[{"article_number":"138","title":"Population structure determines the tradeoff between fixation probability and fixation time","author":[{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"day":"23","file":[{"file_size":1670274,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2019_CommBio_Tkadlec.pdf","date_created":"2019-12-23T13:39:30Z","access_level":"open_access","file_id":"7211","date_updated":"2020-07-14T12:47:53Z","checksum":"d1a69bfe73767e4246f0a38e4e1554dd"}],"publication":"Communications Biology","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)"},"scopus_import":"1","ec_funded":1,"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"pmid":1,"doi":"10.1038/s42003-019-0373-y","quality_controlled":"1","publication_identifier":{"issn":["2399-3642"]},"isi":1,"language":[{"iso":"eng"}],"project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"volume":2,"date_created":"2019-12-23T13:36:50Z","file_date_updated":"2020-07-14T12:47:53Z","oa_version":"Published Version","type":"journal_article","month":"04","abstract":[{"text":"The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.","lang":"eng"}],"date_updated":"2023-09-07T13:19:22Z","_id":"7210","year":"2019","date_published":"2019-04-23T00:00:00Z","ddc":["000"],"oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":" 2","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"citation":{"short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0373-y.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” Communications Biology, vol. 2. Springer Nature, 2019.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0373-y","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138.","mla":"Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology, vol. 2, 138, Springer Nature, 2019, doi:10.1038/s42003-019-0373-y.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2019;2. doi:10.1038/s42003-019-0373-y"},"external_id":{"isi":["000465425700006"],"pmid":["31044163"]},"status":"public"},{"publisher":"BMC","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"publication":"BMC Bioinformatics","scopus_import":"1","article_processing_charge":"No","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)"},"author":[{"full_name":"Aganezov, Sergey","first_name":"Sergey","last_name":"Aganezov"},{"first_name":"Ilya","last_name":"Zban","full_name":"Zban, Ilya"},{"last_name":"Aksenov","first_name":"Vitalii","full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"full_name":"Schatz, Michael C.","last_name":"Schatz","first_name":"Michael C."}],"day":"17","file":[{"file_name":"2019_BMCBioinfo_Aganezov.pdf","file_size":1917374,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"7221","date_updated":"2020-07-14T12:47:54Z","checksum":"7a30357efdcf8f66587ed495c0927724","date_created":"2020-01-02T16:10:58Z","access_level":"open_access"}],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","article_number":"641","isi":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14712105"]},"doi":"10.1186/s12859-019-3208-4","quality_controlled":"1","year":"2019","_id":"7214","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}],"date_updated":"2023-09-06T14:51:06Z","type":"journal_article","oa_version":"Published Version","month":"12","volume":20,"file_date_updated":"2020-07-14T12:47:54Z","date_created":"2019-12-29T23:00:46Z","status":"public","external_id":{"isi":["000511618800007"]},"intvolume":" 20","citation":{"chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4."},"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2019-12-17T00:00:00Z","ddc":["570"]},{"author":[{"first_name":"Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"},{"full_name":"Cook, James","first_name":"James","last_name":"Cook"},{"first_name":"Alex","last_name":"Fabrikant","full_name":"Fabrikant, Alex"},{"last_name":"Gruteser","first_name":"Marco","full_name":"Gruteser, Marco"}],"date_updated":"2023-09-06T14:50:28Z","day":"28","abstract":[{"lang":"eng","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."}],"month":"11","oa_version":"None","type":"conference","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","article_number":"8917514","date_created":"2019-12-29T23:00:47Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"IEEE","department":[{"_id":"HeEd"}],"year":"2019","publication":"2019 IEEE Intelligent Transportation Systems Conference","_id":"7216","article_processing_charge":"No","scopus_import":"1","publication_status":"published","publication_identifier":{"isbn":["9781538670248"]},"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","quality_controlled":"1","external_id":{"isi":["000521238102050"]},"status":"public","isi":1,"conference":{"end_date":"2019-10-30","location":"Auckland, New Zealand","name":"ITSC: Intelligent Transportation Systems Conference","start_date":"2019-10-27"},"language":[{"iso":"eng"}],"citation":{"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.","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.","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.","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"}},{"oa_version":"Published Version","type":"journal_article","month":"12","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-06T14:52:49Z","file_date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-05T23:00:45Z","volume":6,"year":"2019","_id":"7225","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2019-12-03T00:00:00Z","ddc":["620"],"status":"public","external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"citation":{"chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","short":"J. Merrin, Bioengineering 6 (2019).","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","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."},"intvolume":" 6","day":"03","file":[{"checksum":"80f1499e2a4caccdf3aa54b137fd99a0","file_id":"7243","date_updated":"2020-07-14T12:47:54Z","access_level":"open_access","date_created":"2020-01-07T14:49:59Z","file_name":"2019_Bioengineering_Merrin.pdf","creator":"dernst","file_size":2660780,"content_type":"application/pdf","relation":"main_file"}],"author":[{"last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"}],"article_number":"109","title":"Frontiers in microfluidics, a teaching resource review","department":[{"_id":"NanoFab"}],"pmid":1,"publisher":"MDPI","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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)"},"article_type":"review","scopus_import":"1","article_processing_charge":"Yes","publication":"Bioengineering","publication_identifier":{"eissn":["23065354"]},"quality_controlled":"1","doi":"10.3390/bioengineering6040109","issue":"4","language":[{"iso":"eng"}],"isi":1},{"doi":"10.1063/1.5138135","quality_controlled":"1","publication_identifier":{"issn":["00222488"]},"isi":1,"language":[{"iso":"eng"}],"issue":"12","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","article_number":"123504","author":[{"full_name":"Jaksic, Vojkan","last_name":"Jaksic","first_name":"Vojkan"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"day":"01","file":[{"file_id":"7244","date_updated":"2020-07-14T12:47:54Z","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","date_created":"2020-01-07T14:59:13Z","access_level":"open_access","file_name":"2019_JournalMathPhysics_Jaksic.pdf","file_size":1025015,"content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"publication":"Journal of Mathematical Physics","scopus_import":"1","article_processing_charge":"No","article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"ddc":["500"],"date_published":"2019-12-01T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":" 60","citation":{"ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","apa":"Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135"},"external_id":{"isi":["000505529800002"]},"status":"public","volume":60,"date_created":"2020-01-05T23:00:46Z","file_date_updated":"2020-07-14T12:47:54Z","date_updated":"2024-02-28T13:01:45Z","type":"journal_article","month":"12","oa_version":"Published Version","_id":"7226","year":"2019"},{"isi":1,"conference":{"start_date":"2019-08-26","name":"Euro-Par: European Conference on Parallel Processing","location":"Göttingen, Germany","end_date":"2019-08-30"},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-29400-7_23","quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0302-9399-4"],"eissn":["1611-3349"]},"publication":"25th Anniversary of Euro-Par","scopus_import":"1","article_processing_charge":"No","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"title":"Scalable FIFO channels for programming via communicating sequential processes","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Elizarov, Roman","last_name":"Elizarov","first_name":"Roman"}],"day":"13","intvolume":" 11725","citation":{"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.","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.","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","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","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.","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."},"alternative_title":["LNCS"],"status":"public","external_id":{"isi":["000851061400023"]},"date_published":"2019-08-13T00:00:00Z","publication_status":"published","_id":"7228","year":"2019","volume":11725,"date_created":"2020-01-05T23:00:46Z","page":"317-333","abstract":[{"lang":"eng","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. "}],"date_updated":"2023-09-06T14:53:59Z","type":"conference","oa_version":"None","month":"08"},{"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara"},{"full_name":"Derka, Martin","last_name":"Derka","first_name":"Martin"},{"full_name":"Parada, Irene","first_name":"Irene","last_name":"Parada"}],"day":"28","arxiv":1,"title":"Extending simple drawings","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"UlWa"}],"publication":"27th International Symposium on Graph Drawing and Network Visualization","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"]},"doi":"10.1007/978-3-030-35802-0_18","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"conference":{"end_date":"2019-09-20","start_date":"2019-09-17","location":"Prague, Czech Republic","name":"GD: Graph Drawing and Network Visualization"},"isi":1,"language":[{"iso":"eng"}],"page":"230-243","type":"conference","oa_version":"Preprint","month":"11","date_updated":"2023-09-06T14:56:00Z","abstract":[{"lang":"eng","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."}],"volume":11904,"date_created":"2020-01-05T23:00:47Z","year":"2019","_id":"7230","oa":1,"publication_status":"published","date_published":"2019-11-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08129"}],"alternative_title":["LNCS"],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"status":"public","intvolume":" 11904","citation":{"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.","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.","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","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.","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.","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"}},{"quality_controlled":"1","doi":"10.1007/978-3-030-29662-9_8","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"language":[{"iso":"eng"}],"isi":1,"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Amsterdam, The Netherlands","start_date":"2019-08-27","end_date":"2019-08-29"},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"arxiv":1,"title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","day":"13","author":[{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","article_processing_charge":"No","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"date_published":"2019-08-13T00:00:00Z","oa":1,"publication_status":"published","citation":{"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","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","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.","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.","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."},"intvolume":" 11750","status":"public","external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"alternative_title":["LNCS"],"date_created":"2020-01-05T23:00:47Z","volume":11750,"date_updated":"2023-09-06T14:55:15Z","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"}],"oa_version":"Preprint","type":"conference","month":"08","page":"123-141","_id":"7231","year":"2019"},{"citation":{"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","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.","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.","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.","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."},"intvolume":" 11750","status":"public","external_id":{"isi":["000611677700004"]},"alternative_title":["LNCS"],"date_published":"2019-08-13T00:00:00Z","publication_status":"published","_id":"7232","year":"2019","date_created":"2020-01-05T23:00:48Z","volume":11750,"oa_version":"None","month":"08","type":"conference","date_updated":"2023-09-06T14:57:17Z","abstract":[{"lang":"eng","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. "}],"page":"59-75","language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-29","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","location":"Amsterdam, The Netherlands"},"isi":1,"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"quality_controlled":"1","doi":"10.1007/978-3-030-29662-9_4","publication_identifier":{"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"],"issn":["0302-9743"]},"scopus_import":"1","article_processing_charge":"No","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mixed-time signal temporal logic","day":"13","author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"}]},{"quality_controlled":"1","doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","publication_identifier":{"isbn":["9781557528209"]},"publication_status":"published","language":[{"iso":"eng"}],"citation":{"apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019."},"conference":{"start_date":"2019-07-15","name":"NLO: Nonlinear Optics","location":"Waikoloa Beach, Hawaii (HI), United States","end_date":"2019-07-19"},"status":"public","date_created":"2020-01-05T23:00:48Z","article_number":"NM2A.5","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","type":"conference","month":"07","oa_version":"None","abstract":[{"text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm.","lang":"eng"}],"day":"15","date_updated":"2023-10-17T12:14:46Z","author":[{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"scopus_import":"1","article_processing_charge":"No","_id":"7233","publication":"Nonlinear Optics, OSA Technical Digest","department":[{"_id":"JoFi"}],"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group"},{"year":"2019","_id":"73","oa_version":"Published Version","month":"02","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"date_updated":"2023-09-13T09:12:35Z","volume":58,"date_created":"2018-12-11T11:44:29Z","file_date_updated":"2020-07-14T12:47:55Z","status":"public","external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"intvolume":" 58","citation":{"short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1.","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1"},"oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["510"],"date_published":"2019-02-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","department":[{"_id":"JaMa"}],"publication":"Calculus of Variations and Partial Differential Equations","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)"},"article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior"}],"day":"01","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":645565,"file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","date_created":"2019-01-28T15:37:11Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","date_updated":"2020-07-14T12:47:55Z","file_id":"5895"}],"article_number":"19","arxiv":1,"title":"On the geometry of geodesics in discrete optimal transport","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09442669"]},"doi":"10.1007/s00526-018-1456-1","quality_controlled":"1"},{"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)"},"article_processing_charge":"No","scopus_import":"1","publication":"eLife","department":[{"_id":"MaDe"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"eLife Sciences Publications","article_number":"e50793","title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","day":"24","file":[{"success":1,"file_name":"2019_eLife_AminWetzel.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":4817384,"checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","date_updated":"2020-11-19T11:37:41Z","file_id":"8777","access_level":"open_access","date_created":"2020-11-19T11:37:41Z"}],"author":[{"first_name":"Niko Paresh","last_name":"Amin-Wetzel","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","full_name":"Amin-Wetzel, Niko Paresh"},{"full_name":"Neidhardt, Lisa","first_name":"Lisa","last_name":"Neidhardt"},{"full_name":"Yan, Yahui","first_name":"Yahui","last_name":"Yan"},{"last_name":"Mayer","first_name":"Matthias P.","full_name":"Mayer, Matthias P."},{"first_name":"David","last_name":"Ron","full_name":"Ron, David"}],"language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.50793","publication_identifier":{"eissn":["2050084X"]},"_id":"7340","year":"2019","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.","date_created":"2020-01-19T23:00:39Z","file_date_updated":"2020-11-19T11:37:41Z","volume":8,"type":"journal_article","month":"12","oa_version":"Published Version","date_updated":"2023-09-06T14:58:02Z","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"}],"citation":{"short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","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.","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","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.","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.","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"},"intvolume":" 8","status":"public","external_id":{"isi":["000512303700001"],"pmid":["31873072"]},"date_published":"2019-12-24T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"published"},{"publication_identifier":{"issn":["2589-0042"]},"quality_controlled":"1","doi":"10.1016/j.isci.2019.11.025","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"grant_number":"720270","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"issue":"12","language":[{"iso":"eng"}],"day":"20","file":[{"file_id":"7448","date_updated":"2020-07-14T12:47:57Z","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","date_created":"2020-02-04T10:48:36Z","access_level":"open_access","file_name":"2019_iScience_Tabata.pdf","file_size":7197776,"content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"author":[{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","full_name":"Tabata, Shigekazu","first_name":"Shigekazu","last_name":"Tabata"},{"full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo","last_name":"Jevtic"},{"full_name":"Kurashige, Nobutaka","first_name":"Nobutaka","last_name":"Kurashige"},{"first_name":"Hirokazu","last_name":"Fuchida","full_name":"Fuchida, Hirokazu"},{"full_name":"Kido, Munetsugu","last_name":"Kido","first_name":"Munetsugu"},{"full_name":"Tani, Kazushi","first_name":"Kazushi","last_name":"Tani"},{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya","first_name":"Shohei"},{"last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi"},{"full_name":"Itakura, Makoto","last_name":"Itakura","first_name":"Makoto"},{"full_name":"Hamachi, Itaru","last_name":"Hamachi","first_name":"Itaru"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Akio","last_name":"Ojida","full_name":"Ojida, Akio"}],"title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","department":[{"_id":"RySh"}],"pmid":1,"publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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)"},"article_type":"original","ec_funded":1,"article_processing_charge":"No","scopus_import":"1","publication":"iScience","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570"],"date_published":"2019-12-20T00:00:00Z","status":"public","external_id":{"pmid":["31786521"],"isi":[":000504652000020"]},"citation":{"ieee":"S. Tabata et al., “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268. doi:10.1016/j.isci.2019.11.025","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025"},"intvolume":" 22","related_material":{"record":[{"relation":"dissertation_contains","id":"11393","status":"public"}]},"type":"journal_article","oa_version":"Published Version","month":"12","date_updated":"2024-03-25T23:30:07Z","abstract":[{"text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM.","lang":"eng"}],"page":"256-268","date_created":"2020-01-29T15:56:56Z","file_date_updated":"2020-07-14T12:47:57Z","volume":22,"year":"2019","_id":"7391"},{"publication_identifier":{"issn":["2375-2548"]},"doi":"10.1126/sciadv.aav9963","quality_controlled":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}],"isi":1,"language":[{"iso":"eng"}],"issue":"12","author":[{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"file":[{"file_name":"2019_ScienceAdvances_Morales.pdf","relation":"main_file","content_type":"application/pdf","file_size":1869449,"creator":"dernst","date_updated":"2020-07-14T12:47:57Z","file_id":"7442","checksum":"af99a5dcdc66c6d6102051faf3be48d8","date_created":"2020-02-03T13:33:25Z","access_level":"open_access"}],"day":"04","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","article_number":"eaav9963","publisher":"AAAS","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"department":[{"_id":"NiBa"}],"publication":"Science Advances","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2019-12-04T00:00:00Z","status":"public","external_id":{"isi":["000505069600008"],"pmid":["31840052"]},"intvolume":" 5","citation":{"ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019)."},"date_updated":"2023-09-06T15:35:56Z","abstract":[{"text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","month":"12","volume":5,"file_date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-29T15:58:27Z","year":"2019","_id":"7393"},{"publication_identifier":{"issn":["1369-5266"]},"quality_controlled":"1","doi":"10.1016/j.pbi.2019.11.002","issue":"12","language":[{"iso":"eng"}],"isi":1,"day":"01","author":[{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"},{"last_name":"Dagdas","first_name":"Yasin","full_name":"Dagdas, Yasin"}],"title":"Editorial overview: Cell biology in the era of omics?","department":[{"_id":"EvBe"}],"pmid":1,"publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"letter_note","scopus_import":"1","article_processing_charge":"No","publication":"Current Opinion in Plant Biology","publication_status":"published","date_published":"2019-12-01T00:00:00Z","external_id":{"pmid":["31787165"],"isi":["000502890600001"]},"status":"public","citation":{"ama":"Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 2019;52(12):A1-A2. doi:10.1016/j.pbi.2019.11.002","mla":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology, vol. 52, no. 12, Elsevier, 2019, pp. A1–2, doi:10.1016/j.pbi.2019.11.002.","ista":"Benková E, Dagdas Y. 2019. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 52(12), A1–A2.","apa":"Benková, E., & Dagdas, Y. (2019). Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.11.002","ieee":"E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of omics?,” Current Opinion in Plant Biology, vol. 52, no. 12. Elsevier, pp. A1–A2, 2019.","chicago":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.11.002.","short":"E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2."},"intvolume":" 52","type":"journal_article","month":"12","oa_version":"None","date_updated":"2023-09-07T14:56:55Z","page":"A1-A2","date_created":"2020-01-29T16:00:07Z","volume":52,"year":"2019","_id":"7394"},{"date_published":"2019-09-19T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":" 75","citation":{"short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6.","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022.","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019.","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.","ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022"},"status":"public","external_id":{"pmid":["31492636"],"isi":["000486614200006"]},"volume":75,"file_date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-29T16:02:33Z","page":"1131-1146.e6","type":"journal_article","month":"09","oa_version":"Published Version","abstract":[{"text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.","lang":"eng"}],"date_updated":"2023-09-07T14:53:06Z","_id":"7395","year":"2019","doi":"10.1016/j.molcel.2019.07.022","quality_controlled":"1","publication_identifier":{"issn":["1097-2765"]},"isi":1,"issue":"6","language":[{"iso":"eng"}],"project":[{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes"}],"title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","author":[{"id":"322DA418-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9864-3586","full_name":"Letts, James A","last_name":"Letts","first_name":"James A"},{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","first_name":"Karol","last_name":"Fiedorczuk"},{"last_name":"Degliesposti","first_name":"Gianluca","full_name":"Degliesposti, Gianluca"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"file":[{"date_created":"2020-02-04T10:37:28Z","access_level":"open_access","file_id":"7447","date_updated":"2020-07-14T12:47:57Z","checksum":"5202f53a237d6650ece038fbf13bdcea","file_size":9654895,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2019_MolecularCell_Letts.pdf"}],"day":"19","publication":"Molecular Cell","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)"},"ec_funded":1,"article_processing_charge":"No","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Cell Press","department":[{"_id":"LeSa"}],"pmid":1},{"oa":1,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1810.11338","open_access":"1"}],"date_published":"2019-09-18T00:00:00Z","external_id":{"arxiv":["1810.11338"],"isi":["000486661700001"]},"status":"public","citation":{"ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005","apa":"Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005.","mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:10.1103/revmodphys.91.035005.","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.035005.","ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019)."},"intvolume":" 91","date_updated":"2024-02-28T13:15:33Z","abstract":[{"text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting.","lang":"eng"}],"oa_version":"Preprint","type":"journal_article","month":"09","date_created":"2020-01-29T16:04:19Z","volume":91,"year":"2019","_id":"7396","publication_identifier":{"eissn":["1539-0756"],"issn":["0034-6861"]},"quality_controlled":"1","doi":"10.1103/revmodphys.91.035005","project":[{"grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment"}],"language":[{"iso":"eng"}],"issue":"3","isi":1,"day":"18","author":[{"last_name":"Koch","first_name":"Christiane P.","full_name":"Koch, Christiane P."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"last_name":"Sugny","first_name":"Dominique","full_name":"Sugny, Dominique"}],"title":"Quantum control of molecular rotation","arxiv":1,"article_number":"035005 ","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Reviews of Modern Physics"},{"author":[{"id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M"},{"last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"day":"10","arxiv":1,"title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"CUP","department":[{"_id":"BjHo"}],"publication":"Journal of Fluid Mechanics","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"doi":"10.1017/jfm.2019.486","quality_controlled":"1","isi":1,"language":[{"iso":"eng"}],"page":"699-719","abstract":[{"lang":"eng","text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT)."}],"date_updated":"2023-09-06T15:36:36Z","month":"09","type":"journal_article","oa_version":"Preprint","volume":874,"date_created":"2020-01-29T16:05:19Z","year":"2019","_id":"7397","publication_status":"published","oa":1,"date_published":"2019-09-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04080"}],"external_id":{"arxiv":["1808.04080"],"isi":["000475349900001"]},"status":"public","intvolume":" 874","citation":{"ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486","ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719.","mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.","apa":"Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.","chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719."}},{"department":[{"_id":"RySh"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Rockefeller University Press","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication":"The Journal of General Physiology","file":[{"file_id":"7450","date_updated":"2020-07-14T12:47:57Z","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71","date_created":"2020-02-05T07:20:32Z","access_level":"open_access","file_name":"2019_JGP_Erdem.pdf","file_size":2641297,"content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"day":"03","author":[{"full_name":"Erdem, Fatma Asli","first_name":"Fatma Asli","last_name":"Erdem"},{"last_name":"Ilic","first_name":"Marija","full_name":"Ilic, Marija"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner"},{"first_name":"Jakub","last_name":"Gołacki","full_name":"Gołacki, Jakub"},{"first_name":"Gert","last_name":"Lubec","full_name":"Lubec, Gert"},{"last_name":"Freissmuth","first_name":"Michael","full_name":"Freissmuth, Michael"},{"full_name":"Sandtner, Walter","first_name":"Walter","last_name":"Sandtner"}],"title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","issue":"8","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"issn":["0022-1295"],"eissn":["1540-7748"]},"quality_controlled":"1","doi":"10.1085/jgp.201912318","year":"2019","_id":"7398","oa_version":"Published Version","month":"07","type":"journal_article","abstract":[{"text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation.","lang":"eng"}],"date_updated":"2023-09-07T14:52:23Z","page":"1035-1050","file_date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-29T16:06:29Z","volume":151,"external_id":{"pmid":["31270129"],"isi":["000478792500008"]},"status":"public","citation":{"ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. Rockefeller University Press. https://doi.org/10.1085/jgp.201912318","ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318","short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.","ieee":"F. A. Erdem et al., “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” The Journal of General Physiology, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318."},"intvolume":" 151","has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2019-07-03T00:00:00Z","ddc":["570"]},{"ddc":["570"],"date_published":"2019-07-22T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":" 15","citation":{"apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268","mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.","ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268.","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268","short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).","chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268.","ieee":"D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019."},"status":"public","external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"volume":15,"file_date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-29T16:14:07Z","oa_version":"Published Version","type":"journal_article","month":"07","date_updated":"2023-10-17T12:30:27Z","abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"_id":"7399","year":"2019","doi":"10.1371/journal.pgen.1008268","quality_controlled":"1","publication_identifier":{"issn":["1553-7404"]},"isi":1,"issue":"7","language":[{"iso":"eng"}],"article_number":"e1008268","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"full_name":"Muckenhuber, Markus","last_name":"Muckenhuber","first_name":"Markus"},{"first_name":"Philipp C.","last_name":"Bammer","full_name":"Bammer, Philipp C."},{"last_name":"Kulinski","first_name":"Tomasz M.","full_name":"Kulinski, Tomasz M."},{"full_name":"Theussl, Hans-Christian","last_name":"Theussl","first_name":"Hans-Christian"},{"first_name":"Takahiko","last_name":"Shimizu","full_name":"Shimizu, Takahiko"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"first_name":"Quanah J.","last_name":"Hudson","full_name":"Hudson, Quanah J."}],"file":[{"file_name":"2019_PlosGenetics_Andergassen.pdf","creator":"dernst","file_size":2302307,"relation":"main_file","content_type":"application/pdf","checksum":"2f51fc91e4a4199827adc51d432ad864","file_id":"7446","date_updated":"2020-07-14T12:47:57Z","access_level":"open_access","date_created":"2020-02-04T10:11:55Z"}],"day":"22","publication":"PLoS Genetics","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)"},"article_processing_charge":"No","scopus_import":"1","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"pmid":1}]