {150},
  year      = {2024},
  abstract  = {Genome-scale metabolic models are mathematical representations of all known reactions occurring in a cell. Combined with constraints based on physiological measurements, these models have been used to accurately predict metabolic fluxes and effects of perturbations (e.g. knock-outs) and to inform metabolic engineering strategies. Recently, protein-constrained models have been shown to increase predictive potential (especially in overflow metabolism), while alleviating the need for measurement of nutrient uptake rates. The resulting modelling frameworks quantify the upkeep cost of a certain metabolic flux as the minimum amount of enzyme required for catalysis. These improvements are based on the use of in vitro turnover numbers or in vivo apparent catalytic rates of enzymes for model parameterization. In this thesis several tools for the estimation and refinement of these parameters based on in vivo proteomics data of Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii have been developed and applied. The difference between in vitro and in vivo catalytic rate measures for the three microorganisms was systematically analyzed. The results for the facultatively heterotrophic microalga C. reinhardtii considerably expanded the apparent catalytic rate estimates for photosynthetic organisms. Our general finding pointed at a global reduction of enzyme efficiency in heterotrophy compared to other growth scenarios. Independent of the modelled organism, in vivo estimates were shown to improve accuracy of predictions of protein abundances compared to in vitro values for turnover numbers. To further improve the protein abundance predictions, machine learning models were trained that integrate features derived from protein-constrained modelling and codon usage. Combining the two types of features outperformed single feature models and yielded good prediction results without relying on experimental transcriptomic data. The presented work reports valuable advances in the prediction of enzyme allocation in unseen scenarios using protein constrained metabolic models. It marks the first successful application of this modelling framework in the biotechnological important taxon of green microalgae, substantially increasing our knowledge of the enzyme catalytic landscape of phototrophic microorganisms.},
  language  = {en}
}
@phdthesis{Bryant2024,
  author    = {Bryant, Seth},
  title     = {Aggregation and disaggregation in flood risk models},
  doi       = {10.25932/publishup-65095},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-650952},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ix, 116},
  year      = {2024},
  abstract  = {Floods continue to be the leading cause of economic damages and fatalities among natural disasters worldwide. As future climate and exposure changes are projected to intensify these damages, the need for more accurate and scalable flood risk models is rising. Over the past decade, macro-scale flood risk models have evolved from initial proof-of-concepts to indispensable tools for decision-making at global-, nationaland, increasingly, the local-level. This progress has been propelled by the advent of high-performance computing and the availability of global, space-based datasets. However, despite such advancements, these models are rarely validated and consistently fall short of the accuracy achieved by high-resolution local models. While capabilities have improved, significant gaps persist in understanding the behaviours of such macro-scale models, particularly their tendency to overestimate risk. This dissertation aims to address such gaps by examining the scale transfers inherent in the construction and application of coarse macroscale models. To achieve this, four studies are presented that, collectively, address exposure, hazard, and vulnerability components of risk affected by upscaling or downscaling. The first study focuses on a type of downscaling where coarse flood hazard inundation grids are enhanced to a finer resolution. While such inundation downscaling has been employed in numerous global model chains, ours is the first study to focus specifically on this component, providing an evaluation of the state of the art and a novel algorithm. Findings demonstrate that our novel algorithm is eight times faster than existing methods, offers a slight improvement in accuracy, and generates more physically coherent flood maps in hydraulically challenging regions. When applied to a case study, the algorithm generated a 4m resolution inundation map from 30m hydrodynamic model outputs in 33 s, a 60-fold improvement in runtime with a 25\% increase in RMSE compared with direct hydrodynamic modelling. All evaluated downscaling algorithms yielded better accuracy than the coarse hydrodynamic model when compared to observations, demonstrating similar limits of coarse hydrodynamic models reported by others. The substitution of downscaling into flood risk model chains, in place of high-resolution modelling, can drastically improve the lead time of impactbased forecasts and the efficiency of hazard map production. With downscaling, local regions could obtain high resolution local inundation maps by post-processing a global model without the need for expensive modelling or expertise. The second study focuses on hazard aggregation and its implications for exposure, investigating implicit aggregations commonly used to intersect hazard grids with coarse exposure models. This research introduces a novel spatial classification framework to understand the effects of rescaling flood hazard grids to a coarser resolution. The study derives closed-form analytical solutions for the location and direction of bias from flood grid aggregation, showing that bias will always be present in regions near the edge of inundation. For example, inundation area will be positively biased when water depth grids are aggregated, while volume will be negatively biased when water elevation grids are aggregated. Extending the analysis to effects of hazard aggregation on building exposure, this study shows that exposure in regions at the edge of inundation are an order of magnitude more sensitive to aggregation errors than hazard alone. Among the two aggregation routines considered, averaging water surface elevation grids better preserved flood depths at buildings than averaging of water depth grids. The study provides the first mathematical proof and generalizeable treatment of flood hazard grid aggregation, demonstrating important mechanisms to help flood risk modellers understand and control model behaviour. The final two studies focus on the aggregation of vulnerability models or flood damage functions, investigating the practice of applying per-asset functions to aggregate exposure models. Both studies extend Jensen's inequality, a well-known 1906 mathematical proof, to demonstrate how the aggregation of flood damage functions leads to bias. Applying Jensen's proof in this new context, results show that typically concave flood damage functions will introduce a positive bias (overestimation) when aggregated. This behaviour was further investigated with a simulation experiment including 2 million buildings in Germany, four global flood hazard simulations and three aggregation scenarios. The results show that positive aggregation bias is not distributed evenly in space, meaning some regions identified as "hot spots of risk" in assessments may in fact just be hot spots of aggregation bias. This study provides the first application of Jensen's inequality to explain the overestimates reported elsewhere and advice for modellers to minimize such artifacts. In total, this dissertation investigates the complex ways aggregation and disaggregation influence the behaviour of risk models, focusing on the scale-transfers underpinning macro-scale flood risk assessments. Extending a key finding of the flood hazard literature to the broader context of flood risk, this dissertation concludes that all else equal, coarse models overestimate risk. This dissertation goes beyond previous studies by providing mathematical proofs for how and where such bias emerges in aggregation routines, offering a mechanistic explanation for coarse model overestimates. It shows that this bias is spatially heterogeneous, necessitating a deep understanding of how rescaling may bias models to effectively reduce or communicate uncertainties. Further, the dissertation offers specific recommendations to help modellers minimize scale transfers in problematic regions. In conclusion, I argue that such aggregation errors are epistemic, stemming from choices in model structure, and therefore hold greater potential and impetus for study and mitigation. This deeper understanding of uncertainties is essential for improving macro-scale flood risk models and their effectiveness in equitable, holistic, and sustainable flood management.},
  language  = {en}
}
@misc{Weigand2024,
  author    = {Weigand, Susanne},
  title     = {Elisheva Baumgarten, Biblical Women and Jewish Daily Life in the Middle Ages (Philadelphia: University of Pennsylvania Press, 2022), 288 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65130},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651300},
  pages     = {190 -- 192},
  year      = {2024},
  language  = {en}
}
@misc{Tusan2024,
  author    = {Tusan, Michelle Elizabeth},
  title     = {Jaclyn Granick, International Jewish Humanitarianism in the Age of the Great War (Cambridge, UK: Cambridge University Press, 2021), 418 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65129},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651291},
  pages     = {187 -- 190},
  year      = {2024},
  language  = {en}
}
@misc{TiroshSamuelson2024,
  author    = {Tirosh-Samuelson, Hava},
  title     = {Andrea Dara Cooper, Gendering Modern Jewish Thought (Bloomington, IN: Indiana University Press, 2021), 270 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65128},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651289},
  pages     = {185 -- 187},
  year      = {2024},
  language  = {en}
}
@misc{Sun2024,
  author    = {Sun, Cheuk Him Ryan},
  title     = {Kathryn Hellerstein and Song Lihong (eds.), China and Ashkenazic Jewry: Transnational Encounters (Munich: De Gruyter Oldenbourg, 2022), 359 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65127},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651277},
  pages     = {181 -- 185},
  year      = {2024},
  language  = {en}
}
@misc{Sidky2024,
  author    = {Sidky, Sean},
  title     = {Heike Bauer, Andrea Greenbaum, Sarah Lightman, eds., Jewish Women in Comics: Bodies and Borders (Syracuse, NY: Syracuse University Press, 2023), 296 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65126},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651268},
  pages     = {178 -- 180},
  year      = {2024},
  language  = {en}
}
@misc{Shapira2024,
  author    = {Shapira, Elena},
  title     = {Charles Dellheim, Belonging and Betrayal: How Jews Made the Art World Modern (Waltham, MA: Brandeis University Press, 2021), 674 pp., 24 col./96 mono illus.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65125},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651252},
  pages     = {174 -- 177},
  year      = {2024},
  language  = {en}
}
@misc{Arnold2024,
  author    = {Arnold, Rafael D.},
  title     = {Renata Segre, Preludio al Ghetto di Venezia: Gli ebrei sotto i dogi (1250 - 1516) (= Studi di storia, 15). (Venezia: Edizioni Ca' Foscari, 2021). 618 S.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65123},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-651231},
  pages     = {167 -- 170},
  year      = {2024},
  language  = {de}
}
@misc{Piskačova2024,
  author    = {Piskačov{\´a}, Zora},
  title     = {Agnieszka Wierzcholska, Nur Erinnerungen und Steine sind geblieben. Leben und Sterben einer polnisch-j{\"u}dischen Stadt: Tarn{\´o}w 1918 - 1945 (Paderborn: Brill-Sch{\"o}ningh Verlag, 2022), 665 pp.},
  series = {PaRDeS},
  journal   = {PaRDeS},
  number    = {29},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-574-3},
  issn      = {1614-6492},
  doi       = {10.25932/publishup-65053},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-650538},
  pages     = {163 -- 167},
  year      = {2024},
  language  = {en}
}