[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","short":"J. Merrin, Bioengineering 6 (2019).","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109."},"title":"Frontiers in microfluidics, a teaching resource review","article_processing_charge":"Yes","external_id":{"pmid":["31816954"],"isi":["000505590000024"]},"author":[{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"}],"article_number":"109","publication":"Bioengineering","day":"03","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2020-01-05T23:00:45Z","date_published":"2019-12-03T00:00:00Z","doi":"10.3390/bioengineering6040109","oa":1,"publisher":"MDPI","quality_controlled":"1","ddc":["620"],"date_updated":"2023-09-06T14:52:49Z","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"NanoFab"}],"_id":"7225","status":"public","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","article_type":"review","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:54Z","file_size":2660780,"date_created":"2020-01-07T14:49:59Z","file_name":"2019_Bioengineering_Merrin.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7243","checksum":"80f1499e2a4caccdf3aa54b137fd99a0"}],"publication_status":"published","publication_identifier":{"eissn":["23065354"]},"license":"https://creativecommons.org/licenses/by/4.0/","issue":"4","volume":6,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications.","lang":"eng"}],"intvolume":" 6","month":"12","scopus_import":"1"},{"title":"Scalable FIFO channels for programming via communicating sequential processes","article_processing_charge":"No","external_id":{"isi":["000851061400023"]},"author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Elizarov","full_name":"Elizarov, Roman","first_name":"Roman"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333."},"quality_controlled":"1","publisher":"Springer Nature","date_created":"2020-01-05T23:00:46Z","doi":"10.1007/978-3-030-29400-7_23","date_published":"2019-08-13T00:00:00Z","page":"317-333","publication":"25th Anniversary of Euro-Par","day":"13","year":"2019","isi":1,"status":"public","conference":{"name":"Euro-Par: European Conference on Parallel Processing","end_date":"2019-08-30","location":"Göttingen, Germany","start_date":"2019-08-26"},"type":"conference","_id":"7228","department":[{"_id":"DaAl"}],"date_updated":"2023-09-06T14:53:59Z","intvolume":" 11725","month":"08","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"None","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. ","lang":"eng"}],"volume":11725,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9399-4"]}},{"month":"11","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","oa_version":"None","abstract":[{"text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.","lang":"eng"}],"date_created":"2019-12-29T23:00:47Z","date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","language":[{"iso":"eng"}],"publication":"2019 IEEE Intelligent Transportation Systems Conference","day":"28","publication_status":"published","year":"2019","publication_identifier":{"isbn":["9781538670248"]},"isi":1,"status":"public","conference":{"name":"ITSC: Intelligent Transportation Systems Conference","location":"Auckland, New Zealand","end_date":"2019-10-30","start_date":"2019-10-27"},"type":"conference","article_number":"8917514","_id":"7216","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","department":[{"_id":"HeEd"}],"article_processing_charge":"No","external_id":{"isi":["000521238102050"]},"author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","last_name":"Cook","full_name":"Cook, James"},{"first_name":"Alex","last_name":"Fabrikant","full_name":"Fabrikant, Alex"},{"first_name":"Marco","last_name":"Gruteser","full_name":"Gruteser, Marco"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.","ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514.","chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514."},"date_updated":"2023-09-06T14:50:28Z"},{"date_updated":"2023-09-06T14:55:15Z","department":[{"_id":"ToHe"}],"_id":"7231","status":"public","type":"conference","conference":{"end_date":"2019-08-29","location":"Amsterdam, The Netherlands","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"publication_status":"published","volume":11750,"oa_version":"Preprint","abstract":[{"text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature.","lang":"eng"}],"month":"08","intvolume":" 11750","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141."},"title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","author":[{"last_name":"Kong","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"day":"13","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","isi":1,"year":"2019","date_published":"2019-08-13T00:00:00Z","doi":"10.1007/978-3-030-29662-9_8","date_created":"2020-01-05T23:00:47Z","page":"123-141","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"has_accepted_license":"1","isi":1,"year":"2019","day":"24","publication":"eLife","doi":"10.7554/eLife.50793","date_published":"2019-12-24T00:00:00Z","date_created":"2020-01-19T23:00:39Z","acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"citation":{"ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh","first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425"},{"first_name":"Lisa","last_name":"Neidhardt","full_name":"Neidhardt, Lisa"},{"full_name":"Yan, Yahui","last_name":"Yan","first_name":"Yahui"},{"full_name":"Mayer, Matthias P.","last_name":"Mayer","first_name":"Matthias P."},{"first_name":"David","full_name":"Ron, David","last_name":"Ron"}],"article_processing_charge":"No","external_id":{"isi":["000512303700001"],"pmid":["31873072"]},"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","article_number":"e50793","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"file_name":"2019_eLife_AminWetzel.pdf","date_created":"2020-11-19T11:37:41Z","creator":"dernst","file_size":4817384,"date_updated":"2020-11-19T11:37:41Z","success":1,"checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","file_id":"8777","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":8,"abstract":[{"text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"12","intvolume":" 8","date_updated":"2023-09-06T14:58:02Z","ddc":["570"],"department":[{"_id":"MaDe"}],"file_date_updated":"2020-11-19T11:37:41Z","_id":"7340","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)"},"status":"public"},{"quality_controlled":"1","publisher":"AIP Publishing","oa":1,"doi":"10.1063/1.5064867","date_published":"2019-02-07T00:00:00Z","date_created":"2020-01-30T10:34:36Z","day":"07","publication":"The Journal of Chemical Physics","isi":1,"year":"2019","article_number":"054108","title":"eGFRD in all dimensions","author":[{"last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paijmans","full_name":"Paijmans, Joris","first_name":"Joris"},{"first_name":"Laurens","last_name":"Bossen","full_name":"Bossen, Laurens"},{"first_name":"Thomas","full_name":"Miedema, Thomas","last_name":"Miedema"},{"full_name":"Wehrens, Martijn","last_name":"Wehrens","first_name":"Martijn"},{"last_name":"Becker","full_name":"Becker, Nils B.","first_name":"Nils B."},{"full_name":"Kaizu, Kazunari","last_name":"Kaizu","first_name":"Kazunari"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"},{"first_name":"Pieter Rein","full_name":"ten Wolde, Pieter Rein","last_name":"ten Wolde"}],"external_id":{"arxiv":["1708.09364"],"isi":["000458109300009"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.","ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108."},"month":"02","intvolume":" 150","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"volume":150,"issue":"5","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"7422","department":[{"_id":"GaTk"}],"date_updated":"2023-09-06T14:59:28Z"},{"publication":"27th International Symposium on Graph Drawing and Network Visualization","day":"28","year":"2019","isi":1,"date_created":"2020-01-05T23:00:47Z","date_published":"2019-11-28T00:00:00Z","doi":"10.1007/978-3-030-35802-0_18","page":"230-243","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18."},"title":"Extending simple drawings","article_processing_charge":"No","external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670"},{"last_name":"Derka","full_name":"Derka, Martin","first_name":"Martin"},{"first_name":"Irene","full_name":"Parada, Irene","last_name":"Parada"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"]},"ec_funded":1,"volume":11904,"oa_version":"Preprint","abstract":[{"text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.","lang":"eng"}],"intvolume":" 11904","month":"11","main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","date_updated":"2023-09-06T14:56:00Z","department":[{"_id":"UlWa"}],"_id":"7230","status":"public","conference":{"name":"GD: Graph Drawing and Network Visualization","location":"Prague, Czech Republic","end_date":"2019-09-20","start_date":"2019-09-17"},"type":"conference"},{"status":"public","conference":{"name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","location":"Amsterdam, The Netherlands","end_date":"2019-08-29","start_date":"2019-08-27"},"type":"conference","_id":"7232","department":[{"_id":"ToHe"}],"date_updated":"2023-09-06T14:57:17Z","intvolume":" 11750","month":"08","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","abstract":[{"text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. ","lang":"eng"}],"volume":11750,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Mixed-time signal temporal logic","article_processing_charge":"No","external_id":{"isi":["000611677700004"]},"author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4"},"quality_controlled":"1","publisher":"Springer Nature","date_created":"2020-01-05T23:00:48Z","doi":"10.1007/978-3-030-29662-9_4","date_published":"2019-08-13T00:00:00Z","page":"59-75","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","day":"13","year":"2019","isi":1},{"_id":"7420","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-06T15:01:00Z","department":[{"_id":"MiSi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic."}],"month":"06","intvolume":" 132","main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"publication_status":"published","issue":"11","volume":132,"article_number":"jcs233387","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387.","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387."},"title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","author":[{"first_name":"Pranshu","full_name":"Sahgal, Pranshu","last_name":"Sahgal"},{"last_name":"Alanko","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jaroslav","last_name":"Icha","full_name":"Icha, Jaroslav"},{"last_name":"Paatero","full_name":"Paatero, Ilkka","first_name":"Ilkka"},{"last_name":"Hamidi","full_name":"Hamidi, Hellyeh","first_name":"Hellyeh"},{"full_name":"Arjonen, Antti","last_name":"Arjonen","first_name":"Antti"},{"first_name":"Mika","last_name":"Pietilä","full_name":"Pietilä, Mika"},{"first_name":"Anne","full_name":"Rokka, Anne","last_name":"Rokka"},{"first_name":"Johanna","full_name":"Ivaska, Johanna","last_name":"Ivaska"}],"article_processing_charge":"No","external_id":{"isi":["000473327900017"],"pmid":["31076515"]},"quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"day":"07","publication":"Journal of Cell Science","isi":1,"year":"2019","doi":"10.1242/jcs.233387","date_published":"2019-06-07T00:00:00Z","date_created":"2020-01-30T10:31:42Z"},{"title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","author":[{"full_name":"Akemann, Gernot","last_name":"Akemann","first_name":"Gernot"},{"first_name":"Tomasz","last_name":"Checinski","full_name":"Checinski, Tomasz"},{"first_name":"Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","full_name":"Liu, Dangzheng"},{"full_name":"Strahov, Eugene","last_name":"Strahov","first_name":"Eugene"}],"article_processing_charge":"No","external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.","chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.","ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479.","apa":"Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888","mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888."},"doi":"10.1214/18-aihp888","date_published":"2019-02-01T00:00:00Z","date_created":"2020-01-30T10:36:50Z","page":"441-479","day":"01","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","isi":1,"year":"2019","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"department":[{"_id":"LaEr"}],"date_updated":"2023-09-06T14:58:39Z","status":"public","type":"journal_article","article_type":"original","_id":"7423","issue":"1","volume":55,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","month":"02","intvolume":" 55","main_file_link":[{"url":"https://arxiv.org/abs/1704.05224","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.","lang":"eng"}]}]