[{"department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"date_updated":"2023-09-13T08:56:35Z","type":"book_chapter","status":"public","_id":"153","volume":147,"publication_identifier":{"issn":["0091679X"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 147","abstract":[{"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.","lang":"eng"}],"oa_version":"None","pmid":1,"publist_id":"7768","author":[{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"article_processing_charge":"No","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","citation":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"79 - 91","date_published":"2018-07-27T00:00:00Z","doi":"10.1016/bs.mcb.2018.07.004","date_created":"2018-12-11T11:44:54Z","isi":1,"year":"2018","day":"27","publication":"Methods in Cell Biology","quality_controlled":"1","publisher":"Academic Press"},{"volume":47,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"month":"10","intvolume":" 47","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T08:54:38Z","article_type":"review","type":"journal_article","status":"public","_id":"54","page":"3 - 19","doi":"10.1016/j.devcel.2018.09.014","date_published":"2018-10-08T00:00:00Z","date_created":"2018-12-11T11:44:23Z","isi":1,"year":"2018","day":"08","publication":"Developmental Cell","publisher":"Cell Press","quality_controlled":"1","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.","publist_id":"8000","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro"},{"full_name":"Bellaïche, Yohanns","last_name":"Bellaïche","first_name":"Yohanns"}],"article_processing_charge":"No","external_id":{"isi":["000446579900002"]},"title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","citation":{"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","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.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","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.","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"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.","date_published":"2018-06-07T00:00:00Z","doi":"10.1371/journal.pone.0198330","date_created":"2018-12-11T11:45:34Z","day":"07","publication":"PLoS One","has_accepted_license":"1","isi":1,"year":"2018","article_number":"e0198330","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","publist_id":"7626","author":[{"last_name":"Frick","full_name":"Frick, Corina","first_name":"Corina"},{"last_name":"Dettinger","full_name":"Dettinger, Philip","first_name":"Philip"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"first_name":"Annaïse","last_name":"Jauch","full_name":"Jauch, Annaïse"},{"full_name":"Berger, Christoph","last_name":"Berger","first_name":"Christoph"},{"first_name":"Mike","full_name":"Recher, Mike","last_name":"Recher"},{"full_name":"Schroeder, Timm","last_name":"Schroeder","first_name":"Timm"},{"last_name":"Mehling","full_name":"Mehling, Matthias","first_name":"Matthias"}],"article_processing_charge":"No","external_id":{"isi":["000434384900031"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","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"},"month":"06","intvolume":" 13","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"issue":"6","volume":13,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"checksum":"95fc5dc3938b3ad3b7697d10c83cc143","file_id":"5709","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_Plos_Frick.pdf","date_created":"2018-12-17T14:10:32Z","creator":"dernst","file_size":7682167,"date_updated":"2020-07-14T12:45:45Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"276","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:45Z","ddc":["570"],"date_updated":"2023-09-13T09:00:15Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"283","file_date_updated":"2020-07-14T12:45:49Z","department":[{"_id":"EvBe"}],"date_updated":"2023-09-13T08:59:27Z","ddc":["570"],"scopus_import":"1","intvolume":" 8","month":"06","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"}],"oa_version":"Published Version","volume":8,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5707","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T13:04:46Z","file_name":"2018_ScientificReports_Ceinos.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:49Z","file_size":1855324}],"article_number":"8754","article_processing_charge":"No","external_id":{"isi":["000434640800008"]},"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","last_name":"Pagano","first_name":"Cristina"},{"last_name":"Frohlich","full_name":"Frohlich, Nadine","first_name":"Nadine"},{"first_name":"Pietro","last_name":"Negrini","full_name":"Negrini, Pietro"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"first_name":"Daniela","last_name":"Vallone","full_name":"Vallone, Daniela"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"last_name":"Bertolucci","full_name":"Bertolucci, Cristiano","first_name":"Cristiano"},{"first_name":"Nicholas S","full_name":"Foulkes, Nicholas S","last_name":"Foulkes"}],"publist_id":"7616","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","citation":{"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","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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:45:36Z","doi":"10.1038/s41598-018-27080-2","date_published":"2018-06-08T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"08"},{"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Monitoring temporal logic with clock variables","external_id":{"isi":["000884993200004"]},"article_processing_charge":"No","author":[{"first_name":"Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","last_name":"Elgyütt","full_name":"Elgyütt, Adrian"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publist_id":"7973","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","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","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","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.","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."},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:44:31Z","doi":"10.1007/978-3-030-00151-3_4","date_published":"2018-08-26T00:00:00Z","page":"53 - 70","day":"26","year":"2018","isi":1,"has_accepted_license":"1","status":"public","conference":{"end_date":"2018-09-06","location":"Beijing, China","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"type":"conference","_id":"81","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:24:21Z","ddc":["000"],"date_updated":"2023-09-13T08:58:34Z","intvolume":" 11022","month":"08","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Submitted Version","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,"}],"volume":11022,"language":[{"iso":"eng"}],"file":[{"file_size":537219,"date_updated":"2020-10-09T06:24:21Z","creator":"dernst","file_name":"2018_LNCS_Elgyuett.pdf","date_created":"2020-10-09T06:24:21Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","file_id":"8638"}],"publication_status":"published"},{"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"76","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","date_updated":"2023-09-13T09:01:06Z","ddc":["000"],"scopus_import":"1","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","publication_status":"published","file":[{"file_name":"2018_DistributedComputing_Lenzen.pdf","date_created":"2018-12-17T14:21:22Z","creator":"dernst","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","file_id":"5711","checksum":"872db70bba9b401500abe3c6ae2f1a61","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publist_id":"7978","author":[{"first_name":"Christoph","last_name":"Lenzen","full_name":"Lenzen, Christoph"},{"last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000475627800005"]},"article_processing_charge":"Yes (via OA deal)","title":"Near-optimal self-stabilising counting and firing squads","citation":{"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.","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","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","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","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.","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","quality_controlled":"1","oa":1,"doi":"10.1007/s00446-018-0342-6","date_published":"2018-09-12T00:00:00Z","date_created":"2018-12-11T11:44:30Z","has_accepted_license":"1","isi":1,"year":"2018","day":"12","publication":"Distributed Computing"},{"scopus_import":"1","month":"03","intvolume":" 68","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."}],"oa_version":"Preprint","volume":68,"ec_funded":1,"publication_status":"published","file":[{"checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-12T06:47:52Z","file_name":"2018_Edelsbrunner.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:38Z","file_size":708357}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"530","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"HeEd"}],"date_updated":"2023-09-13T08:59:00Z","ddc":["000"],"publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"119 - 133","doi":"10.1016/j.comgeo.2017.06.014","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:59Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Computational Geometry: Theory and Applications","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham"}],"publist_id":"7289","article_processing_charge":"No","external_id":{"isi":["000415778300010"]},"title":"Multiple covers with balls I: Inclusion–exclusion","citation":{"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","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","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","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.","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.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_number":" 043812 ","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"full_name":"Makarov, Alexander","last_name":"Makarov","first_name":"Alexander"},{"first_name":"Vladimir","full_name":"Yudson, Vladimir","last_name":"Yudson"}],"publist_id":"7572","article_processing_charge":"No","external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","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.","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."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"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).","doi":"10.1103/PhysRevA.97.043812","date_published":"2018-04-09T00:00:00Z","date_created":"2018-12-11T11:45:44Z","day":"09","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","isi":1,"year":"2018","status":"public","type":"journal_article","article_type":"original","_id":"307","department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T09:00:41Z","month":"04","intvolume":" 97","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"oa_version":"Submitted Version","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"}],"issue":"4","volume":97,"language":[{"iso":"eng"}],"publication_status":"published"},{"article_number":"67","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (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","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","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."},"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","author":[{"first_name":"Luis","full_name":"Zapata, Luis","last_name":"Zapata"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"publist_id":"7620","article_processing_charge":"No","external_id":{"isi":["000433986200001"]},"quality_controlled":"1","publisher":"BioMed Central","oa":1,"day":"31","publication":"Genome Biology","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1186/s13059-018-1434-0","date_published":"2018-05-31T00:00:00Z","date_created":"2018-12-11T11:45:35Z","_id":"279","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-09-13T09:01:32Z","file_date_updated":"2020-07-14T12:45:47Z","department":[{"_id":"FyKo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"05","intvolume":" 19","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f3e4922486bd9bf1483271bdbed394a7","file_id":"5708","creator":"dernst","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":19,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9811"},{"relation":"research_data","status":"public","id":"9812"}]},"ec_funded":1},{"ddc":["570"],"date_updated":"2023-09-13T09:02:48Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:44:56Z","_id":"145","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T14:17:29Z","file_name":"2018_EMBO_Truckenbrodt.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":2846470}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0261-4189"]},"publication_status":"published","volume":37,"issue":"15","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"month":"08","intvolume":" 37","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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."},"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","author":[{"last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abhiyan","full_name":"Viplav, Abhiyan","last_name":"Viplav"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"last_name":"Vogts","full_name":"Vogts, Angela","first_name":"Angela"},{"first_name":"Annette","full_name":"Denker, Annette","last_name":"Denker"},{"first_name":"Hanna","full_name":"Wildhagen, Hanna","last_name":"Wildhagen"},{"full_name":"Fornasiero, Eugenio","last_name":"Fornasiero","first_name":"Eugenio"},{"first_name":"Silvio","full_name":"Rizzoli, Silvio","last_name":"Rizzoli"}],"publist_id":"7778","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"article_processing_charge":"No","article_number":"e98044","day":"01","publication":"The EMBO Journal","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-08-01T00:00:00Z","doi":"10.15252/embj.201798044","date_created":"2018-12-11T11:44:52Z","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).","publisher":"Wiley","quality_controlled":"1","oa":1}]