[{"file_date_updated":"2020-07-14T12:47:52Z","related_material":{"record":[{"id":"1096","relation":"dissertation_contains","status":"public"},{"id":"7001","relation":"part_of_dissertation","status":"public"}]},"ddc":["570"],"page":"107","date_created":"2019-12-16T14:26:14Z","type":"dissertation","month":"12","author":[{"last_name":"Schwayer","first_name":"Cornelia","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing."}],"alternative_title":["ISTA Thesis"],"_id":"7186","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","day":"16","doi":"10.15479/AT:ISTA:7186","year":"2019","degree_awarded":"PhD","supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"oa":1,"date_updated":"2023-09-07T12:56:42Z","status":"public","publication_status":"published","citation":{"ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","mla":"Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7186.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7186.","apa":"Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186"},"department":[{"_id":"CaHe"}],"file":[{"creator":"cschwayer","file_id":"7194","content_type":"application/zip","date_created":"2019-12-19T15:18:11Z","file_name":"DocumentSourceFiles.zip","access_level":"closed","relation":"source_file","file_size":19431292,"checksum":"585583c1c875c5d9525703a539668a7c","date_updated":"2020-07-14T12:47:52Z"},{"access_level":"open_access","relation":"main_file","checksum":"9b9b24351514948d27cec659e632e2cd","file_size":19226428,"file_name":"Thesis_CS_final.pdf","date_updated":"2020-07-14T12:47:52Z","creator":"cschwayer","date_created":"2019-12-19T15:19:21Z","file_id":"7195","content_type":"application/pdf"}],"oa_version":"Published Version","date_published":"2019-12-16T00:00:00Z"},{"quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"apa":"Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177","chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177.","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177."},"article_type":"original","date_published":"2019-12-16T00:00:00Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","checksum":"382eb67e62a77052a23887332d363f96","file_size":1370022,"file_name":"2019_PhysRevResearch_Huber.pdf","date_updated":"2020-07-14T12:47:52Z","creator":"dernst","date_created":"2019-12-18T07:13:14Z","file_id":"7193","content_type":"application/pdf"}],"year":"2019","issue":"3","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","publication_identifier":{"issn":["2643-1564"]},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"16","article_number":"033177","doi":"10.1103/physrevresearch.1.033177","date_updated":"2024-02-28T13:11:40Z","intvolume":" 1","status":"public","oa":1,"external_id":{"arxiv":["1908.02483"]},"license":"https://creativecommons.org/licenses/by/4.0/","_id":"7190","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"publisher":"American Physical Society","date_created":"2019-12-17T13:03:41Z","file_date_updated":"2020-07-14T12:47:52Z","ddc":["530"],"volume":1,"publication":"Physical Review Research","article_processing_charge":"No","type":"journal_article","author":[{"last_name":"Huber","full_name":"Huber, D.","first_name":"D."},{"last_name":"Hammer","first_name":"H.-W.","full_name":"Hammer, H.-W."},{"first_name":"Artem","full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"language":[{"iso":"eng"}],"month":"12"},{"quality_controlled":"1","citation":{"ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol. 10. Springer Nature, 2019.","mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications, vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4."},"publication_status":"published","date_published":"2019-12-17T00:00:00Z","article_type":"original","department":[{"_id":"MaLo"},{"_id":"BjHo"}],"file":[{"date_created":"2019-12-23T07:34:56Z","file_id":"7208","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:53Z","relation":"main_file","access_level":"open_access","checksum":"a1b44b427ba341383197790d0e8789fa","file_size":8488733,"file_name":"2019_NatureComm_Caldas.pdf"}],"oa_version":"Published Version","year":"2019","title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","has_accepted_license":"1","publication_identifier":{"issn":["2041-1723"]},"isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"5744","doi":"10.1038/s41467-019-13702-4","day":"17","date_updated":"2023-09-07T13:18:51Z","status":"public","intvolume":" 10","oa":1,"external_id":{"isi":["000503009300001"]},"_id":"7197","abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.","lang":"eng"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"date_created":"2019-12-20T12:22:57Z","ddc":["570"],"volume":10,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8358"}]},"file_date_updated":"2020-07-14T12:47:53Z","article_processing_charge":"No","publication":"Nature Communications","scopus_import":"1","month":"12","author":[{"first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin"},{"first_name":"Daniel J. G.","full_name":"Pearce, Daniel J. G.","last_name":"Pearce"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Brugués, Jan","last_name":"Brugués"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"year":"2019","issue":"3","title":"Limit law of a second class particle in TASEP with non-random initial condition","publication_identifier":{"issn":["0246-0203"]},"isi":1,"doi":"10.1214/18-AIHP916","day":"25","date_updated":"2023-10-17T08:53:45Z","status":"public","intvolume":" 55","oa":1,"external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"arxiv":1,"quality_controlled":"1","publication_status":"published","citation":{"mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916."},"date_published":"2019-09-25T00:00:00Z","article_type":"original","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"oa_version":"Preprint","page":"1203-1225","date_created":"2018-12-11T11:44:29Z","volume":55,"article_processing_charge":"No","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","scopus_import":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Ferrari","first_name":"Patrick","full_name":"Ferrari, Patrick"},{"first_name":"Promit","full_name":"Ghosal, Promit","last_name":"Ghosal"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Nejjar, Peter","last_name":"Nejjar"}],"month":"09","type":"journal_article","_id":"72","abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Mathematical Statistics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"project":[{"call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).","lang":"eng"}],"_id":"7200","type":"journal_article","author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","first_name":"Pietro","last_name":"Brighi"},{"first_name":"Marco","full_name":"Grilli, Marco","last_name":"Grilli"},{"last_name":"Leridon","full_name":"Leridon, Brigitte","first_name":"Brigitte"},{"full_name":"Caprara, Sergio","first_name":"Sergio","last_name":"Caprara"}],"month":"11","language":[{"iso":"eng"}],"scopus_import":"1","publication":"Physical Review B","article_processing_charge":"No","volume":100,"date_created":"2019-12-22T23:00:41Z","oa_version":"Preprint","department":[{"_id":"MaSe"}],"article_type":"original","date_published":"2019-11-25T00:00:00Z","publication_status":"published","citation":{"ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019.","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518.","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518","apa":"Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518"},"quality_controlled":"1","arxiv":1,"external_id":{"isi":["000498845700006"],"arxiv":["1907.13579"]},"oa":1,"intvolume":" 100","status":"public","date_updated":"2024-02-28T13:14:08Z","article_number":"174518","day":"25","doi":"10.1103/PhysRevB.100.174518","isi":1,"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"issue":"17","year":"2019"},{"type":"conference","month":"11","conference":{"name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis","location":"Denver, CO, Unites States","start_date":"2019-11-17","end_date":"2019-11-19"},"author":[{"last_name":"Renggli","full_name":"Renggli, Cedric","first_name":"Cedric"},{"id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","last_name":"Ashkboos","first_name":"Saleh","full_name":"Ashkboos, Saleh"},{"last_name":"Aghagolzadeh","full_name":"Aghagolzadeh, Mehdi","first_name":"Mehdi"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Hoefler","full_name":"Hoefler, Torsten","first_name":"Torsten"}],"language":[{"iso":"eng"}],"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","article_processing_charge":"No","scopus_import":"1","date_created":"2019-12-22T23:00:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"publisher":"ACM","ec_funded":1,"abstract":[{"lang":"eng","text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks."}],"_id":"7201","oa":1,"external_id":{"isi":["000545976800011"],"arxiv":["1802.08021"]},"date_updated":"2023-09-06T14:37:55Z","status":"public","title":"SparCML: High-performance sparse communication for machine learning","publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"day":"17","article_number":"a11","doi":"10.1145/3295500.3356222","isi":1,"year":"2019","department":[{"_id":"DaAl"}],"oa_version":"Preprint","date_published":"2019-11-17T00:00:00Z","citation":{"ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222."},"publication_status":"published","quality_controlled":"1","arxiv":1},{"date_published":"2019-11-18T00:00:00Z","article_type":"original","department":[{"_id":"SiHi"}],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:53Z","file_name":"2019_eLife_Llorca.pdf","file_size":2960543,"checksum":"b460ecc33e1a68265e7adea775021f3a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7503","date_created":"2020-02-18T15:19:26Z","creator":"dernst"}],"quality_controlled":"1","citation":{"ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381."},"publication_status":"published","date_updated":"2023-09-06T14:38:39Z","status":"public","intvolume":" 8","oa":1,"external_id":{"isi":["000508156800001"],"pmid":["31736464"]},"year":"2019","has_accepted_license":"1","publication_identifier":{"eissn":["2050084X"]},"title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"e51381","day":"18","doi":"10.7554/eLife.51381","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"eLife Sciences Publications","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF"}],"pmid":1,"_id":"7202","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}],"article_processing_charge":"No","publication":"eLife","scopus_import":"1","month":"11","author":[{"last_name":"Llorca","full_name":"Llorca, Alfredo","first_name":"Alfredo"},{"first_name":"Gabriele","full_name":"Ciceri, Gabriele","last_name":"Ciceri"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie"},{"last_name":"Wong","full_name":"Wong, Fong Kuan","first_name":"Fong Kuan"},{"full_name":"Diana, Giovanni","first_name":"Giovanni","last_name":"Diana"},{"last_name":"Serafeimidou-Pouliou","first_name":"Eleni","full_name":"Serafeimidou-Pouliou, Eleni"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arnold","first_name":"Sebastian J.","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maravall, Miguel","first_name":"Miguel","last_name":"Maravall"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"language":[{"iso":"eng"}],"type":"journal_article","date_created":"2019-12-22T23:00:42Z","ddc":["570"],"volume":8,"file_date_updated":"2020-07-14T12:47:53Z"},{"pmid":1,"_id":"7210","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"}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"}],"date_created":"2019-12-23T13:36:50Z","ddc":["000"],"volume":2,"file_date_updated":"2020-07-14T12:47:53Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"}]},"article_processing_charge":"No","publication":"Communications Biology","scopus_import":"1","month":"04","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","first_name":"Josef"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"type":"journal_article","quality_controlled":"1","publication_status":"published","citation":{"short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","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.","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.","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.","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","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","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."},"date_published":"2019-04-23T00:00:00Z","article_type":"original","department":[{"_id":"KrCh"}],"oa_version":"Published Version","file":[{"file_name":"2019_CommBio_Tkadlec.pdf","checksum":"d1a69bfe73767e4246f0a38e4e1554dd","file_size":1670274,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:53Z","creator":"dernst","content_type":"application/pdf","file_id":"7211","date_created":"2019-12-23T13:39:30Z"}],"year":"2019","publication_identifier":{"issn":["2399-3642"]},"has_accepted_license":"1","title":"Population structure determines the tradeoff between fixation probability and fixation time","isi":1,"day":"23","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"138","doi":"10.1038/s42003-019-0373-y","date_updated":"2023-09-07T13:19:22Z","status":"public","intvolume":" 2","oa":1,"external_id":{"pmid":["31044163"],"isi":["000465425700006"]}},{"citation":{"short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","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.","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.","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","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","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."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"7221","date_created":"2020-01-02T16:10:58Z","file_name":"2019_BMCBioinfo_Aganezov.pdf","file_size":1917374,"checksum":"7a30357efdcf8f66587ed495c0927724","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z"}],"department":[{"_id":"DaAl"}],"date_published":"2019-12-17T00:00:00Z","article_type":"original","isi":1,"article_number":"641","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1186/s12859-019-3208-4","day":"17","has_accepted_license":"1","title":"Recovering rearranged cancer chromosomes from karyotype graphs","publication_identifier":{"eissn":["14712105"]},"year":"2019","external_id":{"isi":["000511618800007"]},"oa":1,"status":"public","intvolume":" 20","date_updated":"2023-09-06T14:51:06Z","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"}],"_id":"7214","publisher":"BMC","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"volume":20,"file_date_updated":"2020-07-14T12:47:54Z","date_created":"2019-12-29T23:00:46Z","month":"12","author":[{"full_name":"Aganezov, Sergey","first_name":"Sergey","last_name":"Aganezov"},{"last_name":"Zban","first_name":"Ilya","full_name":"Zban, Ilya"},{"last_name":"Aksenov","full_name":"Aksenov, Vitalii","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"},{"last_name":"Schatz","first_name":"Michael C.","full_name":"Schatz, Michael C."}],"language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"BMC Bioinformatics"},{"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"}],"publication_status":"published","citation":{"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.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 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.","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","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."},"_id":"7216","quality_controlled":"1","oa_version":"None","publisher":"IEEE","department":[{"_id":"HeEd"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-11-28T00:00:00Z","day":"28","article_number":"8917514","doi":"10.1109/ITSC.2019.8917514","isi":1,"publication_identifier":{"isbn":["9781538670248"]},"title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","date_created":"2019-12-29T23:00:47Z","year":"2019","external_id":{"isi":["000521238102050"]},"type":"conference","author":[{"last_name":"Osang","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"},{"full_name":"Cook, James","first_name":"James","last_name":"Cook"},{"last_name":"Fabrikant","full_name":"Fabrikant, Alex","first_name":"Alex"},{"last_name":"Gruteser","first_name":"Marco","full_name":"Gruteser, Marco"}],"conference":{"start_date":"2019-10-27","end_date":"2019-10-30","name":"ITSC: Intelligent Transportation Systems Conference","location":"Auckland, New Zealand"},"language":[{"iso":"eng"}],"month":"11","scopus_import":"1","status":"public","publication":"2019 IEEE Intelligent Transportation Systems Conference","date_updated":"2023-09-06T14:50:28Z","article_processing_charge":"No"},{"citation":{"ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","short":"J. Merrin, Bioengineering 6 (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.","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","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","file":[{"relation":"main_file","access_level":"open_access","file_size":2660780,"checksum":"80f1499e2a4caccdf3aa54b137fd99a0","file_name":"2019_Bioengineering_Merrin.pdf","date_updated":"2020-07-14T12:47:54Z","creator":"dernst","date_created":"2020-01-07T14:49:59Z","file_id":"7243","content_type":"application/pdf"}],"department":[{"_id":"NanoFab"}],"date_published":"2019-12-03T00:00:00Z","article_type":"review","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.3390/bioengineering6040109","article_number":"109","day":"03","title":"Frontiers in microfluidics, a teaching resource review","publication_identifier":{"eissn":["23065354"]},"issue":"4","has_accepted_license":"1","year":"2019","external_id":{"isi":["000505590000024"],"pmid":["31816954"]},"oa":1,"status":"public","intvolume":" 6","date_updated":"2023-09-06T14:52:49Z","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"}],"_id":"7225","pmid":1,"publisher":"MDPI","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["620"],"volume":6,"file_date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-05T23:00:45Z","author":[{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"}],"month":"12","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"Yes","publication":"Bioengineering"},{"department":[{"_id":"RoSe"}],"file":[{"date_updated":"2020-07-14T12:47:54Z","file_name":"2019_JournalMathPhysics_Jaksic.pdf","file_size":1025015,"checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7244","date_created":"2020-01-07T14:59:13Z","creator":"dernst"}],"oa_version":"Published Version","date_published":"2019-12-01T00:00:00Z","article_type":"letter_note","citation":{"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","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","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.","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.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","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."},"publication_status":"published","quality_controlled":"1","oa":1,"external_id":{"isi":["000505529800002"]},"date_updated":"2024-02-28T13:01:45Z","status":"public","intvolume":" 60","publication_identifier":{"issn":["00222488"]},"title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","issue":"12","has_accepted_license":"1","isi":1,"doi":"10.1063/1.5138135","article_number":"123504","day":"01","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AIP Publishing","_id":"7226","author":[{"last_name":"Jaksic","first_name":"Vojkan","full_name":"Jaksic, Vojkan"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"month":"12","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication":"Journal of Mathematical Physics","scopus_import":"1","volume":60,"ddc":["500"],"file_date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-05T23:00:46Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","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. "}],"_id":"7228","alternative_title":["LNCS"],"conference":{"name":"Euro-Par: European Conference on Parallel Processing","location":"Göttingen, Germany","start_date":"2019-08-26","end_date":"2019-08-30"},"month":"08","language":[{"iso":"eng"}],"author":[{"last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"type":"conference","article_processing_charge":"No","publication":"25th Anniversary of Euro-Par","scopus_import":"1","volume":11725,"page":"317-333","date_created":"2020-01-05T23:00:46Z","department":[{"_id":"DaAl"}],"oa_version":"None","date_published":"2019-08-13T00:00:00Z","publication_status":"published","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.","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","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.","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."},"quality_controlled":"1","external_id":{"isi":["000851061400023"]},"date_updated":"2023-09-06T14:53:59Z","status":"public","intvolume":" 11725","title":"Scalable FIFO channels for programming via communicating sequential processes","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9399-4"]},"isi":1,"day":"13","doi":"10.1007/978-3-030-29400-7_23","year":"2019"},{"ec_funded":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08129"}],"publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"_id":"7230","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"}],"scopus_import":"1","publication":"27th International Symposium on Graph Drawing and Network Visualization","article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M"},{"first_name":"Martin","full_name":"Derka, Martin","last_name":"Derka"},{"first_name":"Irene","full_name":"Parada, Irene","last_name":"Parada"}],"conference":{"start_date":"2019-09-17","end_date":"2019-09-20","name":"GD: Graph Drawing and Network Visualization","location":"Prague, Czech Republic"},"month":"11","date_created":"2020-01-05T23:00:47Z","page":"230-243","volume":11904,"date_published":"2019-11-28T00:00:00Z","oa_version":"Preprint","department":[{"_id":"UlWa"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","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.","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.","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.","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.","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","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"},"intvolume":" 11904","status":"public","date_updated":"2023-09-06T14:56:00Z","external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"oa":1,"year":"2019","doi":"10.1007/978-3-030-35802-0_18","day":"28","isi":1,"title":"Extending simple drawings","publication_identifier":{"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"],"issn":["0302-9743"]}},{"article_processing_charge":"No","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"start_date":"2019-08-27","end_date":"2019-08-29","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Amsterdam, The Netherlands"},"author":[{"full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"first_name":"Yu","full_name":"Jiang, Yu","last_name":"Jiang"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"month":"08","type":"conference","page":"123-141","date_created":"2020-01-05T23:00:47Z","volume":11750,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"_id":"7231","alternative_title":["LNCS"],"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"}],"date_updated":"2023-09-06T14:55:15Z","status":"public","intvolume":" 11750","oa":1,"external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"year":"2019","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"isi":1,"day":"13","doi":"10.1007/978-3-030-29662-9_8","date_published":"2019-08-13T00:00:00Z","department":[{"_id":"ToHe"}],"oa_version":"Preprint","arxiv":1,"quality_controlled":"1","citation":{"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.","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.","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.","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.","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"},"publication_status":"published"},{"_id":"7232","alternative_title":["LNCS"],"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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"page":"59-75","date_created":"2020-01-05T23:00:48Z","volume":11750,"article_processing_charge":"No","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","scopus_import":"1","author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"conference":{"location":"Amsterdam, The Netherlands","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","end_date":"2019-08-29","start_date":"2019-08-27"},"language":[{"iso":"eng"}],"month":"08","type":"conference","quality_controlled":"1","publication_status":"published","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.","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.","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.","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."},"date_published":"2019-08-13T00:00:00Z","department":[{"_id":"ToHe"}],"oa_version":"None","year":"2019","publication_identifier":{"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"],"issn":["0302-9743"]},"title":"Mixed-time signal temporal logic","isi":1,"doi":"10.1007/978-3-030-29662-9_4","day":"13","date_updated":"2023-09-06T14:57:17Z","status":"public","intvolume":" 11750","external_id":{"isi":["000611677700004"]}},{"oa_version":"None","publisher":"Optica Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"date_published":"2019-07-15T00:00:00Z","citation":{"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.","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","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.","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.","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.","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."},"publication_status":"published","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"}],"_id":"7233","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","full_name":"Leuchs, Gerd","first_name":"Gerd"},{"full_name":"Kumari, Madhuri","first_name":"Madhuri","last_name":"Kumari"},{"full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L.","last_name":"Schwefel"}],"month":"07","conference":{"start_date":"2019-07-15","end_date":"2019-07-19","location":"Waikoloa Beach, Hawaii (HI), United States","name":"NLO: Nonlinear Optics"},"type":"conference","status":"public","scopus_import":"1","article_processing_charge":"No","publication":"Nonlinear Optics, OSA Technical Digest","date_updated":"2023-10-17T12:14:46Z","doi":"10.1364/NLO.2019.NM2A.5","article_number":"NM2A.5","day":"15","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","publication_identifier":{"isbn":["9781557528209"]},"year":"2019","date_created":"2020-01-05T23:00:48Z"},{"date_published":"2019-02-01T00:00:00Z","article_type":"original","department":[{"_id":"JaMa"}],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:55Z","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","relation":"main_file","file_size":645565,"checksum":"ba05ac2d69de4c58d2cd338b63512798","file_id":"5895","content_type":"application/pdf","date_created":"2019-01-28T15:37:11Z","creator":"dernst"}],"arxiv":1,"quality_controlled":"1","citation":{"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.","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","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.","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.","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","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"},"publication_status":"published","date_updated":"2023-09-13T09:12:35Z","status":"public","intvolume":" 58","oa":1,"external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"year":"2019","issue":"1","title":"On the geometry of geodesics in discrete optimal transport","publication_identifier":{"issn":["09442669"]},"has_accepted_license":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1007/s00526-018-1456-1","day":"01","article_number":"19","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"_id":"73","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."}],"article_processing_charge":"Yes (via OA deal)","publication":"Calculus of Variations and Partial Differential Equations","scopus_import":"1","month":"02","author":[{"last_name":"Erbar","full_name":"Erbar, Matthias","first_name":"Matthias"},{"last_name":"Maas","full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"language":[{"iso":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:44:29Z","ddc":["510"],"volume":58,"file_date_updated":"2020-07-14T12:47:55Z"},{"publisher":"eLife Sciences Publications","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","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."}],"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.","_id":"7340","pmid":1,"type":"journal_article","month":"12","author":[{"id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","first_name":"Niko Paresh","full_name":"Amin-Wetzel, Niko Paresh","last_name":"Amin-Wetzel"},{"full_name":"Neidhardt, Lisa","first_name":"Lisa","last_name":"Neidhardt"},{"last_name":"Yan","full_name":"Yan, Yahui","first_name":"Yahui"},{"first_name":"Matthias P.","full_name":"Mayer, Matthias P.","last_name":"Mayer"},{"last_name":"Ron","full_name":"Ron, David","first_name":"David"}],"language":[{"iso":"eng"}],"scopus_import":"1","publication":"eLife","article_processing_charge":"No","file_date_updated":"2020-11-19T11:37:41Z","ddc":["570"],"volume":8,"date_created":"2020-01-19T23:00:39Z","oa_version":"Published Version","file":[{"success":1,"date_created":"2020-11-19T11:37:41Z","content_type":"application/pdf","file_id":"8777","creator":"dernst","date_updated":"2020-11-19T11:37:41Z","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","file_size":4817384,"relation":"main_file","access_level":"open_access","file_name":"2019_eLife_AminWetzel.pdf"}],"department":[{"_id":"MaDe"}],"article_type":"original","date_published":"2019-12-24T00:00:00Z","citation":{"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","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.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","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.","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.","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."},"publication_status":"published","quality_controlled":"1","external_id":{"pmid":["31873072"],"isi":["000512303700001"]},"oa":1,"intvolume":" 8","status":"public","date_updated":"2023-09-06T14:58:02Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"24","doi":"10.7554/eLife.50793","article_number":"e50793","isi":1,"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","publication_identifier":{"eissn":["2050084X"]},"has_accepted_license":"1","year":"2019"},{"oa_version":"Published Version","file":[{"file_name":"2019_iScience_Tabata.pdf","relation":"main_file","access_level":"open_access","file_size":7197776,"checksum":"f3e90056a49f09b205b1c4f8c739ffd1","date_updated":"2020-07-14T12:47:57Z","creator":"dernst","file_id":"7448","content_type":"application/pdf","date_created":"2020-02-04T10:48:36Z"}],"department":[{"_id":"RySh"}],"date_published":"2019-12-20T00:00:00Z","article_type":"original","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.","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.","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.","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.","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","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","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."},"publication_status":"published","quality_controlled":"1","external_id":{"isi":[":000504652000020"],"pmid":["31786521"]},"oa":1,"status":"public","intvolume":" 22","date_updated":"2024-03-25T23:30:07Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.isci.2019.11.025","day":"20","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","has_accepted_license":"1","publication_identifier":{"issn":["2589-0042"]},"issue":"12","year":"2019","publisher":"Elsevier","project":[{"grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"abstract":[{"lang":"eng","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."}],"_id":"7391","pmid":1,"month":"12","author":[{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","full_name":"Tabata, Shigekazu","last_name":"Tabata"},{"last_name":"Jevtic","first_name":"Marijo","full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kurashige","full_name":"Kurashige, Nobutaka","first_name":"Nobutaka"},{"first_name":"Hirokazu","full_name":"Fuchida, Hirokazu","last_name":"Fuchida"},{"first_name":"Munetsugu","full_name":"Kido, Munetsugu","last_name":"Kido"},{"last_name":"Tani","full_name":"Tani, Kazushi","first_name":"Kazushi"},{"full_name":"Zenmyo, Naoki","first_name":"Naoki","last_name":"Zenmyo"},{"last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei","first_name":"Shohei"},{"orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi","first_name":"Harumi","last_name":"Harada"},{"last_name":"Itakura","full_name":"Itakura, Makoto","first_name":"Makoto"},{"last_name":"Hamachi","first_name":"Itaru","full_name":"Hamachi, Itaru"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"},{"first_name":"Akio","full_name":"Ojida, Akio","last_name":"Ojida"}],"language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"iScience","ddc":["570"],"volume":22,"related_material":{"record":[{"status":"public","id":"11393","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-29T15:56:56Z","page":"256-268"}]