@misc{vanLeeuwenKunschNergeretal.2019, author = {van Leeuwen, Peter Jan and Kunsch, Hans R. and Nerger, Lars and Potthast, Roland and Reich, Sebastian}, title = {Particle filters for high-dimensional geoscience applications: A review}, series = {Quarterly journal of the Royal Meteorological Society}, volume = {145}, journal = {Quarterly journal of the Royal Meteorological Society}, number = {723}, publisher = {Wiley}, address = {Hoboken}, issn = {0035-9009}, doi = {10.1002/qj.3551}, pages = {2335 -- 2365}, year = {2019}, abstract = {Particle filters contain the promise of fully nonlinear data assimilation. They have been applied in numerous science areas, including the geosciences, but their application to high-dimensional geoscience systems has been limited due to their inefficiency in high-dimensional systems in standard settings. However, huge progress has been made, and this limitation is disappearing fast due to recent developments in proposal densities, the use of ideas from (optimal) transportation, the use of localization and intelligent adaptive resampling strategies. Furthermore, powerful hybrids between particle filters and ensemble Kalman filters and variational methods have been developed. We present a state-of-the-art discussion of present efforts of developing particle filters for high-dimensional nonlinear geoscience state-estimation problems, with an emphasis on atmospheric and oceanic applications, including many new ideas, derivations and unifications, highlighting hidden connections, including pseudo-code, and generating a valuable tool and guide for the community. Initial experiments show that particle filters can be competitive with present-day methods for numerical weather prediction, suggesting that they will become mainstream soon.}, language = {en} } @book{VanLeeuwenChengReich2015, author = {Van Leeuwen, Peter Jan and Cheng, Yuan and Reich, Sebastian}, title = {Nonlinear data assimilation}, series = {Frontiers in applied dynamical systems: reviews and tutorials ; 2}, journal = {Frontiers in applied dynamical systems: reviews and tutorials ; 2}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-18346-6}, doi = {10.1007/978-3-319-18347-3}, pages = {xii, 118}, year = {2015}, abstract = {This book contains two review articles on nonlinear data assimilation that deal with closely related topics but were written and can be read independently. Both contributions focus on so-called particle filters. The first contribution by Jan van Leeuwen focuses on the potential of proposal densities. It discusses the issues with present-day particle filters and explorers new ideas for proposal densities to solve them, converging to particle filters that work well in systems of any dimension, closing the contribution with a high-dimensional example. The second contribution by Cheng and Reich discusses a unified framework for ensemble-transform particle filters. This allows one to bridge successful ensemble Kalman filters with fully nonlinear particle filters, and allows a proper introduction of localization in particle filters, which has been lacking up to now.}, language = {en} } @article{HaaseKrostSauteretal.2017, author = {Haase, Tobias and Krost, Annalena and Sauter, Tilman and Kratz, Karl and Peter, Jan and Kamann, Stefanie and Jung, Friedrich and Lendlein, Andreas and Zohlnh{\"o}fer, Dietlind and R{\"u}der, Constantin}, title = {In vivo biocompatibility assessment of poly (ether imide) electrospun scaffolds}, series = {Journal of Tissue Engineering and Regenerative Medicine}, volume = {11}, journal = {Journal of Tissue Engineering and Regenerative Medicine}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1932-6254}, doi = {10.1002/term.2002}, pages = {1034 -- 1044}, year = {2017}, abstract = {Poly(ether imide) (PEI), which can be chemically functionalized with biologically active ligands, has emerged as a potential biomaterial for medical implants. Electrospun PEI scaffolds have shown advantageous properties, such as enhanced endothelial cell adherence, proliferation and low platelet adhesion in in vitro experiments. In this study, the in vivo behaviour of electrospun PEI scaffolds and PEI films was examined in a murine subcutaneous implantation model. Electrospun PEI scaffolds and films were surgically implanted subcutaneously in the dorsae of mice. The surrounding subcutaneous tissue response was examined via histopathological examination at 7 and 28days after implantation. No serious adverse events were observed for both types of PEI implants. The presence of macrophages or foreign body giant cells in the vicinity of the implants and the formation of a fibrous capsule indicated a normal foreign body reaction towards PEI films and scaffolds. Capsule thickness and inflammatory infiltration cells significantly decreased for PEI scaffolds during days 7-28 while remaining unchanged for PEI films. The infiltration of cells into the implant was observed for PEI scaffolds 7days after implantation and remained stable until 28days of implantation. Additionally some, but not all, PEI scaffold implants induced the formation of functional blood vessels in the vicinity of the implants. Conclusively, this study demonstrates the in vivo biocompatibility of PEI implants, with favourable properties of electrospun PEI scaffolds regarding tissue integration and wound healing.}, language = {en} } @article{RuederSauterKratzetal.2013, author = {R{\"u}der, Constantin and Sauter, Tilman and Kratz, Karl and Haase, Tobias and Peter, Jan and Jung, Friedrich and Lendlein, Andreas and Zohlnh{\"o}fer, Dietlind}, title = {Influence of fibre diameter and orientation of electrospun copolyetheresterurethanes on smooth muscle and endothelial cell behaviour}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {55}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {4}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-131787}, pages = {513 -- 522}, year = {2013}, abstract = {Polymers exhibiting cell-selective effects represent an extensive research field with high relevance for biomedical applications e.g. in the cardiovascular field supporting re-endothelialization while suppressing smooth muscle cell overgrowth. Such an endothelial cell-selective effect could be recently demonstrated for a copolyetheresterurethane (PDC) containing biodegradable poly(p-dioxanone) and poly(epsilon-caprolactone) segments, which selectively enhanced the adhesion of human umbilical vein endothelial cells (HUVEC) while suppressing the attachment of smooth muscle cells (SMC). In this study we investigated the influence of the fibre orientation (random and aligned) and fibre diameter (2 mu m and 500 nm) of electrospun PDC scaffolds on the adhesion, proliferation and apoptosis of HUVEC and SMC. Adhesion, viability and proliferation of HUVEC was diminished when the fibre diameter was reduced to a submicron scale, while the orientation of the microfibres did only slightly influence the cellular behaviour. In contrast, a submicron fibre diameter improved SMC viability. In conclusion, PDC scaffolds with micron-sized single fibres could be promising candidate materials for cell-selective stent coatings.}, language = {en} } @article{RiedlvanLeeuwenSuhrbieretal.2009, author = {Riedl, Maik and van Leeuwen, Peter Jan and Suhrbier, Alexander and Malberg, Hagen and Groenemeyer, Dietrich and Kurths, J{\"u}rgen and Wessel, Niels}, title = {Testing foetal-maternal heart rate synchronization via model-based analyses}, issn = {1364-503X}, doi = {10.1098/rsta.2008.0277}, year = {2009}, abstract = {The investigation of foetal reaction to internal and external conditions and stimuli is an important tool in the characterization of the developing neural integration of the foetus. An interesting example of this is the study of the interrelationship between the foetal and the maternal heart rate. Recent studies have shown a certain likelihood of occasional heart rate synchronization between mother and foetus. In the case of respiratory-induced heart rate changes, the comparison with maternal surrogates suggests that the evidence for detected synchronization is largely statistical and does not result from physiological interaction. Rather, they simply reflect a stochastic, temporary stability of two independent oscillators with time-variant frequencies. We reanalysed three datasets from that study for a more local consideration. Epochs of assumed synchronization associated with short-term regulation of the foetal heart rate were selected and compared with synchronization resulting from white noise instead of the foetal signal. Using data-driven modelling analysis, it was possible to identify the consistent influence of the heartbeat duration of maternal beats preceding the foetal beats during epochs of synchronization. These maternal beats occurred approximately one maternal respiratory cycle prior to the affected foetal beat. A similar effect could not be found in the epochs without synchronization. Simulations based on the fitted models led to a higher likelihood of synchronization in the data segments with assumed foetal-maternal interaction than in the segment without such assumed interaction. We conclude that the data-driven model-based analysis can be a useful tool for the identification of synchronization.}, language = {en} } @article{PathirajaLeeuwen2022, author = {Pathiraja, Sahani Darschika and Leeuwen, Peter Jan van}, title = {Multiplicative Non-Gaussian model error estimation in data assimilation}, series = {Journal of advances in modeling earth systems : JAMES}, volume = {14}, journal = {Journal of advances in modeling earth systems : JAMES}, number = {4}, publisher = {American Geophysical Union}, address = {Washington}, issn = {1942-2466}, doi = {10.1029/2021MS002564}, pages = {23}, year = {2022}, abstract = {Model uncertainty quantification is an essential component of effective data assimilation. Model errors associated with sub-grid scale processes are often represented through stochastic parameterizations of the unresolved process. Many existing Stochastic Parameterization schemes are only applicable when knowledge of the true sub-grid scale process or full observations of the coarse scale process are available, which is typically not the case in real applications. We present a methodology for estimating the statistics of sub-grid scale processes for the more realistic case that only partial observations of the coarse scale process are available. Model error realizations are estimated over a training period by minimizing their conditional sum of squared deviations given some informative covariates (e.g., state of the system), constrained by available observations and assuming that the observation errors are smaller than the model errors. From these realizations a conditional probability distribution of additive model errors given these covariates is obtained, allowing for complex non-Gaussian error structures. Random draws from this density are then used in actual ensemble data assimilation experiments. We demonstrate the efficacy of the approach through numerical experiments with the multi-scale Lorenz 96 system using both small and large time scale separations between slow (coarse scale) and fast (fine scale) variables. The resulting error estimates and forecasts obtained with this new method are superior to those from two existing methods.}, language = {en} }