[{"oa":1,"citation":{"short":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical Review B 95 (2017).","mla":"Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B, vol. 95, no. 11, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125.","chicago":"Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins, and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125.","ama":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125","ieee":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene, “Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American Physical Society, 2017.","apa":"Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene, R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.95.115125","ista":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 95(11)."},"main_file_link":[{"url":"http://dspace.mit.edu/handle/1721.1/109835","open_access":"1"}],"publication":"Physical Review B","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.95.115125","date_published":"2017-03-13T00:00:00Z","day":"13","month":"03","publisher":"American Physical Society","intvolume":" 95","status":"public","title":"Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ","publication_status":"published","_id":"392","acknowledgement":"Optical pump-probe work was supported by the Gordon and Betty Moore Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization was supported by AFOSR FA95501410332 and NSF DMR1410665.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","volume":95,"oa_version":"None","date_updated":"2021-01-12T07:53:12Z","date_created":"2018-12-11T11:46:13Z","author":[{"last_name":"Vishik","first_name":"Inna","full_name":"Vishik, Inna"},{"full_name":"Mahmood, Fahad","first_name":"Fahad","last_name":"Mahmood"},{"full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"},{"full_name":"Gedik, Nuh","first_name":"Nuh","last_name":"Gedik"},{"first_name":"Joshu","last_name":"Higgins","full_name":"Higgins, Joshu"},{"full_name":"Greene, Richard","last_name":"Greene","first_name":"Richard"}],"type":"journal_article","extern":"1","issue":"11","publist_id":"7437","abstract":[{"text":"We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static.","lang":"eng"}]},{"has_accepted_license":"1","day":"30","date_published":"2017-01-30T00:00:00Z","citation":{"chicago":"Hardie, Rae, Ellen Van Dam, Mark Cowley, Ting Han, Seher Balaban, Marina Pajic, Mark Pinese, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism. BioMed Central, 2017. https://doi.org/10.1186/s40170-017-0164-1.","short":"R. Hardie, E. Van Dam, M. Cowley, T. Han, S. Balaban, M. Pajic, M. Pinese, M. Iconomou, R. Shearer, J. Mckenna, D. Miller, N. Waddell, J. Pearson, S. Grimmond, L.A. Sazanov, A. Biankin, S. Villas Boas, A. Hoy, N. Turner, D. Saunders, Cancer & Metabolism 5 (2017).","mla":"Hardie, Rae, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism, vol. 5, no. 2, BioMed Central, 2017, doi:10.1186/s40170-017-0164-1.","apa":"Hardie, R., Van Dam, E., Cowley, M., Han, T., Balaban, S., Pajic, M., … Saunders, D. (2017). Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. BioMed Central. https://doi.org/10.1186/s40170-017-0164-1","ieee":"R. Hardie et al., “Mitochondrial mutations and metabolic adaptation in pancreatic cancer,” Cancer & Metabolism, vol. 5, no. 2. BioMed Central, 2017.","ista":"Hardie R, Van Dam E, Cowley M, Han T, Balaban S, Pajic M, Pinese M, Iconomou M, Shearer R, Mckenna J, Miller D, Waddell N, Pearson J, Grimmond S, Sazanov LA, Biankin A, Villas Boas S, Hoy A, Turner N, Saunders D. 2017. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 5(2).","ama":"Hardie R, Van Dam E, Cowley M, et al. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 2017;5(2). doi:10.1186/s40170-017-0164-1"},"publication":"Cancer & Metabolism","issue":"2","abstract":[{"text":"Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":1609174,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Cancer_Hardie.pdf","checksum":"337a65786875f64a1fe9fc0ac24767dc","date_updated":"2020-07-14T12:46:29Z","date_created":"2019-01-22T08:17:56Z","relation":"main_file","file_id":"5868"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"443","intvolume":" 5","status":"public","ddc":["570"],"title":"Mitochondrial mutations and metabolic adaptation in pancreatic cancer","month":"01","doi":"10.1186/s40170-017-0164-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"7380","file_date_updated":"2020-07-14T12:46:29Z","extern":"1","author":[{"last_name":"Hardie","first_name":"Rae","full_name":"Hardie, Rae"},{"full_name":"Van Dam, Ellen","last_name":"Van Dam","first_name":"Ellen"},{"full_name":"Cowley, Mark","first_name":"Mark","last_name":"Cowley"},{"first_name":"Ting","last_name":"Han","full_name":"Han, Ting"},{"full_name":"Balaban, Seher","first_name":"Seher","last_name":"Balaban"},{"first_name":"Marina","last_name":"Pajic","full_name":"Pajic, Marina"},{"last_name":"Pinese","first_name":"Mark","full_name":"Pinese, Mark"},{"full_name":"Iconomou, Mary","last_name":"Iconomou","first_name":"Mary"},{"full_name":"Shearer, Robert","first_name":"Robert","last_name":"Shearer"},{"last_name":"Mckenna","first_name":"Jessie","full_name":"Mckenna, Jessie"},{"full_name":"Miller, David","first_name":"David","last_name":"Miller"},{"full_name":"Waddell, Nicola","first_name":"Nicola","last_name":"Waddell"},{"full_name":"Pearson, John","last_name":"Pearson","first_name":"John"},{"first_name":"Sean","last_name":"Grimmond","full_name":"Grimmond, Sean"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"full_name":"Biankin, Andrew","last_name":"Biankin","first_name":"Andrew"},{"last_name":"Villas Boas","first_name":"Silas","full_name":"Villas Boas, Silas"},{"full_name":"Hoy, Andrew","first_name":"Andrew","last_name":"Hoy"},{"full_name":"Turner, Nigel","first_name":"Nigel","last_name":"Turner"},{"full_name":"Saunders, Darren","last_name":"Saunders","first_name":"Darren"}],"volume":5,"date_created":"2018-12-11T11:46:30Z","date_updated":"2021-01-12T07:56:55Z","year":"2017","publisher":"BioMed Central","publication_status":"published"},{"_id":"444","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","publisher":"Royal Society of Chemistry","department":[{"_id":"LeSa"}],"editor":[{"first_name":"Mårten","last_name":"Wikström","full_name":"Wikström, Mårten"}],"author":[{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"date_updated":"2021-01-12T07:56:59Z","date_created":"2018-12-11T11:46:30Z","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations."}],"publist_id":"7379","publication":"Mechanisms of primary energy transduction in biology ","citation":{"chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025.","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025"},"quality_controlled":"1","page":"25 - 59","date_published":"2017-11-29T00:00:00Z","doi":"10.1039/9781788010405-00025","language":[{"iso":"eng"}],"series_title":"Mechanisms of Primary Energy Transduction in Biology ","month":"11","day":"29","publication_identifier":{"isbn":["978-1-78262-865-1"]}},{"date_published":"2017-07-12T00:00:00Z","doi":"10.1103/PhysRevB.96.014202","quality_controlled":0,"main_file_link":[{"url":"https://arxiv.org/abs/1701.07772","open_access":"1"}],"oa":1,"citation":{"mla":"Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1, American Physical Society, 2017, doi:10.1103/PhysRevB.96.014202.","short":"M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","chicago":"Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.014202.","ama":"Serbyn M, Abanin D. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 2017;96(1). doi:10.1103/PhysRevB.96.014202","ista":"Serbyn M, Abanin D. 2017. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 96(1).","apa":"Serbyn, M., & Abanin, D. (2017). Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.014202","ieee":"M. Serbyn and D. Abanin, “Loschmidt echo in many body localized phases,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1. American Physical Society, 2017."},"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"12","month":"07","volume":96,"date_updated":"2021-01-12T07:57:03Z","date_created":"2018-12-11T11:46:31Z","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"full_name":"Abanin, Dimitry A","last_name":"Abanin","first_name":"Dimitry"}],"publisher":"American Physical Society","intvolume":" 96","title":"Loschmidt echo in many body localized phases","publication_status":"published","status":"public","_id":"445","year":"2017","acknowledgement":"This research was supported in part by the National\nScience Foundation under Grant No. NSF PHY11-25915.\nM.S. was supported by Gordon and Betty Moore Foundation’s\nEPiQS Initiative through Grant No. GBMF4307. D.A. also\nacknowledges support by Swiss National Science Foundation.","extern":1,"publist_id":"7378","issue":"1","abstract":[{"text":"The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","issue":"8","publist_id":"7370","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"452","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting was supported by the ETH Zurich/Marie Curie COFUND Postdoctoral Fellowship. \r\nFirst and foremost, we would like to thank our editor Steve Marschner for his invaluable feedback. We were fortunate to get further help from Maurizio Nitti for model design, Romain Prévost for Make-It-Stand comparisons, Alexander Sorkine-Hornung, Kaan Yücer, and Changil Kim for video and photo assistance, Ronnie Gänsli for metal casting, Alec Jacobson for the posed Elephant and Armadillo models, and Romain Prévost and Amit Bermano for print preparation. Model sources include: Woven Ring: generated by “Sculpture Generator 1” by Carlo H. Séquin, UC Berkeley; Elephant: De Espona model library, courtesy of Robert Sumner; T-Rex: TurboSquid; Armadillo: Stanford Computer Graphics Laboratory; and Utah Teapot: Martin Newell, University of Utah. ","year":"2017","intvolume":" 60","publisher":"ACM","status":"public","publication_status":"published","title":"Spin it: Optimizing moment of inertia for spinnable objects","author":[{"full_name":"Bächer, Moritz","last_name":"Bächer","first_name":"Moritz"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Emily","last_name":"Whiting","full_name":"Whiting, Emily"},{"full_name":"Sorkine Hornung, Olga","first_name":"Olga","last_name":"Sorkine Hornung"}],"oa_version":"None","volume":60,"date_created":"2018-12-11T11:46:33Z","date_updated":"2022-03-18T12:55:28Z","scopus_import":"1","article_processing_charge":"No","month":"08","day":"01","citation":{"ista":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. 2017. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 60(8), 92–99.","apa":"Bächer, M., Bickel, B., Whiting, E., & Sorkine Hornung, O. (2017). Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. ACM. https://doi.org/10.1145/3068766","ieee":"M. Bächer, B. Bickel, E. Whiting, and O. Sorkine Hornung, “Spin it: Optimizing moment of inertia for spinnable objects,” Communications of the ACM, vol. 60, no. 8. ACM, pp. 92–99, 2017.","ama":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 2017;60(8):92-99. doi:10.1145/3068766","chicago":"Bächer, Moritz, Bernd Bickel, Emily Whiting, and Olga Sorkine Hornung. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM. ACM, 2017. https://doi.org/10.1145/3068766.","mla":"Bächer, Moritz, et al. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM, vol. 60, no. 8, ACM, 2017, pp. 92–99, doi:10.1145/3068766.","short":"M. Bächer, B. Bickel, E. Whiting, O. Sorkine Hornung, Communications of the ACM 60 (2017) 92–99."},"publication":"Communications of the ACM","page":"92 - 99","doi":"10.1145/3068766","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}]},{"publist_id":"7369","file_date_updated":"2020-07-14T12:46:31Z","author":[{"full_name":"Fallesen, Todd","first_name":"Todd","last_name":"Fallesen"},{"full_name":"Roostalu, Johanna","last_name":"Roostalu","first_name":"Johanna"},{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","first_name":"Christian F","last_name":"Düllberg","full_name":"Düllberg, Christian F"},{"full_name":"Pruessner, Gunnar","first_name":"Gunnar","last_name":"Pruessner"},{"first_name":"Thomas","last_name":"Surrey","full_name":"Surrey, Thomas"}],"volume":113,"date_created":"2018-12-11T11:46:33Z","date_updated":"2021-01-12T07:59:28Z","year":"2017","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","publisher":"Biophysical Society","department":[{"_id":"MaLo"}],"publication_status":"published","month":"11","doi":"10.1016/j.bpj.2017.09.006","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","issue":"9","abstract":[{"text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.","lang":"eng"}],"type":"journal_article","pubrep_id":"965","file":[{"relation":"main_file","file_id":"5052","checksum":"99a2474088e20ac74b1882c4fbbb45b1","date_created":"2018-12-12T10:14:03Z","date_updated":"2020-07-14T12:46:31Z","access_level":"open_access","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","file_size":977192,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"453","intvolume":" 113","status":"public","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"07","date_published":"2017-11-07T00:00:00Z","citation":{"chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006"},"publication":"Biophysical Journal","page":"2055 - 2067","article_type":"original"},{"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["1410.0833"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"doi":"10.23638/LMCS-13(3:26)2017","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["1860-5974"]},"year":"2017","publication_status":"published","publisher":"International Federation of Computational Logic","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"related_material":{"record":[{"id":"1661","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:46:37Z","date_updated":"2023-02-23T10:08:55Z","volume":13,"article_number":"26","file_date_updated":"2020-07-14T12:46:32Z","ec_funded":1,"publist_id":"7357","license":"https://creativecommons.org/licenses/by-nd/4.0/","publication":"Logical Methods in Computer Science","citation":{"mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26.","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017"},"date_published":"2017-09-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"464","ddc":["004"],"title":"Improved algorithms for parity and Streett objectives","status":"public","intvolume":" 13","pubrep_id":"956","file":[{"content_type":"application/pdf","file_size":582940,"creator":"system","file_name":"IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:32Z","date_created":"2018-12-12T10:13:27Z","checksum":"12d469ae69b80361333d7dead965cf5d","relation":"main_file","file_id":"5010"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years."}],"issue":"3"},{"file_date_updated":"2020-07-14T12:46:34Z","ec_funded":1,"publist_id":"7350","article_number":"103","date_updated":"2023-02-23T12:20:26Z","date_created":"2018-12-11T11:46:39Z","volume":36,"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"year":"2017","month":"07","publication_identifier":{"issn":["07300301"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3072959.3073678","quality_controlled":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"oa":1,"abstract":[{"lang":"eng","text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios."}],"issue":"4","type":"journal_article","file":[{"creator":"wojtan","file_size":13131683,"content_type":"application/pdf","file_name":"wavepackets_final.pdf","access_level":"open_access","date_created":"2020-01-24T09:32:35Z","date_updated":"2020-07-14T12:46:34Z","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","file_id":"7359","relation":"main_file"}],"oa_version":"Published Version","title":"Water wave packets","ddc":["006"],"status":"public","intvolume":" 36","_id":"470","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017.","apa":"Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","ama":"Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678"}},{"abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"471","status":"public","title":"Faster statistical model checking for unbounded temporal properties","intvolume":" 18","day":"01","scopus_import":1,"date_published":"2017-05-01T00:00:00Z","publication":"ACM Transactions on Computational Logic (TOCL)","citation":{"mla":"Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017."},"publist_id":"7349","ec_funded":1,"article_number":"12","author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}],"related_material":{"record":[{"id":"1234","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-21T16:48:11Z","date_created":"2018-12-11T11:46:39Z","volume":18,"year":"2017","publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"month":"05","publication_identifier":{"issn":["15293785"]},"doi":"10.1145/3060139","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}]},{"type":"journal_article","extern":"1","publist_id":"7348","issue":"25","abstract":[{"text":"α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission.","lang":"eng"}],"publisher":"Wiley-Blackwell","intvolume":" 37","publication_status":"published","status":"public","title":"Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held","_id":"472","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","oa_version":"None","volume":37,"date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:51Z","author":[{"first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku"},{"last_name":"Taoufiq","first_name":"Zachari","full_name":"Taoufiq, Zachari"},{"first_name":"Oliver","last_name":"Thorn Seshold","full_name":"Thorn Seshold, Oliver"},{"full_name":"Trauner, Dirk","first_name":"Dirk","last_name":"Trauner"},{"first_name":"Masato","last_name":"Hasegawa","full_name":"Hasegawa, Masato"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"publication_identifier":{"issn":["02706474"]},"day":"21","month":"06","page":"6043 - 6052","quality_controlled":"1","citation":{"ista":"Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. 2017. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 37(25), 6043–6052.","ieee":"K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, and T. Takahashi, “Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held,” European Journal of Neuroscience, vol. 37, no. 25. Wiley-Blackwell, pp. 6043–6052, 2017.","apa":"Eguchi, K., Taoufiq, Z., Thorn Seshold, O., Trauner, D., Hasegawa, M., & Takahashi, T. (2017). Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.0179-17.2017","ama":"Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 2017;37(25):6043-6052. doi:10.1523/JNEUROSCI.0179-17.2017","chicago":"Eguchi, Kohgaku, Zachari Taoufiq, Oliver Thorn Seshold, Dirk Trauner, Masato Hasegawa, and Tomoyuki Takahashi. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1523/JNEUROSCI.0179-17.2017.","mla":"Eguchi, Kohgaku, et al. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience, vol. 37, no. 25, Wiley-Blackwell, 2017, pp. 6043–52, doi:10.1523/JNEUROSCI.0179-17.2017.","short":"K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, T. Takahashi, European Journal of Neuroscience 37 (2017) 6043–6052."},"publication":"European Journal of Neuroscience","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0179-17.2017","date_published":"2017-06-21T00:00:00Z"},{"scopus_import":1,"has_accepted_license":"1","day":"13","citation":{"chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050.","short":"T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050"},"publication":"International Journal of Computational Geometry and Applications","page":"211 - 229","date_published":"2017-04-13T00:00:00Z","type":"journal_article","issue":"3-4","abstract":[{"text":"We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"481","intvolume":" 26","ddc":["004","514","516"],"title":"Planar matchings for weighted straight skeletons","status":"public","pubrep_id":"949","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","content_type":"application/pdf","file_size":769296,"creator":"system","relation":"main_file","file_id":"4758","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","date_created":"2018-12-12T10:09:34Z","date_updated":"2020-07-14T12:46:35Z"}],"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1142/S0218195916600050","language":[{"iso":"eng"}],"publist_id":"7338","file_date_updated":"2020-07-14T12:46:35Z","year":"2017","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","publisher":"World Scientific Publishing","department":[{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"id":"10892","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"full_name":"Huber, Stefan","last_name":"Huber","first_name":"Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"volume":26,"date_updated":"2023-02-21T16:06:22Z","date_created":"2018-12-11T11:46:43Z"},{"date_published":"2017-01-01T00:00:00Z","page":"683 - 738","publication":"Advances in Theoretical and Mathematical Physics","citation":{"short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738."},"day":"01","scopus_import":1,"oa_version":"Submitted Version","status":"public","title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","intvolume":" 21","_id":"484","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory."}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.4310/ATMP.2017.v21.n3.a4","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.04631"}],"oa":1,"month":"01","publication_identifier":{"issn":["10950761"]},"date_created":"2018-12-11T11:46:43Z","date_updated":"2021-01-12T08:00:58Z","volume":21,"author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","first_name":"Phan"},{"last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"International Press","year":"2017","ec_funded":1,"publist_id":"7336"},{"ec_funded":1,"publist_id":"7337","author":[{"first_name":"Paul","last_name":"Bourgade","full_name":"Bourgade, Paul"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"volume":21,"date_created":"2018-12-11T11:46:43Z","date_updated":"2021-01-12T08:00:57Z","year":"2017","department":[{"_id":"LaEr"}],"publisher":"International Press","publication_status":"published","publication_identifier":{"issn":["10950761"]},"month":"08","doi":"10.4310/ATMP.2017.v21.n3.a5","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1602.02312","open_access":"1"}],"oa":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","issue":"3","abstract":[{"lang":"eng","text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices."}],"type":"journal_article","oa_version":"Submitted Version","_id":"483","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 21","status":"public","title":"Universality for a class of random band matrices","day":"25","scopus_import":1,"date_published":"2017-08-25T00:00:00Z","citation":{"ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5."},"publication":"Advances in Theoretical and Mathematical Physics","page":"739 - 800"},{"citation":{"ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.","short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367."},"publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","page":"2 - 14","quality_controlled":"1","date_published":"2017-11-28T00:00:00Z","doi":"10.1145/3143361.3143367","conference":{"name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies","end_date":"2017-12-15","start_date":"2017-12-12","location":"Incheon, South Korea"},"language":[{"iso":"eng"}],"scopus_import":1,"publication_identifier":{"isbn":["978-145035422-6"]},"month":"11","day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"487","year":"2017","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","status":"public","title":"Towards unlicensed cellular networks in TV white spaces","author":[{"full_name":"Baig, Ghufran","first_name":"Ghufran","last_name":"Baig"},{"first_name":"Bozidar","last_name":"Radunovic","full_name":"Radunovic, Bozidar"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Balkwill, Matthew","last_name":"Balkwill","first_name":"Matthew"},{"full_name":"Karagiannis, Thomas","last_name":"Karagiannis","first_name":"Thomas"},{"first_name":"Lili","last_name":"Qiu","full_name":"Qiu, Lili"}],"oa_version":"None","date_updated":"2023-02-23T12:21:11Z","date_created":"2018-12-11T11:46:45Z","type":"conference","publist_id":"7333","abstract":[{"lang":"eng","text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x."}]},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","publication":"Nature Communications","citation":{"ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017)."},"abstract":[{"lang":"eng","text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:14:31Z","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","relation":"main_file","file_id":"5083","file_size":2948357,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","access_level":"open_access"}],"pubrep_id":"937","ddc":["571"],"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","status":"public","intvolume":" 8","_id":"514","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms16032","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:46:36Z","publist_id":"7305","article_number":"16032","date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:16Z","volume":8,"author":[{"full_name":"Simonnet, Jean","first_name":"Jean","last_name":"Simonnet"},{"last_name":"Nassar","first_name":"Mérie","full_name":"Nassar, Mérie"},{"full_name":"Stella, Federico","first_name":"Federico","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148"},{"first_name":"Ivan","last_name":"Cohen","full_name":"Cohen, Ivan"},{"first_name":"Bertrand","last_name":"Mathon","full_name":"Mathon, Bertrand"},{"full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","first_name":"Charlotte"},{"full_name":"Miles, Richard","last_name":"Miles","first_name":"Richard"},{"first_name":"Desdemona","last_name":"Fricker","full_name":"Fricker, Desdemona"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoCs"}],"year":"2017"},{"ec_funded":1,"publist_id":"7304","file_date_updated":"2020-07-14T12:46:36Z","year":"2017","department":[{"_id":"LeSa"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"first_name":"James A","last_name":"Letts","id":"322DA418-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9864-3586","full_name":"Letts, James A"},{"first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"volume":24,"date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:17Z","publication_identifier":{"issn":["15459993"]},"month":"10","oa":1,"project":[{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","doi":"10.1038/nsmb.3460","language":[{"iso":"eng"}],"type":"journal_article","issue":"10","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"_id":"515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","ddc":["572"],"status":"public","file":[{"access_level":"open_access","file_name":"29893_2_merged_1501257589_red.pdf","file_size":4118385,"content_type":"application/pdf","creator":"lsazanov","relation":"main_file","file_id":"6993","checksum":"9bc7e8c41b43636dd7566289e511f096","date_created":"2019-11-07T12:51:07Z","date_updated":"2020-07-14T12:46:36Z"}],"oa_version":"Submitted Version","scopus_import":1,"has_accepted_license":"1","day":"05","citation":{"ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460","chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808."},"publication":"Nature Structural and Molecular Biology","page":"800 - 808","article_type":"original","date_published":"2017-10-05T00:00:00Z"},{"_id":"513","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","intvolume":" 2","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","status":"public","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","author":[{"full_name":"Klotz, Lukasz","last_name":"Klotz","first_name":"Lukasz","orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87"},{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M","last_name":"Lemoult","full_name":"Lemoult, Grégoire M"},{"first_name":"Idalia","last_name":"Frontczak","full_name":"Frontczak, Idalia"},{"first_name":"Laurette","last_name":"Tuckerman","full_name":"Tuckerman, Laurette"},{"last_name":"Wesfreid","first_name":"José","full_name":"Wesfreid, José"}],"volume":2,"oa_version":"Preprint","date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:16Z","type":"journal_article","article_number":"043904","issue":"4","publist_id":"7306","abstract":[{"text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02619"}],"citation":{"ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904."},"publication":"Physical Review Fluids","quality_controlled":"1","date_published":"2017-04-01T00:00:00Z","doi":"10.1103/PhysRevFluids.2.043904","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"04"},{"month":"03","publication_identifier":{"issn":["21615063"]},"doi":"10.1021/acssynbio.6b00235","language":[{"iso":"eng"}],"external_id":{"pmid":["27936615"]},"quality_controlled":"1","publist_id":"7298","author":[{"first_name":"Wei","last_name":"Du","full_name":"Du, Wei"},{"full_name":"Angermayr, Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","first_name":"Andreas","last_name":"Angermayr"},{"full_name":"Jongbloets, Joeri","last_name":"Jongbloets","first_name":"Joeri"},{"full_name":"Molenaar, Douwe","first_name":"Douwe","last_name":"Molenaar"},{"full_name":"Bachmann, Herwig","last_name":"Bachmann","first_name":"Herwig"},{"full_name":"Hellingwerf, Klaas","first_name":"Klaas","last_name":"Hellingwerf"},{"full_name":"Branco Dos Santos, Filipe","first_name":"Filipe","last_name":"Branco Dos Santos"}],"date_updated":"2021-01-12T08:01:21Z","date_created":"2018-12-11T11:46:56Z","volume":6,"year":"2017","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"ToBo"}],"day":"17","scopus_import":1,"date_published":"2017-03-17T00:00:00Z","publication":"ACS Synthetic Biology","citation":{"ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235","ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017.","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235."},"article_type":"letter_note","page":"395 - 401","abstract":[{"lang":"eng","text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here."}],"issue":"3","type":"journal_article","oa_version":"None","_id":"520","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","intvolume":" 6"},{"day":"01","month":"01","publication_identifier":{"issn":["01668641"]},"doi":"10.1016/j.topol.2016.10.005","date_published":"2017-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Topology and its Applications","main_file_link":[{"url":"https://arxiv.org/abs/1608.03954v1","open_access":"1"}],"citation":{"chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005"},"oa":1,"quality_controlled":"1","page":"45 - 57","abstract":[{"lang":"eng","text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension."}],"publist_id":"7299","type":"journal_article","author":[{"first_name":"Kyle","last_name":"Austin","full_name":"Austin, Kyle"},{"full_name":"Virk, Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga","last_name":"Virk"}],"date_created":"2018-12-11T11:46:56Z","date_updated":"2021-01-12T08:01:21Z","volume":215,"oa_version":"Submitted Version","year":"2017","_id":"521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Higson compactification and dimension raising","publication_status":"published","intvolume":" 215","department":[{"_id":"HeEd"}],"publisher":"Elsevier"},{"publication":"Current Biology","citation":{"ama":"von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060","ieee":"D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017.","apa":"von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060","ista":"von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174.","short":"D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174.","mla":"von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060.","chicago":"Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.01.060."},"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/983","open_access":"1"}],"oa":1,"quality_controlled":0,"page":"R172 - R174","date_published":"2017-03-06T00:00:00Z","doi":"10.1016/j.cub.2017.01.060","month":"03","day":"06","year":"2017","_id":"525","acknowledgement":"Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t","status":"public","publication_status":"published","title":"Plant biology: Building barriers… in roots","intvolume":" 27","publisher":"Cell Press","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Daniel von Wangenheim"},{"full_name":"Goh, Tatsuaki","first_name":"Tatsuaki","last_name":"Goh"},{"full_name":"Dietrich, Daniela","first_name":"Daniela","last_name":"Dietrich"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm J"}],"pubrep_id":"983","date_created":"2018-12-11T11:46:58Z","date_updated":"2021-01-12T08:01:23Z","file":[{"file_name":"IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2840413,"file_id":"5330","relation":"main_file","date_created":"2018-12-12T10:18:11Z","date_updated":"2020-07-14T12:46:38Z","checksum":"81fd4475c5a2a2c6f4313beeab215ed9"}],"volume":27,"type":"journal_article","abstract":[{"lang":"eng","text":"The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. "}],"file_date_updated":"2020-07-14T12:46:38Z","issue":"5","publist_id":"7294","extern":1},{"publication":"Brain Research","citation":{"ama":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 2017;1657:297-303. doi:10.1016/j.brainres.2016.12.026","ista":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303.","apa":"Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., & Brǎiloiu, E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2016.12.026","ieee":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects of VPAC1 activation in nucleus ambiguus neurons,” Brain Research, vol. 1657. Elsevier, pp. 297–303, 2017.","mla":"Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research, vol. 1657, Elsevier, 2017, pp. 297–303, doi:10.1016/j.brainres.2016.12.026.","short":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain Research 1657 (2017) 297–303.","chicago":"Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.brainres.2016.12.026."},"quality_controlled":0,"page":"297 - 303","date_published":"2017-02-15T00:00:00Z","doi":"10.1016/j.brainres.2016.12.026","day":"15","month":"02","year":"2017","_id":"529","acknowledgement":"This study was supported by startup funds from the Jefferson College of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30 DA 013429 to Center for Substance Abuse Research, Temple University.","title":"Effects of VPAC1 activation in nucleus ambiguus neurons","publication_status":"published","status":"public","publisher":"Elsevier","intvolume":" 1657","author":[{"last_name":"Gherghina","first_name":"Florin","full_name":"Gherghina, Florin L"},{"first_name":"Andrei","last_name":"Tica","full_name":"Tica, Andrei A"},{"last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Elena Deliu"},{"first_name":"Mary","last_name":"Abood","full_name":"Abood, Mary E"},{"last_name":"Brailoiu","first_name":"G.","full_name":"Brailoiu, G. Christina"},{"full_name":"Brǎiloiu, Eugen","first_name":"Eugen","last_name":"Brǎiloiu"}],"date_created":"2018-12-11T11:46:59Z","date_updated":"2021-01-12T08:01:26Z","volume":1657,"type":"journal_article","abstract":[{"lang":"eng","text":"The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological processes. Although some sympathetic stimulatory effects of this system have been reported, its central cardiovascular regulatory properties are poorly characterized. VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto transient reduction in heart rate of conscious rats. Therefore we demonstrate a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart rate, adding to the complexity of PACAP-mediated cardiovascular modulation."}],"publist_id":"7290","extern":1},{"intvolume":" 58","status":"public","title":"Finding non-orientable surfaces in 3-Manifolds","_id":"534","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"page":"871 - 888","article_type":"original","citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0."},"publication":"Discrete & Computational Geometry","date_published":"2017-06-09T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"09","department":[{"_id":"UlWa"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":58,"date_updated":"2023-02-21T17:01:34Z","date_created":"2018-12-11T11:47:01Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1379"}]},"author":[{"first_name":"Benjamin","last_name":"Burton","full_name":"Burton, Benjamin"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"publist_id":"7283","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.07907","open_access":"1"}],"external_id":{"arxiv":["1602.07907"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-017-9900-0","publication_identifier":{"issn":["01795376"]},"month":"06"},{"ec_funded":1,"publist_id":"7279","file_date_updated":"2020-07-14T12:46:39Z","volume":129,"date_created":"2018-12-11T11:47:02Z","date_updated":"2021-01-12T08:01:33Z","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"publisher":"Wiley","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publication_status":"published","year":"2017","month":"05","language":[{"iso":"eng"}],"doi":"10.1002/ange.201611998","project":[{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"16","abstract":[{"lang":"ger","text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. "}],"type":"journal_article","file":[{"relation":"main_file","file_id":"5007","date_updated":"2020-07-14T12:46:39Z","date_created":"2018-12-12T10:13:24Z","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","access_level":"open_access","file_size":1668557,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"932","intvolume":" 129","title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","ddc":["571"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"538","has_accepted_license":"1","day":"20","date_published":"2017-05-20T00:00:00Z","page":"4679 - 4682","citation":{"apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998."},"publication":"Angewandte Chemie"},{"pubrep_id":"931","oa_version":"Published Version","file":[{"file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","access_level":"open_access","file_size":4106772,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4944","date_created":"2018-12-12T10:12:26Z","date_updated":"2020-07-14T12:46:44Z","checksum":"1aa20f19a1e90664fadce6e7d5284fdc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"540","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","ddc":["576","616"],"status":"public","intvolume":" 13","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"issue":"12","type":"journal_article","date_published":"2017-12-01T00:00:00Z","publication":"PLoS Pathogens","citation":{"chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758"},"day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"last_name":"Khamina","first_name":"Kseniya","full_name":"Khamina, Kseniya"},{"full_name":"Lercher, Alexander","first_name":"Alexander","last_name":"Lercher"},{"last_name":"Caldera","first_name":"Michael","full_name":"Caldera, Michael"},{"full_name":"Schliehe, Christopher","last_name":"Schliehe","first_name":"Christopher"},{"full_name":"Vilagos, Bojan","first_name":"Bojan","last_name":"Vilagos"},{"last_name":"Sahin","first_name":"Mehmet","full_name":"Sahin, Mehmet"},{"last_name":"Kosack","first_name":"Lindsay","full_name":"Kosack, Lindsay"},{"full_name":"Bhattacharya, Anannya","first_name":"Anannya","last_name":"Bhattacharya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"full_name":"Stukalov, Alexey","first_name":"Alexey","last_name":"Stukalov"},{"first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto"},{"first_name":"Leo","last_name":"James","full_name":"James, Leo"},{"full_name":"Pinschewer, Daniel","first_name":"Daniel","last_name":"Pinschewer"},{"full_name":"Bennett, Keiryn","first_name":"Keiryn","last_name":"Bennett"},{"last_name":"Menche","first_name":"Jörg","full_name":"Menche, Jörg"},{"last_name":"Bergthaler","first_name":"Andreas","full_name":"Bergthaler, Andreas"}],"date_created":"2018-12-11T11:47:03Z","date_updated":"2021-01-12T08:01:48Z","volume":13,"year":"2017","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:46:44Z","publist_id":"7276","article_number":"e1006758","doi":"10.1371/journal.ppat.1006758","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"12","publication_identifier":{"issn":["15537366"]}},{"scopus_import":1,"has_accepted_license":"1","day":"03","citation":{"ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017","ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017."},"publication":"Logical Methods in Computer Science","date_published":"2017-07-03T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"466","intvolume":" 13","ddc":["004"],"status":"public","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","pubrep_id":"957","oa_version":"Published Version","file":[{"creator":"system","file_size":511832,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","checksum":"bfa405385ec6229ad5ead89ab5751639","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:18:32Z","file_id":"5354","relation":"main_file"}],"publication_identifier":{"issn":["18605974"]},"month":"07","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.23638/LMCS-13(2:15)2017","language":[{"iso":"eng"}],"article_number":"15","publist_id":"7355","ec_funded":1,"file_date_updated":"2020-07-14T12:46:33Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","publication_status":"published","related_material":{"record":[{"id":"1657","status":"public","relation":"earlier_version"},{"id":"5429","status":"public","relation":"earlier_version"},{"id":"5435","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Křetínská, Zuzana","first_name":"Zuzana","last_name":"Křetínská"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"}],"volume":13,"date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-11T11:46:38Z"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1656"},{"status":"public","relation":"earlier_version","id":"5415"},{"id":"5436","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"volume":18,"date_updated":"2023-02-23T12:26:19Z","date_created":"2018-12-11T11:46:38Z","year":"2017","publisher":"ACM","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","publist_id":"7354","ec_funded":1,"article_number":"31","doi":"10.1145/3152769","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1606.03598"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","publication_identifier":{"issn":["15293785"]},"month":"12","oa_version":"Preprint","_id":"467","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 18","status":"public","title":"Nested weighted automata","issue":"4","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"type":"journal_article","date_published":"2017-12-01T00:00:00Z","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769."},"publication":"ACM Transactions on Computational Logic (TOCL)","day":"01","scopus_import":1},{"citation":{"ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017)."},"publication":"Logical Methods in Computer Science","date_published":"2017-09-13T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"465","intvolume":" 13","status":"public","ddc":["004"],"title":"Edit distance for pushdown automata","pubrep_id":"955","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5090","date_created":"2018-12-12T10:14:37Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","file_name":"IST-2015-321-v1+1_main.pdf","access_level":"open_access","file_size":279071,"content_type":"application/pdf","creator":"system"},{"file_id":"5091","relation":"main_file","date_created":"2018-12-12T10:14:38Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","access_level":"open_access","creator":"system","file_size":279071,"content_type":"application/pdf"}],"type":"journal_article","issue":"3","abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"project":[{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.23638/LMCS-13(3:23)2017","language":[{"iso":"eng"}],"publication_identifier":{"issn":["18605974"]},"month":"09","year":"2017","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","publication_status":"published","related_material":{"record":[{"id":"1610","status":"public","relation":"earlier_version"},{"id":"5438","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"volume":13,"date_updated":"2023-02-23T12:26:25Z","date_created":"2018-12-11T11:46:37Z","ec_funded":1,"publist_id":"7356","file_date_updated":"2020-07-14T12:46:33Z"},{"article_number":"82","file_date_updated":"2020-07-14T12:46:36Z","publist_id":"7307","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","year":"2017","date_created":"2018-12-11T11:46:53Z","date_updated":"2023-02-23T12:26:57Z","volume":7,"author":[{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5449"}]},"month":"03","publication_identifier":{"issn":["20452322"]},"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41598-017-00107-w","type":"journal_article","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ","lang":"eng"}],"issue":"1","title":"Amplification on undirected population structures: Comets beat stars","ddc":["004"],"status":"public","intvolume":" 7","_id":"512","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","file_size":1536783,"file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:18:35Z","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","file_id":"5357","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"938","scopus_import":1,"day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"Scientific Reports","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. 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Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017)."},"article_type":"original","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}],"issue":"POPL","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2021-12-07T08:06:28Z","date_updated":"2021-12-07T08:06:28Z","success":1,"checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","file_id":"10421","relation":"main_file","creator":"cchlebak","file_size":460188,"content_type":"application/pdf","file_name":"2017_ACMProgLang_Chatterjee.pdf","access_level":"open_access"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10416","ddc":["000"],"status":"public","title":"Optimal Dyck reachability for data-dependence and Alias analysis","intvolume":" 2","month":"12","publication_identifier":{"eissn":["2475-1421"]},"conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"doi":"10.1145/3158118","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1910.00241"]},"quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"file_date_updated":"2021-12-07T08:06:28Z","ec_funded":1,"article_number":"30","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5455"}]},"date_created":"2021-12-05T23:01:48Z","date_updated":"2023-02-23T12:27:13Z","volume":2,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","year":"2017","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}]},{"citation":{"apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1."},"page":"37","date_published":"2017-10-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23","_id":"5455","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Optimal Dyck reachability for data-dependence and alias analysis","ddc":["000"],"status":"public","pubrep_id":"870","file":[{"checksum":"177a84a46e3ac17e87b31534ad16a4c9","date_created":"2018-12-12T11:54:02Z","date_updated":"2020-07-14T12:46:59Z","file_id":"5524","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":960491,"access_level":"open_access","file_name":"IST-2017-870-v1+1_main.pdf"}],"oa_version":"Published Version","type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks."}],"oa":1,"doi":"10.15479/AT:IST-2017-870-v1-1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"month":"10","year":"2017","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","related_material":{"record":[{"id":"10416","relation":"later_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bhavya","last_name":"Choudhary","full_name":"Choudhary, Bhavya"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"date_updated":"2023-02-21T15:54:10Z","date_created":"2018-12-12T11:39:26Z","file_date_updated":"2020-07-14T12:46:59Z"},{"type":"report","file_date_updated":"2020-07-14T12:46:59Z","abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"extern":0,"year":"2017","_id":"5450","title":"Implementing the institutional data repository IST DataRep","status":"public","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","author":[{"last_name":"Petritsch","first_name":"Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","full_name":"Barbara Petritsch"}],"pubrep_id":"724","date_updated":"2020-07-14T23:05:03Z","date_created":"2018-12-12T11:39:24Z","file":[{"date_created":"2018-12-12T11:53:22Z","date_updated":"2020-07-14T12:46:59Z","checksum":"6321792dcfa82bf490f17615a9b22355","relation":"main_file","file_id":"5483","file_size":3460985,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","access_level":"open_access"}],"month":"06","day":"26","oa":1,"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/724.","open_access":"1"}],"publication_date":"2017-06-26","citation":{"ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017."},"date_published":"2017-06-26T00:00:00Z"},{"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10417","intvolume":" 2","title":"Data-centric dynamic partial order reduction","status":"public","issue":"POPL","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"type":"journal_article","date_published":"2017-12-27T00:00:00Z","citation":{"apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","article_processing_charge":"No","day":"27","scopus_import":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5448"},{"relation":"earlier_version","status":"public","id":"5456"}]},"author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"full_name":"Vaidya, Kapil","first_name":"Kapil","last_name":"Vaidya"}],"volume":2,"date_updated":"2023-02-23T12:27:16Z","date_created":"2021-12-05T23:01:49Z","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","publication_status":"published","ec_funded":1,"article_number":"31","doi":"10.1145/3158119","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","start_date":"2018-01-07","location":"Los Angeles, CA, United States"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"external_id":{"arxiv":["1610.01188"]},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","publication_identifier":{"eissn":["2475-1421"]},"month":"12"},{"_id":"5456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publisher":"IST Austria","department":[{"_id":"KrCh"}],"title":"Data-centric dynamic partial order reduction","ddc":["000"],"status":"public","publication_status":"published","pubrep_id":"872","related_material":{"record":[{"relation":"later_version","status":"public","id":"10417"},{"id":"5448","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chalupa, Marek","first_name":"Marek","last_name":"Chalupa"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Sinha, Nishant","last_name":"Sinha","first_name":"Nishant"},{"full_name":"Vaidya, Kapil","last_name":"Vaidya","first_name":"Kapil"}],"oa_version":"Published Version","file":[{"date_created":"2018-12-12T11:53:26Z","date_updated":"2020-07-14T12:46:59Z","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","file_id":"5487","relation":"main_file","creator":"system","file_size":910347,"content_type":"application/pdf","file_name":"IST-2017-872-v1+1_main.pdf","access_level":"open_access"}],"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-02-23T12:26:54Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:59Z","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.","lang":"eng"}],"citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1"},"oa":1,"page":"36","date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-872-v1-1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"10","day":"23"},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61."},"publication":"Leibniz International Proceedings in Informatics","date_published":"2017-11-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. "}],"_id":"551","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 83","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","status":"public","ddc":["004"],"pubrep_id":"924","file":[{"date_created":"2018-12-12T10:18:04Z","date_updated":"2020-07-14T12:47:00Z","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","relation":"main_file","file_id":"5322","file_size":535077,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.4230/LIPIcs.MFCS.2017.61","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25"},"language":[{"iso":"eng"}],"article_number":"61","publist_id":"7263","file_date_updated":"2020-07-14T12:47:00Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"volume":83,"date_updated":"2021-01-12T08:02:34Z","date_created":"2018-12-11T11:47:08Z"},{"_id":"552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["004"],"title":"Faster algorithms for mean-payoff parity games","intvolume":" 83","pubrep_id":"923","oa_version":"Published Version","file":[{"file_size":610339,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:57Z","date_updated":"2020-07-14T12:47:00Z","checksum":"c67f4866ddbfd555afef1f63ae9a8fc7","relation":"main_file","file_id":"5248"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective)."}],"publication":"Leibniz International Proceedings in Informatics","citation":{"ama":"Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39","ista":"Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.","apa":"Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39","ieee":"K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.","short":"K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39."},"date_published":"2017-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"date_created":"2018-12-11T11:47:08Z","date_updated":"2023-02-14T10:06:46Z","volume":83,"article_number":"39","file_date_updated":"2020-07-14T12:47:00Z","publist_id":"7262","ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"doi":"10.4230/LIPIcs.MFCS.2017.39","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"isbn":["978-395977046-0"]}},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"553","status":"public","ddc":["004"],"title":"Strategy complexity of concurrent safety games","intvolume":" 83","pubrep_id":"922","file":[{"file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","access_level":"open_access","creator":"system","file_size":549967,"content_type":"application/pdf","file_id":"4753","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:09:29Z","checksum":"7101facb56ade363205c695d72dbd173"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. "}],"publication":"Leibniz International Proceedings in Informatics","citation":{"chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.","mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.","apa":"Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55"},"date_published":"2017-11-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kristofer","last_name":"Hansen","full_name":"Hansen, Kristofer"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:47:08Z","date_updated":"2021-01-12T08:02:35Z","volume":83,"article_number":"55","file_date_updated":"2020-07-14T12:47:00Z","publist_id":"7261","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://arxiv.org/abs/1506.02434","open_access":"1"}],"quality_controlled":"1","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21"},"doi":"10.4230/LIPIcs.MFCS.2017.55","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"isbn":["978-395977046-0"]}},{"publist_id":"7256","ec_funded":1,"article_number":"0104","author":[{"full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jentzen, Arnulf","last_name":"Jentzen","first_name":"Arnulf"},{"full_name":"Salimova, Diyora","last_name":"Salimova","first_name":"Diyora"}],"volume":473,"date_updated":"2021-01-12T08:03:04Z","date_created":"2018-12-11T11:47:11Z","year":"2017","publisher":"Royal Society of London","department":[{"_id":"JaMa"}],"publication_status":"published","publication_identifier":{"issn":["13645021"]},"month":"11","doi":"10.1098/rspa.2017.0104","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1702.03229","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","issue":"2207","abstract":[{"text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"560","intvolume":" 473","title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","status":"public","day":"01","scopus_import":1,"date_published":"2017-11-01T00:00:00Z","citation":{"short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.","chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.","apa":"Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104."},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences"},{"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"quality_controlled":"1","doi":"10.1090/cln/028","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9-781-4704-3648-3"],"eisbn":["978-1-4704-4194-4"]},"month":"01","year":"2017","department":[{"_id":"LaEr"}],"publisher":"American Mathematical Society","publication_status":"published","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"}],"volume":28,"date_updated":"2022-05-24T06:57:28Z","date_created":"2018-12-11T11:47:13Z","publist_id":"7247","ec_funded":1,"citation":{"chicago":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028.","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017.","mla":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.","ieee":"L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017.","apa":"Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028","ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","ama":"Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028"},"page":"226","date_published":"2017-01-01T00:00:00Z","series_title":"Courant Lecture Notes","article_processing_charge":"No","day":"01","_id":"567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 28","status":"public","title":"A Dynamical Approach to Random Matrix Theory","oa_version":"None","type":"book","alternative_title":["Courant Lecture Notes"],"abstract":[{"text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n","lang":"eng"}]},{"day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.","ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342."},"publication":"Homology, Homotopy and Applications","page":"313 - 342","issue":"2","abstract":[{"text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"568","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","title":"Persistence of zero sets","status":"public","publication_identifier":{"issn":["15320073"]},"month":"01","doi":"10.4310/HHA.2017.v19.n2.a16","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1507.04310","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","publist_id":"7246","ec_funded":1,"author":[{"first_name":"Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter"},{"full_name":"Krcál, Marek","last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"volume":19,"date_updated":"2021-01-12T08:03:12Z","date_created":"2018-12-11T11:47:14Z","year":"2017","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"International Press","publication_status":"published"},{"citation":{"short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921."},"publication":"eLife","date_published":"2017-11-13T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"570","intvolume":" 6","title":"Regulatory network structure determines patterns of intermolecular epistasis","ddc":["576"],"status":"public","pubrep_id":"918","oa_version":"Published Version","file":[{"creator":"system","file_size":8453470,"content_type":"application/pdf","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:42Z","date_updated":"2020-07-14T12:47:10Z","checksum":"273ab17f33305e4eaafd911ff88e7c5b","file_id":"5096","relation":"main_file"},{"file_id":"5097","relation":"main_file","date_created":"2018-12-12T10:14:43Z","date_updated":"2020-07-14T12:47:10Z","checksum":"b433f90576c7be597cd43367946f8e7f","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1953221}],"type":"journal_article","abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.7554/eLife.28921","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050084X"]},"month":"11","year":"2017","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan"},{"orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","first_name":"Hande","full_name":"Acar, Hande"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"volume":6,"date_updated":"2021-01-12T08:03:15Z","date_created":"2018-12-11T11:47:14Z","article_number":"e28921","ec_funded":1,"publist_id":"7244","file_date_updated":"2020-07-14T12:47:10Z"},{"day":"06","has_accepted_license":"1","scopus_import":1,"date_published":"2017-11-06T00:00:00Z","publication":"eLife","citation":{"apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","ieee":"F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867."},"abstract":[{"lang":"eng","text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"system","file_size":9666973,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","checksum":"ba09c1451153d39e4f4b7cee013e314c","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:40Z","file_id":"4829","relation":"main_file"},{"relation":"main_file","file_id":"4830","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:41Z","checksum":"01eb51f1d6ad679947415a51c988e137","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","access_level":"open_access","file_size":5951246,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"919","ddc":["570"],"title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","status":"public","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"569","month":"11","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.30867","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7245","article_number":"e30867","date_created":"2018-12-11T11:47:14Z","date_updated":"2023-02-23T12:30:29Z","volume":6,"author":[{"first_name":"Felix","last_name":"Spira","full_name":"Spira, Felix"},{"full_name":"Cuylen Haering, Sara","first_name":"Sara","last_name":"Cuylen Haering"},{"full_name":"Mehta, Shalin","first_name":"Shalin","last_name":"Mehta"},{"full_name":"Samwer, Matthias","last_name":"Samwer","first_name":"Matthias"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne"},{"full_name":"Verma, Amitabh","first_name":"Amitabh","last_name":"Verma"},{"last_name":"Oldenbourg","first_name":"Rudolf","full_name":"Oldenbourg, Rudolf"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Gerlich","full_name":"Gerlich, Daniel"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"MiSi"}],"year":"2017"},{"day":"30","scopus_import":1,"date_published":"2017-11-30T00:00:00Z","page":"1368 - 1382","publication":"Cell Press","citation":{"mla":"Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.","short":"F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382.","chicago":"Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.11.001.","ama":"Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382. doi:10.1016/j.cell.2017.11.001","ista":"Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.","apa":"Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001","ieee":"F. R. Gärtner et al., “Migrating platelets are mechano scavengers that collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017."},"abstract":[{"lang":"eng","text":"Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface."}],"issue":"6","type":"journal_article","oa_version":"None","status":"public","title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","intvolume":" 171","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"571","month":"11","publication_identifier":{"issn":["00928674"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.11.001","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"publist_id":"7243","ec_funded":1,"date_created":"2018-12-11T11:47:15Z","date_updated":"2021-01-12T08:03:15Z","volume":171,"author":[{"full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","first_name":"Florian R"},{"full_name":"Ahmad, Zerkah","last_name":"Ahmad","first_name":"Zerkah"},{"last_name":"Rosenberger","first_name":"Gerhild","full_name":"Rosenberger, Gerhild"},{"first_name":"Shuxia","last_name":"Fan","full_name":"Fan, Shuxia"},{"full_name":"Nicolai, Leo","last_name":"Nicolai","first_name":"Leo"},{"full_name":"Busch, Benjamin","first_name":"Benjamin","last_name":"Busch"},{"full_name":"Yavuz, Gökce","last_name":"Yavuz","first_name":"Gökce"},{"last_name":"Luckner","first_name":"Manja","full_name":"Luckner, Manja"},{"full_name":"Ishikawa Ankerhold, Hellen","first_name":"Hellen","last_name":"Ishikawa Ankerhold"},{"first_name":"Roman","last_name":"Hennel","full_name":"Hennel, Roman"},{"full_name":"Benechet, Alexandre","first_name":"Alexandre","last_name":"Benechet"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"full_name":"Chandraratne, Sue","last_name":"Chandraratne","first_name":"Sue"},{"full_name":"Schubert, Irene","first_name":"Irene","last_name":"Schubert"},{"first_name":"Sebastian","last_name":"Helmer","full_name":"Helmer, Sebastian"},{"full_name":"Striednig, Bianca","last_name":"Striednig","first_name":"Bianca"},{"first_name":"Konstantin","last_name":"Stark","full_name":"Stark, Konstantin"},{"full_name":"Janko, Marek","last_name":"Janko","first_name":"Marek"},{"full_name":"Böttcher, Ralph","first_name":"Ralph","last_name":"Böttcher"},{"full_name":"Verschoor, Admar","first_name":"Admar","last_name":"Verschoor"},{"last_name":"Leon","first_name":"Catherine","full_name":"Leon, Catherine"},{"last_name":"Gachet","first_name":"Christian","full_name":"Gachet, Christian"},{"first_name":"Thomas","last_name":"Gudermann","full_name":"Gudermann, Thomas"},{"full_name":"Mederos Y Schnitzler, Michael","first_name":"Michael","last_name":"Mederos Y Schnitzler"},{"full_name":"Pincus, Zachary","last_name":"Pincus","first_name":"Zachary"},{"first_name":"Matteo","last_name":"Iannacone","full_name":"Iannacone, Matteo"},{"last_name":"Haas","first_name":"Rainer","full_name":"Haas, Rainer"},{"full_name":"Wanner, Gerhard","first_name":"Gerhard","last_name":"Wanner"},{"full_name":"Lauber, Kirsten","first_name":"Kirsten","last_name":"Lauber"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"}],"year":"2017"},{"ddc":["580"],"title":"Control of endogenous auxin levels in plant root development","status":"public","intvolume":" 18","_id":"572","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","access_level":"open_access","content_type":"application/pdf","file_size":920962,"creator":"system","relation":"main_file","file_id":"4718","date_created":"2018-12-12T10:08:55Z","date_updated":"2020-07-14T12:47:10Z","checksum":"82d51f11e493f7eec02976d9a9a9805e"}],"oa_version":"Published Version","pubrep_id":"917","type":"journal_article","abstract":[{"lang":"eng","text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture."}],"issue":"12","publication":"International Journal of Molecular Sciences","citation":{"ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587."},"date_published":"2017-12-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","year":"2017","date_created":"2018-12-11T11:47:15Z","date_updated":"2021-01-12T08:03:16Z","volume":18,"author":[{"full_name":"Olatunji, Damilola","first_name":"Damilola","last_name":"Olatunji"},{"full_name":"Geelen, Danny","first_name":"Danny","last_name":"Geelen"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"}],"article_number":"2587","file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7242","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.3390/ijms18122587","month":"12"},{"extern":"1","issue":"1","abstract":[{"text":"This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":59,"date_updated":"2021-01-12T08:03:34Z","date_created":"2019-01-08T20:42:08Z","author":[{"first_name":"Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"publisher":"Springer Nature","intvolume":" 59","status":"public","publication_status":"published","title":"On the functionality and usefulness of Quadraginta octants of naive sphere","_id":"5800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_identifier":{"issn":["09249907"]},"month":"09","day":"01","language":[{"iso":"eng"}],"date_published":"2017-09-01T00:00:00Z","doi":"10.1007/s10851-017-0718-4","page":"69-83","quality_controlled":"1","citation":{"ama":"Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83. doi:10.1007/s10851-017-0718-4","apa":"Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4","ieee":"R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol. 59, no. 1. Springer Nature, pp. 69–83, 2017.","ista":"Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.","short":"R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017) 69–83.","mla":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision, vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4."},"publication":"Journal of Mathematical Imaging and Vision"},{"publication_identifier":{"issn":["0166-218X"]},"day":"10","month":"01","citation":{"ama":"Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017","ista":"Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 216, 362–375.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier, pp. 362–375, 2017.","apa":"Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2015.11.017","mla":"Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017) 362–375.","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017."},"publication":"Discrete Applied Mathematics","page":"362-375","quality_controlled":"1","date_published":"2017-01-10T00:00:00Z","doi":"10.1016/j.dam.2015.11.017","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space.","lang":"eng"}],"extern":"1","_id":"5799","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 216","publisher":"Elsevier","status":"public","publication_status":"published","title":"On the polyhedra of graceful spheres and circular geodesics","author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"},{"first_name":"Valentin E.","last_name":"Brimkov","full_name":"Brimkov, Valentin E."}],"oa_version":"None","volume":216,"date_created":"2019-01-08T20:41:12Z","date_updated":"2021-01-12T08:03:33Z"},{"author":[{"first_name":"Shivam","last_name":"Dwivedi","full_name":"Dwivedi, Shivam"},{"full_name":"Gupta, Aniket","first_name":"Aniket","last_name":"Gupta"},{"full_name":"Roy, Siddhant","first_name":"Siddhant","last_name":"Roy"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"volume":10502,"oa_version":"None","date_updated":"2022-01-27T15:34:25Z","date_created":"2019-01-08T20:42:22Z","year":"2017","_id":"5801","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 10502","publisher":"Springer Nature","publication_status":"published","status":"public","title":"Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space","abstract":[{"lang":"eng","text":"Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space."}],"extern":"1","type":"conference","place":"Cham","alternative_title":["LNCS"],"date_published":"2017-08-22T00:00:00Z","doi":"10.1007/978-3-319-66272-5_28","conference":{"name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","location":"Vienna, Austria","start_date":"2017-09-19","end_date":"2017-09-21"},"language":[{"iso":"eng"}],"citation":{"ista":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.","ieee":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 347–359.","apa":"Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28","ama":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359. doi:10.1007/978-3-319-66272-5_28","chicago":"Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.","mla":"Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28.","short":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 347–359."},"publication":"20th IAPR International Conference","page":"347-359","quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-319-66271-8"],"issn":["0302-9743"],"eisbn":["978-3-319-66272-5"]},"article_processing_charge":"No","month":"08","day":"22"},{"page":"93-104","citation":{"chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8.","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","apa":"Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256, pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8","ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:10.1007/978-3-319-59108-7_8"},"publication":"Combinatorial image analysis","date_published":"2017-05-17T00:00:00Z","article_processing_charge":"No","day":"17","intvolume":" 10256","status":"public","title":"Construction of persistent Voronoi diagram on 3D digital plane","_id":"5803","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","alternative_title":["LNCS"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept."}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-59108-7_8","conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","location":"Plovdiv, Bulgaria","start_date":"2017-06-19","end_date":"2017-06-21"},"publication_identifier":{"isbn":["978-3-319-59107-0","978-3-319-59108-7"],"issn":["0302-9743","1611-3349"]},"month":"05","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2017","volume":10256,"date_created":"2019-01-08T20:42:56Z","date_updated":"2022-01-28T07:48:24Z","author":[{"full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"place":"Cham","extern":"1"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-66272-5_31","date_published":"2017-08-22T00:00:00Z","conference":{"location":"Vienna, Austria","start_date":"2017-09-19","end_date":"2017-09-21","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery"},"page":"388-398","quality_controlled":"1","citation":{"ista":"Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted focal set. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.","ieee":"E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 388–398.","apa":"Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined by weighted focal set. In 20th IAPR International Conference (Vol. 10502, pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31","ama":"Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31","chicago":"Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives Defined by Weighted Focal Set.” In 20th IAPR International Conference, 10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.","mla":"Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98, doi:10.1007/978-3-319-66272-5_31.","short":"E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 388–398."},"publication":"20th IAPR International Conference","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-66272-5"],"eissn":["1611-3349"],"isbn":["978-3-319-66271-8"]},"article_processing_charge":"No","day":"22","month":"08","volume":10502,"oa_version":"None","date_updated":"2022-01-27T15:38:35Z","date_created":"2019-01-08T20:42:39Z","author":[{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"intvolume":" 10502","publisher":"Springer Nature","status":"public","publication_status":"published","title":"Digital primitives defined by weighted focal set","_id":"5802","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2017","extern":"1","abstract":[{"text":"This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination.","lang":"eng"}],"place":"Cham","alternative_title":["LNCS"],"type":"conference"},{"date_created":"2018-12-11T11:47:23Z","date_updated":"2021-01-12T08:05:16Z","oa_version":"None","volume":118,"author":[{"full_name":"Engelsen, Nils","first_name":"Nils","last_name":"Engelsen"},{"last_name":"Krishnakumar","first_name":"Rajiv","full_name":"Krishnakumar, Rajiv"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur"},{"full_name":"Kasevich, Mark","last_name":"Kasevich","first_name":"Mark"}],"publication_status":"published","status":"public","title":"Bell correlations in spin-squeezed states of 500 000 atoms","intvolume":" 118","publisher":"American Physical Society","_id":"593","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","extern":"1","abstract":[{"lang":"eng","text":"Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements."}],"publist_id":"7212","issue":"14","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.118.140401","date_published":"2017-04-03T00:00:00Z","publication":"Physical Review Letters","citation":{"short":"N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017).","mla":"Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.140401.","chicago":"Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401.","ama":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401","ieee":"N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol. 118, no. 14. American Physical Society, 2017.","apa":"Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401","ista":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14)."},"month":"04","day":"03"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.03.003","date_published":"2017-03-23T00:00:00Z","page":"120 - 131.e22","quality_controlled":"1","citation":{"chicago":"Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.03.003.","mla":"Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003.","short":"C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.","ista":"Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22.","ieee":"C. Engel et al., “Structural basis of RNA polymerase I transcription initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.","apa":"Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003","ama":"Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003"},"publication":"Cell","publication_identifier":{"issn":["00928674"]},"article_processing_charge":"No","day":"23","month":"03","oa_version":"None","volume":169,"date_created":"2018-12-11T11:47:25Z","date_updated":"2021-01-12T08:05:36Z","author":[{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"},{"first_name":"Tobias","last_name":"Gubbey","full_name":"Gubbey, Tobias"},{"first_name":"Simon","last_name":"Neyer","full_name":"Neyer, Simon"},{"full_name":"Sainsbury, Sarah","last_name":"Sainsbury","first_name":"Sarah"},{"full_name":"Oberthuer, Christiane","first_name":"Christiane","last_name":"Oberthuer"},{"full_name":"Baejen, Carlo","first_name":"Carlo","last_name":"Baejen"},{"first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"publisher":"Cell Press","intvolume":" 169","title":"Structural basis of RNA polymerase I transcription initiation","status":"public","publication_status":"published","_id":"600","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","extern":"1","issue":"1","publist_id":"7204","abstract":[{"lang":"eng","text":"Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase."}],"type":"journal_article"}]