[{"author":[{"full_name":"Hross, Sabrina","last_name":"Hross","first_name":"Sabrina"},{"full_name":"Theis, Fabian J.","first_name":"Fabian J.","last_name":"Theis"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Hasenauer, Jan","last_name":"Hasenauer","first_name":"Jan"}],"date_updated":"2023-09-13T08:55:05Z","date_created":"2019-01-20T22:59:18Z","volume":15,"year":"2018","publication_status":"published","publisher":"Royal Society Publishing","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:13Z","article_number":"20180600","doi":"10.1098/rsif.2018.0600","language":[{"iso":"eng"}],"external_id":{"isi":["000456783800011"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"month":"12","publication_identifier":{"issn":["17425689"]},"file":[{"content_type":"application/pdf","file_size":1464288,"creator":"dernst","access_level":"open_access","file_name":"2018_Interface_Hross.pdf","checksum":"56eb4308a15b7190bff938fab1f780e8","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:46:44Z","relation":"main_file","file_id":"5925"}],"oa_version":"Published Version","_id":"5858","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","ddc":["570"],"intvolume":" 15","abstract":[{"text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.","lang":"eng"}],"issue":"149","type":"journal_article","date_published":"2018-12-05T00:00:00Z","publication":"Journal of the Royal Society Interface","citation":{"ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600."},"day":"05","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":1838431,"creator":"system","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:45:04Z","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","relation":"main_file","file_id":"5043"}],"pubrep_id":"1062","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","status":"public","ddc":["532"],"intvolume":" 3","_id":"16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives."}],"issue":"10","type":"journal_article","date_published":"2018-10-16T00:00:00Z","article_type":"original","publication":"Physical Review Fluids","citation":{"apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303."},"day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-13T08:57:05Z","date_created":"2018-12-11T11:44:10Z","volume":3,"author":[{"last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","year":"2018","file_date_updated":"2020-07-14T12:45:04Z","ec_funded":1,"publist_id":"8039","article_number":"103303","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.3.103303","isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"external_id":{"isi":["000447469200001"]},"month":"10"},{"day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-02T00:00:00Z","page":"10690 - 10695","publication":"PNAS","citation":{"apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115."},"abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"issue":"42","type":"journal_article","oa_version":"Submitted Version","file":[{"file_id":"6258","relation":"main_file","date_created":"2019-04-09T08:02:50Z","date_updated":"2020-07-14T12:46:26Z","checksum":"df7ac544a587c06b75692653b9fabd18","file_name":"2018_PNAS_Rybicki.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4070777}],"pubrep_id":"1063","status":"public","ddc":["570","577"],"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","intvolume":" 115","_id":"43","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1721061115","isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["000447491300057"]},"file_date_updated":"2020-07-14T12:46:26Z","ec_funded":1,"publist_id":"8011","date_updated":"2023-09-13T08:57:38Z","date_created":"2018-12-11T11:44:19Z","volume":115,"author":[{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"full_name":"Anttila, Jani","last_name":"Anttila","first_name":"Jani"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"National Academy of Sciences","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","year":"2018"},{"doi":"10.1145/3197517.3201381","language":[{"iso":"eng"}],"external_id":{"isi":["000448185000097"]},"oa":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","month":"08","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/"}]},"author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"full_name":"Giorgi, Daniela","first_name":"Daniela","last_name":"Giorgi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"volume":37,"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-13T08:56:07Z","year":"2018","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","publist_id":"8043","ec_funded":1,"file_date_updated":"2020-07-14T12:44:43Z","article_number":"136","date_published":"2018-08-04T00:00:00Z","citation":{"short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136."},"publication":"ACM Trans. Graph.","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","pubrep_id":"1038","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","file_size":91939066,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5374","checksum":"61d46273dca4de626accef1d17a0aaad","date_created":"2018-12-12T10:18:52Z","date_updated":"2020-07-14T12:44:43Z"}],"_id":"13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 37","title":"Metamolds: Computational design of silicone molds","status":"public","ddc":["004"],"issue":"4","abstract":[{"lang":"eng","text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery."}],"type":"journal_article"},{"month":"07","doi":"10.1038/s41589-018-0108-2","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718","open_access":"1"}],"oa":1,"external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publist_id":"7786","author":[{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"full_name":"Wulff, Andreas","first_name":"Andreas","last_name":"Wulff"},{"first_name":"Vanessa","last_name":"Vongsouthi","full_name":"Vongsouthi, Vanessa"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"first_name":"Polina","last_name":"Gulakova","full_name":"Gulakova, Polina"},{"first_name":"Daniel","last_name":"Minge","full_name":"Minge, Daniel"},{"first_name":"Björn","last_name":"Breithausen","full_name":"Breithausen, Björn"},{"full_name":"Schoch, Susanne","last_name":"Schoch","first_name":"Susanne"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"}],"volume":14,"date_created":"2018-12-11T11:44:49Z","date_updated":"2023-09-13T08:58:05Z","pmid":1,"year":"2018","department":[{"_id":"HaJa"}],"publisher":"Nature Publishing Group","publication_status":"published","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","citation":{"mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2"},"publication":"Nature Chemical Biology","page":"861 - 869","article_type":"original","issue":"9","abstract":[{"text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"137","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","status":"public","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS"},{"author":[{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"full_name":"Reversat, Anne","last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"volume":147,"date_updated":"2023-09-13T08:56:35Z","date_created":"2018-12-11T11:44:54Z","pmid":1,"year":"2018","publisher":"Academic Press","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publication_status":"published","publist_id":"7768","doi":"10.1016/bs.mcb.2018.07.004","language":[{"iso":"eng"}],"external_id":{"isi":["000452412300006"],"pmid":["30165964"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0091679X"]},"month":"07","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"153","intvolume":" 147","status":"public","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"type":"book_chapter","date_published":"2018-07-27T00:00:00Z","citation":{"ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004."},"publication":"Methods in Cell Biology","page":"79 - 91","article_processing_charge":"No","day":"27","scopus_import":"1"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics."}],"_id":"54","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 47","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"08","citation":{"ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","apa":"Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19."},"publication":"Developmental Cell","page":"3 - 19","article_type":"review","date_published":"2018-10-08T00:00:00Z","publist_id":"8000","year":"2018","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","department":[{"_id":"CaHe"}],"publisher":"Cell Press","publication_status":"published","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","first_name":"Diana C","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C"},{"full_name":"Bellaïche, Yohanns","first_name":"Yohanns","last_name":"Bellaïche"}],"volume":47,"date_updated":"2023-09-13T08:54:38Z","date_created":"2018-12-11T11:44:23Z","month":"10","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"external_id":{"isi":["000446579900002"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2018.09.014","language":[{"iso":"eng"}]},{"month":"06","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0198330","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434384900031"]},"oa":1,"file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7626","article_number":"e0198330","date_updated":"2023-09-13T09:00:15Z","date_created":"2018-12-11T11:45:34Z","volume":13,"author":[{"last_name":"Frick","first_name":"Corina","full_name":"Frick, Corina"},{"full_name":"Dettinger, Philip","first_name":"Philip","last_name":"Dettinger"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"Jauch, Annaïse","last_name":"Jauch","first_name":"Annaïse"},{"full_name":"Berger, Christoph","first_name":"Christoph","last_name":"Berger"},{"last_name":"Recher","first_name":"Mike","full_name":"Recher, Mike"},{"last_name":"Schroeder","first_name":"Timm","full_name":"Schroeder, Timm"},{"last_name":"Mehling","first_name":"Matthias","full_name":"Mehling, Matthias"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Public Library of Science","year":"2018","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-07T00:00:00Z","article_type":"original","publication":"PLoS One","citation":{"short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330.","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330","ieee":"C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330."},"abstract":[{"lang":"eng","text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":7682167,"content_type":"application/pdf","file_name":"2018_Plos_Frick.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T14:10:32Z","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","file_id":"5709","relation":"main_file"}],"ddc":["570"],"title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","status":"public","intvolume":" 13","_id":"276","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-27080-2","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434640800008"]},"oa":1,"month":"06","volume":8,"date_updated":"2023-09-13T08:59:27Z","date_created":"2018-12-11T11:45:36Z","author":[{"full_name":"Ceinos, Rosa Maria","last_name":"Ceinos","first_name":"Rosa Maria"},{"first_name":"Elena","last_name":"Frigato","full_name":"Frigato, Elena"},{"full_name":"Pagano, Cristina","first_name":"Cristina","last_name":"Pagano"},{"full_name":"Frohlich, Nadine","last_name":"Frohlich","first_name":"Nadine"},{"full_name":"Negrini, Pietro","first_name":"Pietro","last_name":"Negrini"},{"full_name":"Cavallari, Nicola","first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vallone","first_name":"Daniela","full_name":"Vallone, Daniela"},{"last_name":"Fuselli","first_name":"Silvia","full_name":"Fuselli, Silvia"},{"full_name":"Bertolucci, Cristiano","first_name":"Cristiano","last_name":"Bertolucci"},{"last_name":"Foulkes","first_name":"Nicholas S","full_name":"Foulkes, Nicholas S"}],"publisher":"Nature Publishing Group","department":[{"_id":"EvBe"}],"publication_status":"published","year":"2018","publist_id":"7616","file_date_updated":"2020-07-14T12:45:49Z","article_number":"8754","date_published":"2018-06-08T00:00:00Z","citation":{"chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2","ieee":"R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2"},"publication":"Scientific Reports","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","file":[{"file_id":"5707","relation":"main_file","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","date_created":"2018-12-17T13:04:46Z","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","file_name":"2018_ScientificReports_Ceinos.pdf","creator":"dernst","file_size":1855324,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 8","ddc":["570"],"status":"public","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","_id":"283","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"type":"journal_article"},{"month":"08","language":[{"iso":"eng"}],"conference":{"location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"doi":"10.1007/978-3-030-00151-3_4","quality_controlled":"1","isi":1,"project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000884993200004"]},"file_date_updated":"2020-10-09T06:24:21Z","publist_id":"7973","date_updated":"2023-09-13T08:58:34Z","date_created":"2018-12-11T11:44:31Z","volume":11022,"author":[{"full_name":"Elgyütt, Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","last_name":"Elgyütt","first_name":"Adrian"},{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"year":"2018","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-08-26T00:00:00Z","page":"53 - 70","citation":{"mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4"},"abstract":[{"lang":"eng","text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"date_updated":"2020-10-09T06:24:21Z","date_created":"2020-10-09T06:24:21Z","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","success":1,"relation":"main_file","file_id":"8638","content_type":"application/pdf","file_size":537219,"creator":"dernst","file_name":"2018_LNCS_Elgyuett.pdf","access_level":"open_access"}],"status":"public","title":"Monitoring temporal logic with clock variables","ddc":["000"],"intvolume":" 11022","_id":"81","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"status":"public","title":"Near-optimal self-stabilising counting and firing squads","ddc":["000"],"_id":"76","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"5711","checksum":"872db70bba9b401500abe3c6ae2f1a61","date_created":"2018-12-17T14:21:22Z","date_updated":"2020-07-14T12:48:01Z","access_level":"open_access","file_name":"2018_DistributedComputing_Lenzen.pdf","content_type":"application/pdf","file_size":799337,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions."}],"citation":{"ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6."},"publication":"Distributed Computing","date_published":"2018-09-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"12","department":[{"_id":"DaAl"}],"publisher":"Springer","publication_status":"published","year":"2018","date_updated":"2023-09-13T09:01:06Z","date_created":"2018-12-11T11:44:30Z","author":[{"first_name":"Christoph","last_name":"Lenzen","full_name":"Lenzen, Christoph"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel"}],"publist_id":"7978","file_date_updated":"2020-07-14T12:48:01Z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000475627800005"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00446-018-0342-6","month":"09"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"_id":"530","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Multiple covers with balls I: Inclusion–exclusion","ddc":["000"],"status":"public","intvolume":" 68","file":[{"relation":"main_file","file_id":"5953","date_updated":"2020-07-14T12:46:38Z","date_created":"2019-02-12T06:47:52Z","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_name":"2018_Edelsbrunner.pdf","access_level":"open_access","file_size":708357,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Preprint","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Computational Geometry: Theory and Applications","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014"},"page":"119 - 133","date_published":"2018-03-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:38Z","publist_id":"7289","ec_funded":1,"year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"HeEd"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"date_created":"2018-12-11T11:46:59Z","date_updated":"2023-09-13T08:59:00Z","volume":68,"month":"03","external_id":{"isi":["000415778300010"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems"}],"doi":"10.1016/j.comgeo.2017.06.014","language":[{"iso":"eng"}]},{"article_type":"original","citation":{"apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812."},"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","date_published":"2018-04-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"09","intvolume":" 97","status":"public","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","_id":"307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. ","lang":"eng"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10127"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043812","month":"04","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2018","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","volume":97,"date_created":"2018-12-11T11:45:44Z","date_updated":"2023-09-13T09:00:41Z","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"full_name":"Makarov, Alexander","last_name":"Makarov","first_name":"Alexander"},{"last_name":"Yudson","first_name":"Vladimir","full_name":"Yudson, Vladimir"}],"article_number":" 043812 ","publist_id":"7572"},{"volume":19,"date_created":"2018-12-11T11:45:35Z","date_updated":"2023-09-13T09:01:32Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"relation":"research_data","status":"public","id":"9812"}]},"author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","first_name":"Stephan","last_name":"Ossowski"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"publisher":"BioMed Central","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2018","publist_id":"7620","ec_funded":1,"file_date_updated":"2020-07-14T12:45:47Z","article_number":"67","language":[{"iso":"eng"}],"doi":"10.1186/s13059-018-1434-0","project":[{"name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000433986200001"]},"month":"05","file":[{"content_type":"application/pdf","file_size":1414722,"creator":"dernst","access_level":"open_access","file_name":"2018_GenomeBiology_Zapata.pdf","checksum":"f3e4922486bd9bf1483271bdbed394a7","date_created":"2018-12-17T14:05:01Z","date_updated":"2020-07-14T12:45:47Z","relation":"main_file","file_id":"5708"}],"oa_version":"Published Version","intvolume":" 19","ddc":["570"],"status":"public","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"279","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"type":"journal_article","date_published":"2018-05-31T00:00:00Z","citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"publication":"Genome Biology","has_accepted_license":"1","article_processing_charge":"No","day":"31","scopus_import":"1"},{"date_published":"2018-08-01T00:00:00Z","article_type":"original","citation":{"ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044."},"publication":"The EMBO Journal","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","date_updated":"2020-07-14T12:44:56Z","date_created":"2018-12-17T14:17:29Z","access_level":"open_access","file_name":"2018_EMBO_Truckenbrodt.pdf","content_type":"application/pdf","file_size":2846470,"creator":"dernst"}],"intvolume":" 37","ddc":["570"],"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"145","issue":"15","abstract":[{"lang":"eng","text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.15252/embj.201798044","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"publication_identifier":{"issn":["0261-4189"]},"month":"08","volume":37,"date_created":"2018-12-11T11:44:52Z","date_updated":"2023-09-13T09:02:48Z","author":[{"full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"last_name":"Jähne","first_name":"Sebsatian","full_name":"Jähne, Sebsatian"},{"full_name":"Vogts, Angela","first_name":"Angela","last_name":"Vogts"},{"first_name":"Annette","last_name":"Denker","full_name":"Denker, Annette"},{"last_name":"Wildhagen","first_name":"Hanna","full_name":"Wildhagen, Hanna"},{"full_name":"Fornasiero, Eugenio","last_name":"Fornasiero","first_name":"Eugenio"},{"full_name":"Rizzoli, Silvio","last_name":"Rizzoli","first_name":"Silvio"}],"department":[{"_id":"JoDa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","year":"2018","publist_id":"7778","file_date_updated":"2020-07-14T12:44:56Z","article_number":"e98044"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"quality_controlled":"1","isi":1,"doi":"10.1111/pce.13153","language":[{"iso":"eng"}],"month":"05","pmid":1,"acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","year":"2018","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"first_name":"Ligang","last_name":"Fan","full_name":"Fan, Ligang"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"first_name":"Wei","last_name":"Hu","full_name":"Hu, Wei"},{"last_name":"Li","first_name":"Weina","full_name":"Li, Weina"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shen, Jinbo","last_name":"Shen","first_name":"Jinbo"},{"full_name":"Jiang, Liwen","last_name":"Jiang","first_name":"Liwen"},{"last_name":"Qiu","first_name":"Quan","full_name":"Qiu, Quan"}],"volume":41,"date_updated":"2023-09-13T09:03:18Z","date_created":"2018-12-11T11:46:36Z","publist_id":"7359","file_date_updated":"2020-07-14T12:46:32Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","citation":{"ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153."},"publication":"Plant, Cell and Environment","page":"850 - 864","article_type":"original","date_published":"2018-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"462","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 41","status":"public","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","ddc":["580"],"oa_version":"Submitted Version","file":[{"file_name":"2018_PlantCellEnv_Fan.pdf","access_level":"open_access","file_size":1937976,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7042","date_updated":"2020-07-14T12:46:32Z","date_created":"2019-11-18T16:22:22Z","checksum":"6a20f843565f962cb20281cdf5e40914"}],"type":"journal_article","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}]},{"article_type":"original","page":"427 - 441","publication":"Journal of Magnetism and Magnetic Materials","citation":{"chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073"},"date_published":"2018-04-15T00:00:00Z","scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","ddc":["530"],"status":"public","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","intvolume":" 452","_id":"519","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"checksum":"431f5cd4a628d7ca21161f82b14ccb4f","date_created":"2020-05-14T14:41:17Z","date_updated":"2020-07-14T12:46:37Z","file_id":"7838","relation":"main_file","creator":"dernst","file_size":17309535,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Magnetism_Altmeyer.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. "}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000425547700061"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jmmm.2017.12.073","month":"04","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Elsevier","year":"2018","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","date_created":"2018-12-11T11:46:56Z","date_updated":"2023-09-13T09:03:44Z","volume":452,"author":[{"full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","last_name":"Altmeyer","first_name":"Sebastian"}],"file_date_updated":"2020-07-14T12:46:37Z","publist_id":"7297"},{"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5679","intvolume":" 11275","title":"New approaches for almost-sure termination of probabilistic programs","status":"public","abstract":[{"text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2018-12-01T00:00:00Z","citation":{"chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11"},"page":"181-201","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Huang, Mingzhang","last_name":"Huang","first_name":"Mingzhang"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"volume":11275,"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-09-13T09:02:22Z","year":"2018","publisher":"Springer","department":[{"_id":"KrCh"}],"editor":[{"full_name":"Ryu, Sukyoung","last_name":"Ryu","first_name":"Sukyoung"}],"doi":"10.1007/978-3-030-02768-1_11","conference":{"end_date":"2018-12-06","location":"Wellington, New Zealand","start_date":"2018-12-02","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"oa":1,"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"month":"12"},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Current Opinion in Neurobiology","citation":{"ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138."},"page":"131 - 138","date_published":"2018-02-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies.","lang":"eng"}],"issue":"2","_id":"546","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Neural stem cells in neuropsychiatric disorders","status":"public","intvolume":" 48","oa_version":"None","month":"02","external_id":{"isi":["000427101600018"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.conb.2017.12.005","language":[{"iso":"eng"}],"publist_id":"7268","year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"author":[{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco","first_name":"Roberto","full_name":"Sacco, Roberto"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-13T09:01:56Z","date_created":"2018-12-11T11:47:06Z","volume":48},{"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401414.v1","citation":{"apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 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