[{"citation":{"chicago":"Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” The Cryosphere. Copernicus Publications, 2018. https://doi.org/10.5194/tc-12-1811-2018.","short":"S. Herreid, F. Pellicciotti, The Cryosphere 12 (2018) 1811–1829.","mla":"Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” The Cryosphere, vol. 12, no. 5, Copernicus Publications, 2018, pp. 1811–29, doi:10.5194/tc-12-1811-2018.","ieee":"S. Herreid and F. Pellicciotti, “Automated detection of ice cliffs within supraglacial debris cover,” The Cryosphere, vol. 12, no. 5. Copernicus Publications, pp. 1811–1829, 2018.","apa":"Herreid, S., & Pellicciotti, F. (2018). Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. Copernicus Publications. https://doi.org/10.5194/tc-12-1811-2018","ista":"Herreid S, Pellicciotti F. 2018. Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. 12(5), 1811–1829.","ama":"Herreid S, Pellicciotti F. Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. 2018;12(5):1811-1829. doi:10.5194/tc-12-1811-2018"},"publication":"The Cryosphere","page":"1811-1829","article_type":"original","date_published":"2018-05-31T00:00:00Z","scopus_import":"1","keyword":["Earth-Surface Processes","Water Science and Technology"],"article_processing_charge":"No","day":"31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12606","intvolume":" 12","status":"public","title":"Automated detection of ice cliffs within supraglacial debris cover","oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"text":"Ice cliffs within a supraglacial debris cover have been identified as a source for high ablation relative to the surrounding debris-covered area. Due to their small relative size and steep orientation, ice cliffs are difficult to detect using nadir-looking space borne sensors. The method presented here uses surface slopes calculated from digital elevation model (DEM) data to map ice cliff geometry and produce an ice cliff probability map. Surface slope thresholds, which can be sensitive to geographic location and/or data quality, are selected automatically. The method also attempts to include area at the (often narrowing) ends of ice cliffs which could otherwise be neglected due to signal saturation in surface slope data. The method was calibrated in the eastern Alaska Range, Alaska, USA, against a control ice cliff dataset derived from high-resolution visible and thermal data. Using the same input parameter set that performed best in Alaska, the method was tested against ice cliffs manually mapped in the Khumbu Himal, Nepal. Our results suggest the method can accommodate different glaciological settings and different DEM data sources without a data intensive (high-resolution, multi-data source) recalibration.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/tc-12-1811-2018"}],"quality_controlled":"1","doi":"10.5194/tc-12-1811-2018","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1994-0424"]},"month":"05","year":"2018","publisher":"Copernicus Publications","publication_status":"published","author":[{"full_name":"Herreid, Sam","first_name":"Sam","last_name":"Herreid"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"volume":12,"date_updated":"2023-02-28T11:39:26Z","date_created":"2023-02-20T08:13:36Z","extern":"1"},{"oa_version":"Published Version","intvolume":" 115","status":"public","title":"Reversible photoswitching of encapsulated azobenzenes in water","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13376","issue":"38","abstract":[{"text":"Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.","lang":"eng"}],"type":"journal_article","date_published":"2018-05-01T00:00:00Z","page":"9379-9384","article_type":"original","citation":{"mla":"Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences, vol. 115, no. 38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115.","short":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn, Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.","chicago":"Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115.","ama":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115","ista":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 115(38), 9379–9384.","apa":"Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., & Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1712787115","ieee":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn, “Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the National Academy of Sciences, pp. 9379–9384, 2018."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"01","keyword":["Multidisciplinary"],"scopus_import":"1","volume":115,"date_created":"2023-08-01T09:40:00Z","date_updated":"2023-08-07T10:58:11Z","author":[{"full_name":"Samanta, Dipak","last_name":"Samanta","first_name":"Dipak"},{"full_name":"Gemen, Julius","first_name":"Julius","last_name":"Gemen"},{"full_name":"Chu, Zonglin","first_name":"Zonglin","last_name":"Chu"},{"full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner","first_name":"Yael"},{"first_name":"Linda J. W.","last_name":"Shimon","full_name":"Shimon, Linda J. W."},{"first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"year":"2018","extern":"1","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1712787115","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1712787115","open_access":"1"}],"external_id":{"pmid":["29717041"]},"oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"05"},{"oa_version":"Published Version","intvolume":" 9","status":"public","title":"Reversible chromism of spiropyran in the cavity of a flexible coordination cage","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13374","abstract":[{"lang":"eng","text":"Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments."}],"type":"journal_article","date_published":"2018-02-13T00:00:00Z","article_type":"original","citation":{"chicago":"Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.","short":"D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L. Avram, P. Král, R. Klajn, Nature Communications 9 (2018).","mla":"Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer Nature, 2018, doi:10.1038/s41467-017-02715-6.","ieee":"D. Samanta et al., “Reversible chromism of spiropyran in the cavity of a flexible coordination cage,” Nature Communications, vol. 9. Springer Nature, 2018.","apa":"Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner, Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02715-6","ista":"Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 9, 641.","ama":"Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 2018;9. doi:10.1038/s41467-017-02715-6"},"publication":"Nature Communications","article_processing_charge":"No","day":"13","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"scopus_import":"1","volume":9,"date_created":"2023-08-01T09:39:32Z","date_updated":"2023-08-07T10:54:05Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-018-03701-2","relation":"erratum"}]},"author":[{"last_name":"Samanta","first_name":"Dipak","full_name":"Samanta, Dipak"},{"first_name":"Daria","last_name":"Galaktionova","full_name":"Galaktionova, Daria"},{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"first_name":"Linda J. W.","last_name":"Shimon","full_name":"Shimon, Linda J. W."},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"full_name":"Avram, Liat","first_name":"Liat","last_name":"Avram"},{"full_name":"Král, Petr","first_name":"Petr","last_name":"Král"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2018","extern":"1","article_number":"641","language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-02715-6","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-017-02715-6"}],"oa":1,"external_id":{"pmid":["29440687"]},"publication_identifier":{"eissn":["2041-1723"]},"month":"02"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures."}],"issue":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13377","title":"“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles","status":"public","intvolume":" 57","oa_version":"Published Version","scopus_import":"1","keyword":["General Chemistry","Catalysis"],"day":"11","article_processing_charge":"No","publication":"Angewandte Chemie International Edition","citation":{"chicago":"Chu, Zonglin, Yanxiao Han, Petr Král, and Rafal Klajn. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201800673.","short":"Z. Chu, Y. Han, P. Král, R. Klajn, Angewandte Chemie International Edition 57 (2018) 7023–7027.","mla":"Chu, Zonglin, et al. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” Angewandte Chemie International Edition, vol. 57, no. 24, Wiley, 2018, pp. 7023–27, doi:10.1002/anie.201800673.","ieee":"Z. Chu, Y. Han, P. Král, and R. Klajn, “‘Precipitation on nanoparticles’: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles,” Angewandte Chemie International Edition, vol. 57, no. 24. Wiley, pp. 7023–7027, 2018.","apa":"Chu, Z., Han, Y., Král, P., & Klajn, R. (2018). “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201800673","ista":"Chu Z, Han Y, Král P, Klajn R. 2018. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 57(24), 7023–7027.","ama":"Chu Z, Han Y, Král P, Klajn R. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 2018;57(24):7023-7027. doi:10.1002/anie.201800673"},"article_type":"original","page":"7023-7027","date_published":"2018-06-11T00:00:00Z","extern":"1","year":"2018","pmid":1,"publication_status":"published","publisher":"Wiley","author":[{"full_name":"Chu, Zonglin","first_name":"Zonglin","last_name":"Chu"},{"first_name":"Yanxiao","last_name":"Han","full_name":"Han, Yanxiao"},{"first_name":"Petr","last_name":"Král","full_name":"Král, Petr"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"date_created":"2023-08-01T09:40:16Z","date_updated":"2023-08-07T11:14:28Z","volume":57,"month":"06","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"external_id":{"pmid":["29673022"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1002/anie.201800673","open_access":"1"}],"quality_controlled":"1","doi":"10.1002/anie.201800673","language":[{"iso":"eng"}]},{"article_number":"1700827","extern":"1","publication_status":"published","publisher":"Wiley","year":"2018","pmid":1,"date_created":"2023-08-01T09:40:48Z","date_updated":"2023-08-07T11:16:49Z","volume":39,"author":[{"full_name":"Bléger, David","last_name":"Bléger","first_name":"David"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"month":"01","publication_identifier":{"eissn":["1521-3927"],"issn":["1022-1336"]},"quality_controlled":"1","external_id":{"pmid":["29314396"]},"main_file_link":[{"url":"https://doi.org/10.1002/marc.201700827","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/marc.201700827","type":"journal_article","issue":"1","status":"public","title":"Integrating macromolecules with molecular switches","intvolume":" 39","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13379","oa_version":"Published Version","keyword":["Materials Chemistry","Polymers and Plastics","Organic Chemistry"],"scopus_import":"1","day":"08","article_processing_charge":"No","article_type":"letter_note","publication":"Macromolecular Rapid Communications","citation":{"ista":"Bléger D, Klajn R. 2018. Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. 39(1), 1700827.","ieee":"D. Bléger and R. Klajn, “Integrating macromolecules with molecular switches,” Macromolecular Rapid Communications, vol. 39, no. 1. Wiley, 2018.","apa":"Bléger, D., & Klajn, R. (2018). Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. Wiley. https://doi.org/10.1002/marc.201700827","ama":"Bléger D, Klajn R. Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. 2018;39(1). doi:10.1002/marc.201700827","chicago":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” Macromolecular Rapid Communications. Wiley, 2018. https://doi.org/10.1002/marc.201700827.","mla":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” Macromolecular Rapid Communications, vol. 39, no. 1, 1700827, Wiley, 2018, doi:10.1002/marc.201700827.","short":"D. Bléger, R. Klajn, Macromolecular Rapid Communications 39 (2018)."},"date_published":"2018-01-08T00:00:00Z"},{"intvolume":" 615","status":"public","title":"Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13475","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Stars stripped of their hydrogen-rich envelope through interaction with a binary companion are generally not considered when accounting for ionizing radiation from stellar populations, despite the expectation that stripped stars emit hard ionizing radiation, form frequently, and live 10–100 times longer than single massive stars. We compute the first grid of evolutionary and spectral models specially made for stars stripped in binaries for a range of progenitor masses (2–20 M⊙) and metallicities ranging from solar to values representative for pop II stars. For stripped stars with masses in the range 0.3–7 M⊙, we find consistently high effective temperatures (20 000–100 000 K, increasing with mass), small radii (0.2–1 R⊙), and high bolometric luminosities, comparable to that of their progenitor before stripping. The spectra show a continuous sequence that naturally bridges subdwarf-type stars at the low-mass end and Wolf-Rayet-like spectra at the high-mass end. For intermediate masses we find hybrid spectral classes showing a mixture of absorption and emission lines. These appear for stars with mass-loss rates of 10−8−10−6 M⊙ yr−1, which have semi-transparent atmospheres. At low metallicity, substantial hydrogen-rich layers are left at the surface and we predict spectra that resemble O-type stars instead. We obtain spectra undistinguishable from subdwarfs for stripped stars with masses up to 1.7 M⊙, which questions whether the widely adopted canonical value of 0.47 M⊙ is uniformly valid. Only a handful of stripped stars of intermediate mass have currently been identified observationally. Increasing this sample will provide necessary tests for the physics of interaction, internal mixing, and stellar winds. We use our model spectra to investigate the feasibility to detect stripped stars next to an optically bright companion and recommend systematic searches for their UV excess and possible emission lines, most notably HeII λ4686 in the optical and HeII λ1640 in the UV. Our models are publicly available for further investigations or inclusion in spectral synthesis simulations."}],"article_type":"original","citation":{"ista":"Götberg YLL, de Mink SE, Groh JH, Kupfer T, Crowther PA, Zapartas E, Renzo M. 2018. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. 615, A78.","ieee":"Y. L. L. Götberg et al., “Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars,” Astronomy & Astrophysics, vol. 615. EDP Sciences, 2018.","apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Kupfer, T., Crowther, P. A., Zapartas, E., & Renzo, M. (2018). Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732274","ama":"Götberg YLL, de Mink SE, Groh JH, et al. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201732274","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, T. Kupfer, P. A. Crowther, E. Zapartas, and M. Renzo. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201732274.","mla":"Götberg, Ylva Louise Linsdotter, et al. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” Astronomy & Astrophysics, vol. 615, A78, EDP Sciences, 2018, doi:10.1051/0004-6361/201732274.","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, T. Kupfer, P.A. Crowther, E. Zapartas, M. Renzo, Astronomy & Astrophysics 615 (2018)."},"publication":"Astronomy & Astrophysics","date_published":"2018-07-17T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","article_processing_charge":"No","day":"17","publisher":"EDP Sciences","publication_status":"published","year":"2018","volume":615,"date_updated":"2023-08-09T11:22:17Z","date_created":"2023-08-03T10:15:00Z","author":[{"first_name":"Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter"},{"last_name":"de Mink","first_name":"S. E.","full_name":"de Mink, S. E."},{"full_name":"Groh, J. H.","first_name":"J. H.","last_name":"Groh"},{"full_name":"Kupfer, T.","first_name":"T.","last_name":"Kupfer"},{"full_name":"Crowther, P. A.","last_name":"Crowther","first_name":"P. A."},{"last_name":"Zapartas","first_name":"E.","full_name":"Zapartas, E."},{"full_name":"Renzo, M.","first_name":"M.","last_name":"Renzo"}],"article_number":"A78","extern":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201732274","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1802.03018"]},"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201732274","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"07"},{"oa_version":"Published Version","_id":"13473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 615","status":"public","title":"Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei","abstract":[{"text":"Stripped-envelope stars form in binary systems after losing mass through Roche-lobe overflow. They bear astrophysical significance as sources of UV and ionizing radiation in older stellar populations and, if sufficiently massive, as stripped supernova progenitors. Binary evolutionary models predict that they are common, but only a handful of subdwarfs with B-type companions are known. The question is whether a large population of such systems has evaded detection as a result of biases, or whether the model predictions are wrong. We reanalyze the well-studied post-interaction binary φ Persei. Recently, new data have improved the orbital solution of the system, which contains an ~1.2M⊙ stripped-envelope star and a rapidly rotating ~9.6M⊙ Be star. We compare with an extensive grid of evolutionary models using a Bayesian approach and constrain the initial masses of the progenitor to 7.2 ± 0.4M⊙ for the stripped star and 3.8 ± 0.4M⊙ for the Be star. The system must have evolved through near-conservative mass transfer. These findings are consistent with earlier studies. The age we obtain, 57 ± 9 Myr, is in excellent agreement with the age of the α Persei cluster. We note that neither star was initially massive enough to produce a core-collapse supernova, but mass exchange pushed the Be star above the mass threshold. We find that the subdwarf is overluminous for its mass by almost an order of magnitude, compared to the expectations for a helium core burning star. We can only reconcile this if the subdwarf resides in a late phase of helium shell burning, which lasts only 2–3% of the total lifetime as a subdwarf. Assuming continuous star formation implies that up to ~50 less evolved, dimmer subdwarfs exist for each system similar to φ Persei, but have evaded detection so far. Our findings can be interpreted as a strong indication that a substantial population of stripped-envelope stars indeed exists, but has so far evaded detection because of observational biases and lack of large-scale systematic searches.","lang":"eng"}],"type":"journal_article","date_published":"2018-07-06T00:00:00Z","citation":{"mla":"Schootemeijer, A., et al. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy & Astrophysics, vol. 615, A30, EDP Sciences, 2018, doi:10.1051/0004-6361/201731194.","short":"A. Schootemeijer, Y.L.L. Götberg, S.E. de Mink, D. Gies, E. Zapartas, Astronomy & Astrophysics 615 (2018).","chicago":"Schootemeijer, A., Ylva Louise Linsdotter Götberg, S. E. de Mink, D. Gies, and E. Zapartas. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201731194.","ama":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. 2018;615. doi:10.1051/0004-6361/201731194","ista":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. 2018. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. 615, A30.","ieee":"A. Schootemeijer, Y. L. L. Götberg, S. E. de Mink, D. Gies, and E. Zapartas, “Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei,” Astronomy & Astrophysics, vol. 615. EDP Sciences, 2018.","apa":"Schootemeijer, A., Götberg, Y. L. L., de Mink, S. E., Gies, D., & Zapartas, E. (2018). Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201731194"},"publication":"Astronomy & Astrophysics","article_type":"original","article_processing_charge":"No","day":"06","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"author":[{"full_name":"Schootemeijer, A.","last_name":"Schootemeijer","first_name":"A."},{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"full_name":"de Mink, S. E.","first_name":"S. E.","last_name":"de Mink"},{"last_name":"Gies","first_name":"D.","full_name":"Gies, D."},{"first_name":"E.","last_name":"Zapartas","full_name":"Zapartas, E."}],"volume":615,"date_created":"2023-08-03T10:14:37Z","date_updated":"2023-08-09T12:22:52Z","year":"2018","publisher":"EDP Sciences","publication_status":"published","extern":"1","article_number":"A30","doi":"10.1051/0004-6361/201731194","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.02379"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201731194","open_access":"1"}],"quality_controlled":"1","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"month":"07"},{"_id":"13474","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 475","title":"Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries","status":"public","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Recent surveys of the Magellanic Clouds have revealed a subtype of Wolf–Rayet (WR) star with peculiar properties. WN3/O3 spectra exhibit both WR-like emission and O3 V-like absorption – but at lower luminosity than O3 V or WN stars. We examine the projected spatial distribution of WN3/O3 stars in the Large Magellanic Cloud as compared to O-type stars. Surprisingly, WN3/O3 stars are among the most isolated of all classes of massive stars; they have a distribution similar to red supergiants dominated by initial masses of 10–15 M⊙, and are far more dispersed than classical WR stars or luminous blue variables. Their lack of association with clusters of O-type stars suggests strongly that WN3/O3 stars are not the descendants of single massive stars (30 M⊙ or above). Instead, they are likely products of interacting binaries at lower initial mass (10–18 M⊙). Comparison with binary models suggests a probable origin with primaries in this mass range that were stripped of their H envelopes through non-conservative mass transfer by a low-mass secondary. We show that model spectra and positions on the Hertzsprung–Russell diagram for binary-stripped stars are consistent with WN3/O3 stars. Monitoring radial velocities with high-resolution spectra can test for low-mass companions or runaway velocities. With lower initial mass and environments that avoid very massive stars, the WN3/O3 stars fit expectations for progenitors of Type Ib and possibly Type Ibn supernovae."}],"citation":{"apa":"Smith, N., Götberg, Y. L. L., & de Mink, S. E. (2018). Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx3181","ieee":"N. Smith, Y. L. L. Götberg, and S. E. de Mink, “Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries,” Monthly Notices of the Royal Astronomical Society, vol. 475, no. 1. Oxford University Press, pp. 772–782, 2018.","ista":"Smith N, Götberg YLL, de Mink SE. 2018. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. 475(1), 772–782.","ama":"Smith N, Götberg YLL, de Mink SE. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. 2018;475(1):772-782. doi:10.1093/mnras/stx3181","chicago":"Smith, Nathan, Ylva Louise Linsdotter Götberg, and Selma E de Mink. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/stx3181.","short":"N. Smith, Y.L.L. Götberg, S.E. de Mink, Monthly Notices of the Royal Astronomical Society 475 (2018) 772–782.","mla":"Smith, Nathan, et al. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” Monthly Notices of the Royal Astronomical Society, vol. 475, no. 1, Oxford University Press, 2018, pp. 772–82, doi:10.1093/mnras/stx3181."},"publication":"Monthly Notices of the Royal Astronomical Society","page":"772-782","article_type":"original","date_published":"2018-03-01T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_processing_charge":"No","day":"01","year":"2018","publisher":"Oxford University Press","publication_status":"published","author":[{"last_name":"Smith","first_name":"Nathan","full_name":"Smith, Nathan"},{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"last_name":"de Mink","first_name":"Selma E","full_name":"de Mink, Selma E"}],"volume":475,"date_updated":"2023-08-09T12:17:34Z","date_created":"2023-08-03T10:14:47Z","extern":"1","main_file_link":[{"url":"https://doi.org/10.1093/mnras/stx3181","open_access":"1"}],"external_id":{"arxiv":["1704.03516"]},"oa":1,"quality_controlled":"1","doi":"10.1093/mnras/stx3181","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"03"},{"article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-06-11T00:00:00Z","page":"40.1 - 40.14","citation":{"ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40."},"abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Submitted Version","intvolume":" 99","title":"The ℤ2-Genus of Kuratowski minors","status":"public","_id":"186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.40","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"arxiv":["1803.05085"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"oa":1,"publist_id":"7734","volume":99,"date_created":"2018-12-11T11:45:05Z","date_updated":"2023-08-14T12:43:51Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"11593"}]},"author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2018"},{"volume":8,"date_created":"2023-08-10T06:34:48Z","date_updated":"2023-08-22T07:42:07Z","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","extern":"1","article_number":"031060","language":[{"iso":"eng"}],"doi":"10.1103/physrevx.8.031060","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1103/PhysRevX.8.031060"}],"oa":1,"publication_identifier":{"eissn":["2160-3308"]},"month":"07","oa_version":"Published Version","intvolume":" 8","title":"Chiral discrimination through bielliptical high-harmonic spectroscopy","status":"public","_id":"14003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"Molecular chirality plays an essential role in most biochemical processes. The observation and quantification of chirality-sensitive signals, however, remains extremely challenging, especially on ultrafast timescales and in dilute media. Here, we describe the experimental realization of an all-optical and ultrafast scheme for detecting chiral dynamics in molecules. This technique is based on high-harmonic generation by a combination of two-color counterrotating femtosecond laser pulses with polarization states tunable from linear to circular. We demonstrate two different implementations of chiral-sensitive high-harmonic spectroscopy on an ensemble of randomly oriented methyloxirane molecules in the gas phase. Using two elliptically polarized fields, we observe that the ellipticities maximizing the harmonic signal reach up to \r\n4.4\r\n±\r\n0.2\r\n%\r\n (at 17.6 eV). Using two circularly polarized fields, we observe circular dichroisms ranging up to \r\n13\r\n±\r\n6\r\n%\r\n (28.3–33.1 eV). Our theoretical analysis confirms that the observed chiral response originates from subfemtosecond electron dynamics driven by the magnetic component of the driving laser field. This assignment is supported by the experimental observation of a strong intensity dependence of the chiral effects and its agreement with theory. We moreover report and explain a pronounced variation of the signal strength and dichroism with the driving-field ellipticities and harmonic orders. Finally, we demonstrate the sensitivity of the experimental observables to the shape of the electron hole. This technique for chiral discrimination will yield femtosecond temporal resolution when integrated in a pump-probe scheme and subfemtosecond resolution on chiral charge migration in a self-probing scheme.","lang":"eng"}],"type":"journal_article","date_published":"2018-07-01T00:00:00Z","article_type":"original","citation":{"ama":"Baykusheva DR, Wörner HJ. Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. 2018;8(3). doi:10.1103/physrevx.8.031060","ista":"Baykusheva DR, Wörner HJ. 2018. Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. 8(3), 031060.","ieee":"D. R. Baykusheva and H. J. Wörner, “Chiral discrimination through bielliptical high-harmonic spectroscopy,” Physical Review X, vol. 8, no. 3. American Physical Society, 2018.","apa":"Baykusheva, D. R., & Wörner, H. J. (2018). Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.8.031060","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” Physical Review X, vol. 8, no. 3, 031060, American Physical Society, 2018, doi:10.1103/physrevx.8.031060.","short":"D.R. Baykusheva, H.J. Wörner, Physical Review X 8 (2018).","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” Physical Review X. American Physical Society, 2018. https://doi.org/10.1103/physrevx.8.031060."},"publication":"Physical Review X","article_processing_charge":"No","day":"01","keyword":["General Physics and Astronomy"],"scopus_import":"1"},{"publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"year":"2018","date_updated":"2023-08-24T14:39:32Z","date_created":"2018-12-11T11:46:27Z","volume":10692,"author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"related_material":{"record":[{"id":"5857","relation":"later_version","status":"public"}]},"publist_id":"7390","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"external_id":{"arxiv":["1708.08037"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"GD 2017: Graph Drawing and Network Visualization","location":"Boston, MA, United States","start_date":"201-09-25","end_date":"2017-09-27"},"doi":"10.1007/978-3-319-73915-1_14","month":"01","status":"public","title":"Thrackles: An improved upper bound","intvolume":" 10692","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"433","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"page":"160 - 166","citation":{"ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14."},"date_published":"2018-01-21T00:00:00Z","scopus_import":1,"day":"21"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","year":"2018","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","date_updated":"2023-08-24T14:50:26Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","month":"10","day":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"citation":{"apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113."},"oa":1,"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113"},{"_id":"5457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"Cost analysis of nondeterministic probabilistic programs","ddc":["000"],"publication_status":"published","status":"public","publisher":"IST Austria","author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"full_name":"Anonymous, 2","last_name":"Anonymous","first_name":"2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"full_name":"Anonymous, 4","first_name":"4","last_name":"Anonymous"},{"full_name":"Anonymous, 5","last_name":"Anonymous","first_name":"5"},{"first_name":"6","last_name":"Anonymous","full_name":"Anonymous, 6"}],"pubrep_id":"1066","related_material":{"record":[{"id":"6175","status":"public","relation":"later_version"}]},"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-08-25T08:07:48Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5493","checksum":"ba3adafd36fe200385ccda583063b9eb","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T11:53:32Z","access_level":"open_access","file_name":"IST-2018-1066-v1+1_techreport.pdf","file_size":4202966,"content_type":"application/pdf","creator":"system"},{"content_type":"text/plain","file_size":322,"creator":"dernst","access_level":"closed","file_name":"authors-names.txt","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","date_updated":"2020-07-14T12:47:00Z","date_created":"2019-05-10T13:22:12Z","relation":"main_file","file_id":"6402"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:00Z","oa":1,"citation":{"mla":"Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria; 2018.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, & Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs. IST Austria.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, Cost analysis of nondeterministic probabilistic programs. IST Austria, 2018."},"page":"27","date_published":"2018-11-11T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"11","month":"11","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1"},{"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","year":"2018","publication_status":"published","department":[{"_id":"VlKo"}],"editor":[{"full_name":"Czelakowski, J","last_name":"Czelakowski","first_name":"J"}],"publisher":"Springer Nature","author":[{"full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","last_name":"Kazda"},{"first_name":"Marcin","last_name":"Kozik","full_name":"Kozik, Marcin"},{"first_name":"Ralph","last_name":"McKenzie","full_name":"McKenzie, Ralph"},{"full_name":"Moore, Matthew","first_name":"Matthew","last_name":"Moore"}],"date_created":"2022-03-18T10:30:32Z","date_updated":"2023-09-05T15:37:18Z","volume":16,"place":"Cham","external_id":{"arxiv":["1502.01072"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"quality_controlled":"1","doi":"10.1007/978-3-319-74772-9_7","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eisbn":["9783319747729"],"issn":["2211-2758"],"eissn":["2211-2766"],"isbn":["9783319747712"]},"_id":"10864","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Absorption and directed Jónsson terms","intvolume":" 16","oa_version":"Preprint","type":"book_chapter","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","citation":{"ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7."},"page":"203-220","date_published":"2018-03-21T00:00:00Z","scopus_import":"1","series_title":"OCTR","day":"21","article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:45:18Z","publist_id":"7736","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","first_name":"Zuzana","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","volume":99,"year":"2018","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"06","conference":{"location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2018.41","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","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"type":"conference","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"oa_version":"Published Version","file":[{"checksum":"d12bdd60f04a57307867704b5f930afd","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-17T16:35:02Z","file_id":"5725","relation":"main_file","creator":"dernst","file_size":718414,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Goaoc.pdf"}],"_id":"184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["516","000"],"status":"public","title":"Shellability is NP-complete","intvolume":" 99","day":"11","has_accepted_license":"1","scopus_import":1,"date_published":"2018-06-11T00:00:00Z","citation":{"ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41."},"page":"41:1 - 41:16"},{"oa_version":"Submitted Version","file":[{"file_id":"5713","relation":"main_file","date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-17T15:32:38Z","checksum":"530d084116778135d5bffaa317479cac","file_name":"2018_LIPIcs_Huszar.pdf","access_level":"open_access","creator":"dernst","file_size":642522,"content_type":"application/pdf"}],"intvolume":" 99","title":"On the treewidth of triangulated 3-manifolds","status":"public","ddc":["516","000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"285","abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2018-06-01T00:00:00Z","citation":{"ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46.","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":1,"volume":99,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-06T11:13:41Z","related_material":{"record":[{"id":"7093","status":"public","relation":"later_version"}]},"author":[{"last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2018","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","publist_id":"7614","file_date_updated":"2020-07-14T12:45:51Z","article_number":"46","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.46","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"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,"external_id":{"arxiv":["1712.00434"]},"publication_identifier":{"issn":["18688969"]},"month":"06"},{"date_updated":"2023-09-06T14:32:51Z","date_created":"2023-05-23T16:08:20Z","oa_version":"Published Version","author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"full_name":"Magis, Cedrik","first_name":"Cedrik","last_name":"Magis"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"full_name":"Notredame, Cedric","first_name":"Cedric","last_name":"Notredame"}],"related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","ddc":["570"],"status":"public","publisher":"Zenodo","department":[{"_id":"FyKo"}],"_id":"13059","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"type":"research_data_reference","doi":"10.5281/ZENODO.2025846","date_published":"2018-12-07T00:00:00Z","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"},"citation":{"chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"month":"12","day":"07","article_processing_charge":"No"},{"publist_id":"8005","file_date_updated":"2020-07-14T12:46:35Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"publication_status":"published","year":"2018","date_updated":"2023-09-07T12:27:43Z","date_created":"2018-12-11T11:44:21Z","author":[{"last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07","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"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"doi":"10.15479/AT:ISTA:th_1033","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.","lang":"eng"}],"title":"Ge hut wires - from growth to hole spin resonance","status":"public","ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"49","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:35Z","date_created":"2019-04-09T07:13:28Z","checksum":"b653b5216251f938ddbeafd1de88667c","file_id":"6249","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":85539748,"file_name":"2018_Thesis_Watzinger.pdf","access_level":"open_access"},{"creator":"dernst","file_size":21830697,"content_type":"application/zip","access_level":"closed","file_name":"2018_Thesis_Watzinger_source.zip","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","date_created":"2019-04-09T07:13:27Z","date_updated":"2020-07-14T12:46:35Z","file_id":"6250","relation":"source_file"}],"pubrep_id":"1033","has_accepted_license":"1","article_processing_charge":"No","day":"30","page":"77","citation":{"ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033."},"date_published":"2018-07-30T00:00:00Z"},{"month":"06","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_1026","degree_awarded":"PhD","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:45:24Z","publist_id":"7712","author":[{"full_name":"Iglesias Ham, Mabel","first_name":"Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:45:10Z","date_updated":"2023-09-07T12:25:32Z","year":"2018","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","day":"11","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-06-11T00:00:00Z","citation":{"mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026"},"page":"171","abstract":[{"text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1026","file":[{"relation":"source_file","file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05","date_created":"2019-02-05T07:43:31Z","date_updated":"2020-07-14T12:45:24Z","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","file_size":11827713,"content_type":"application/zip","creator":"kschuh"},{"checksum":"ba163849a190d2b41d66fef0e4983294","date_created":"2019-02-05T07:43:45Z","date_updated":"2020-07-14T12:45:24Z","file_id":"5919","relation":"main_file","creator":"kschuh","file_size":4783846,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"201","title":"Multiple covers with balls","status":"public","ddc":["514","516"]},{"citation":{"chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048"},"page":"92","date_published":"2018-09-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"68","ddc":["004","519"],"status":"public","title":"Learning from dependent data","pubrep_id":"1048","file":[{"access_level":"open_access","file_name":"2018_Thesis_Zimin.pdf","creator":"dernst","content_type":"application/pdf","file_size":1036137,"file_id":"6253","relation":"main_file","checksum":"e849dd40a915e4d6c5572b51b517f098","date_created":"2019-04-09T07:32:47Z","date_updated":"2020-07-14T12:47:40Z"},{"file_name":"2018_Thesis_Zimin_Source.zip","access_level":"closed","content_type":"application/zip","file_size":637490,"creator":"dernst","relation":"source_file","file_id":"6254","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","checksum":"da092153cec55c97461bd53c45c5d139"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability.","lang":"eng"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:TH1048","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"year":"2018","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Zimin, Alexander","last_name":"Zimin","first_name":"Alexander","id":"37099E9C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:29:07Z","date_created":"2018-12-11T11:44:27Z","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"publist_id":"7986"},{"article_processing_charge":"No","has_accepted_license":"1","day":"05","citation":{"ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.","mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018."},"page":"59","date_published":"2018-09-05T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"_id":"83","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004"],"title":"Proof systems for sustainable decentralized cryptocurrencies","status":"public","pubrep_id":"1046","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","checksum":"c4b5f7d111755d1396787f41886fc674","file_id":"6245","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":876241,"file_name":"2018_Thesis_Abusalah.pdf","access_level":"open_access"},{"access_level":"closed","file_name":"2018_Thesis_Abusalah_source.tar.gz","creator":"dernst","file_size":2029190,"content_type":"application/x-gzip","file_id":"6246","relation":"source_file","checksum":"0f382ac56b471c48fd907d63eb87dafe","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","oa":1,"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:TH_1046","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"ec_funded":1,"publist_id":"7971","file_date_updated":"2020-07-14T12:48:11Z","year":"2018","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"1229","status":"public","relation":"part_of_dissertation"},{"id":"1235","relation":"part_of_dissertation","status":"public"},{"id":"1236","status":"public","relation":"part_of_dissertation"},{"id":"559","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M","full_name":"Abusalah, Hamza M"}],"date_created":"2018-12-11T11:44:32Z","date_updated":"2023-09-07T12:30:23Z"},{"date_published":"2018-05-25T00:00:00Z","page":"113","citation":{"ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021."},"has_accepted_license":"1","article_processing_charge":"No","day":"25","file":[{"checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","date_created":"2018-12-12T10:14:57Z","date_updated":"2020-07-14T12:45:22Z","file_id":"5113","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":12918758,"access_level":"open_access","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf"},{"access_level":"closed","file_name":"2018_Thesis_Kolesnikov_source.zip","content_type":"application/zip","file_size":55973760,"creator":"dernst","relation":"source_file","file_id":"6225","checksum":"bc66973b086da5a043f1162dcfb1fde4","date_created":"2019-04-05T09:34:49Z","date_updated":"2020-07-14T12:45:22Z"}],"oa_version":"Published Version","pubrep_id":"1021","ddc":["004"],"status":"public","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","_id":"197","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1021","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"05","date_created":"2018-12-11T11:45:09Z","date_updated":"2023-09-07T12:51:46Z","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"}],"department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","year":"2018","ec_funded":1,"publist_id":"7718","file_date_updated":"2020-07-14T12:45:22Z"},{"file_date_updated":"2020-07-14T12:47:40Z","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2018","volume":2,"date_updated":"2023-09-07T13:10:36Z","date_created":"2019-08-08T06:47:40Z","related_material":{"record":[{"id":"6681","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský","first_name":"Marek","full_name":"Filakovský, Marek"},{"full_name":"Franek, Peter","first_name":"Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8878-8397"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"},{"id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"month":"12","project":[{"call_identifier":"FWF","name":"Robust invariants of Nonlinear Systems","grant_number":"M01980","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"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,"language":[{"iso":"eng"}],"doi":"10.1007/s41468-018-0021-5","type":"journal_article","issue":"3-4","abstract":[{"lang":"eng","text":"A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) ."}],"intvolume":" 2","ddc":["514"],"title":"Computing simplicial representatives of homotopy group elements","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6774","file":[{"file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","access_level":"open_access","file_size":1056278,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6775","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-08T06:55:21Z","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8"}],"oa_version":"Published Version","has_accepted_license":"1","day":"01","page":"177-231","article_type":"original","citation":{"chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5.","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","apa":"Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5"},"publication":"Journal of Applied and Computational Topology","date_published":"2018-12-01T00:00:00Z"},{"has_accepted_license":"1","day":"13","scopus_import":1,"date_published":"2018-08-13T00:00:00Z","citation":{"short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21."},"abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"1039","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":745438,"creator":"system","file_name":"IST-2018-853-v2+2_concur2018.pdf","access_level":"open_access","date_created":"2018-12-12T10:18:46Z","date_updated":"2020-07-14T12:44:44Z","checksum":"c90895f4c5fafc18ddc54d1c8848077e","relation":"main_file","file_id":"5368"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"133","intvolume":" 118","title":"Synchronizing the asynchronous","status":"public","ddc":["000"],"publication_identifier":{"issn":["18688969"]},"month":"08","doi":"10.4230/LIPIcs.CONCUR.2018.21","conference":{"name":"CONCUR: International Conference on Concurrency Theory","end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04"},"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,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"7790","file_date_updated":"2020-07-14T12:44:44Z","article_number":"21","related_material":{"record":[{"id":"6426","relation":"earlier_version","status":"public"},{"id":"8332","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"volume":118,"date_updated":"2023-09-07T13:18:00Z","date_created":"2018-12-11T11:44:48Z","year":"2018","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published"},{"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14"},"doi":"10.4230/LIPIcs.SoCG.2018.34","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","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"month":"06","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"9317"},{"relation":"dissertation_contains","status":"public","id":"9056"}]},"date_created":"2018-12-11T11:45:05Z","date_updated":"2023-09-07T13:29:00Z","volume":99,"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2018","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"7732","article_number":"34","date_published":"2018-06-11T00:00:00Z","citation":{"short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34."},"day":"11","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"file_id":"5738","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-18T09:27:22Z","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","access_level":"open_access","creator":"dernst","file_size":528018,"content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"187","title":"The multi-cover persistence of Euclidean balls","status":"public","ddc":["516"],"intvolume":" 99","abstract":[{"text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"]},{"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,"external_id":{"isi":["000431418800004"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1007/s10711-017-0265-6","language":[{"iso":"eng"}],"month":"06","year":"2018","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"}],"date_created":"2018-12-11T11:47:57Z","date_updated":"2023-09-08T11:40:29Z","volume":194,"file_date_updated":"2020-07-14T12:47:44Z","publist_id":"7014","ec_funded":1,"publication":"Geometriae Dedicata","citation":{"ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6","ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6","chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6."},"article_type":"original","page":"55 - 64","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","_id":"692","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["510"],"title":"3-Webs generated by confocal conics and circles","intvolume":" 194","oa_version":"Published Version","file":[{"file_size":1140860,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2018_Springer_Akopyan.pdf","checksum":"1febcfc1266486053a069e3425ea3713","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T11:35:08Z","relation":"main_file","file_id":"7222"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them."}],"issue":"1"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"25","article_type":"original","citation":{"chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.","mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018.","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4"},"publication":"Nature Communications","date_published":"2018-09-25T00:00:00Z","type":"journal_article","issue":"3902 ","abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}],"intvolume":" 9","title":"A germanium hole spin qubit","status":"public","ddc":["530"],"_id":"77","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-17T10:28:30Z","date_updated":"2020-07-14T12:48:02Z","checksum":"e7148c10a64497e279c4de570b6cc544","relation":"main_file","file_id":"5687","content_type":"application/pdf","file_size":1063469,"creator":"dernst","file_name":"2018_NatureComm_Watzinger.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"09","project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7"},{"grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000445560800010"]},"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"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-018-06418-4","ec_funded":1,"file_date_updated":"2020-07-14T12:48:02Z","publisher":"Nature Publishing Group","department":[{"_id":"GeKa"}],"publication_status":"published","year":"2018","volume":9,"date_created":"2018-12-11T11:44:30Z","date_updated":"2023-09-08T11:44:02Z","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"id":"7996","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip"},{"orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukusic","first_name":"Lada","full_name":"Vukusic, Lada"},{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"first_name":"Ting","last_name":"Wang","full_name":"Wang, Ting"},{"last_name":"Schäffler","first_name":"Friedrich","full_name":"Schäffler, Friedrich"},{"first_name":"Jian","last_name":"Zhang","full_name":"Zhang, Jian"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}]},{"file":[{"creator":"system","content_type":"application/pdf","file_size":3780491,"file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:45Z","date_updated":"2020-07-14T12:46:22Z","checksum":"87a427bc2e8724be3dd22a4efdd21a33","file_id":"4902","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"996","title":"A biochemical network controlling basal myosin oscillation","status":"public","ddc":["539","570"],"intvolume":" 9","_id":"401","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"issue":"1","type":"journal_article","date_published":"2018-03-23T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5.","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5"},"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_created":"2018-12-11T11:46:16Z","date_updated":"2023-09-08T11:41:45Z","volume":9,"author":[{"full_name":"Qin, Xiang","first_name":"Xiang","last_name":"Qin"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"last_name":"Mangeat","first_name":"Thomas","full_name":"Mangeat, Thomas"},{"full_name":"Liu, Chang","last_name":"Liu","first_name":"Chang"},{"full_name":"Majumder, Pralay","last_name":"Majumder","first_name":"Pralay"},{"full_name":"Liu, Jjiaying","last_name":"Liu","first_name":"Jjiaying"},{"last_name":"Choesmel Cadamuro","first_name":"Valerie","full_name":"Choesmel Cadamuro, Valerie"},{"full_name":"Mcdonald, Jocelyn","first_name":"Jocelyn","last_name":"Mcdonald"},{"full_name":"Liu, Yinyao","last_name":"Liu","first_name":"Yinyao"},{"first_name":"Bin","last_name":"Yi","full_name":"Yi, Bin"},{"last_name":"Wang","first_name":"Xiaobo","full_name":"Wang, Xiaobo"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"EdHa"}],"year":"2018","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7427","article_number":"1210","language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-03574-5","isi":1,"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,"external_id":{"isi":["000428165400009"]},"month":"03"},{"day":"26","article_processing_charge":"No","scopus_import":"1","date_published":"2018-02-26T00:00:00Z","page":"405 - 406","publication":"Developmental Cell","citation":{"ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009","apa":"Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009.","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009."},"abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Published Version","title":"A fat lot of good for wound healing","status":"public","intvolume":" 44","_id":"318","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.02.009","isi":1,"quality_controlled":"1","external_id":{"isi":["000426150700002"],"pmid":["29486189"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189"}],"publist_id":"7547","date_updated":"2023-09-08T11:42:28Z","date_created":"2018-12-11T11:45:47Z","volume":44,"author":[{"full_name":"Casano, Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6009-6804","first_name":"Alessandra M","last_name":"Casano"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"}],"acknowledgement":"Short Survey","year":"2018","pmid":1},{"doi":"10.1038/s41598-018-23247-z","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":{"isi":["000428234100005"]},"quality_controlled":"1","isi":1,"month":"03","author":[{"full_name":"Masís, Javier","first_name":"Javier","last_name":"Masís"},{"full_name":"Mankus, David","first_name":"David","last_name":"Mankus"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"full_name":"Guitchounts, Grigori","first_name":"Grigori","last_name":"Guitchounts"},{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"},{"last_name":"Cox","first_name":"David","full_name":"Cox, David"}],"date_updated":"2023-09-08T11:48:39Z","date_created":"2018-12-11T11:46:19Z","volume":8,"year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:46:23Z","publist_id":"7419","article_number":"5184","date_published":"2018-03-26T00:00:00Z","publication":"Scientific Reports","citation":{"mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z"},"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","pubrep_id":"994","oa_version":"Published Version","file":[{"file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2359430,"file_id":"4831","relation":"main_file","date_updated":"2020-07-14T12:46:23Z","date_created":"2018-12-12T10:10:42Z","checksum":"653fcb852f899c75b00ceee2a670d738"}],"_id":"410","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571","572"],"title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","status":"public","intvolume":" 8","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"issue":"1","type":"journal_article"},{"month":"06","doi":"10.1007/s11103-018-0747-4","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000438981700009"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7625","author":[{"full_name":"Dokládal, Ladislav","last_name":"Dokládal","first_name":"Ladislav"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"full_name":"Dupláková, Nikoleta","first_name":"Nikoleta","last_name":"Dupláková"},{"first_name":"Lan","last_name":"Lee","full_name":"Lee, Lan"},{"full_name":"Gelvin, Stanton","first_name":"Stanton","last_name":"Gelvin"},{"full_name":"Sýkorová, Eva","last_name":"Sýkorová","first_name":"Eva"}],"date_updated":"2023-09-08T13:21:05Z","date_created":"2018-12-11T11:45:34Z","volume":97,"year":"2018","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-06-12T00:00:00Z","publication":"Plant Molecular Biology","citation":{"chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4.","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4","ieee":"L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4"},"article_type":"original","page":"407 - 420","abstract":[{"text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.","lang":"eng"}],"issue":"5","type":"journal_article","file":[{"relation":"main_file","file_id":"7834","checksum":"451ae47616e6af2533099f596b2a47fb","date_created":"2020-05-14T12:23:08Z","date_updated":"2020-07-14T12:45:45Z","access_level":"open_access","file_name":"2018_PlantMolecBio_Dokladal.pdf","file_size":1150679,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","_id":"277","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"An armadillo-domain protein participates in a telomerase interaction network","status":"public","ddc":["580"],"intvolume":" 97"},{"date_updated":"2023-09-08T11:52:02Z","date_created":"2018-12-11T11:45:41Z","volume":10806,"author":[{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"full_name":"Lebeltel, Olivier","last_name":"Lebeltel","first_name":"Olivier"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas"},{"full_name":"Ulus, Dogan","first_name":"Dogan","last_name":"Ulus"}],"related_material":{"record":[{"id":"10861","relation":"later_version","status":"public"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","editor":[{"last_name":"Beyer","first_name":"Dirk","full_name":"Beyer, Dirk"},{"last_name":"Huisman","first_name":"Marieke","full_name":"Huisman, Marieke"}],"year":"2018","file_date_updated":"2020-07-14T12:45:58Z","publist_id":"7582","language":[{"iso":"eng"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Thessaloniki, Greece","start_date":"2018-04-14","end_date":"2018-04-20"},"doi":"10.1007/978-3-319-89963-3_18","quality_controlled":"1","isi":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,"external_id":{"isi":["00445822600018"]},"month":"04","file":[{"file_name":"2018_LNCS_Nickovic.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3267209,"creator":"dernst","relation":"main_file","file_id":"5928","date_created":"2019-02-06T07:33:05Z","date_updated":"2020-07-14T12:45:58Z","checksum":"e11db3b9c8e27a1c7d1c738cc5e4d25a"}],"oa_version":"Published Version","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","ddc":["000"],"status":"public","intvolume":" 10806","_id":"299","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2018-04-14T00:00:00Z","page":"303 - 319","citation":{"chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319.","mla":"Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18"},"day":"14","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"oa_version":"Published Version","intvolume":" 115","status":"public","title":"Ants avoid superinfections by performing risk-adjusted sanitary care","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"413","issue":"11","abstract":[{"lang":"eng","text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk."}],"type":"journal_article","date_published":"2018-03-13T00:00:00Z","page":"2782 - 2787","citation":{"short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115.","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787."},"publication":"PNAS","article_processing_charge":"No","day":"13","scopus_import":"1","volume":115,"date_updated":"2023-09-08T13:22:21Z","date_created":"2018-12-11T11:46:20Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/"}]},"author":[{"last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias"},{"orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher","full_name":"Pull, Christopher"},{"full_name":"Metzler, Sina","last_name":"Metzler","first_name":"Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seif, Katharina","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D","last_name":"Seif","first_name":"Katharina"},{"full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"publisher":"National Academy of Sciences","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"year":"2018","ec_funded":1,"publist_id":"7416","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1713501115","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000427245400069"],"pmid":["29463746"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746"}],"month":"03"},{"type":"journal_article","issue":"4","abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"intvolume":" 98","status":"public","title":"Anyonic statistics of quantum impurities in two dimensions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"195","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"15","citation":{"ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018.","apa":"Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402."},"publication":"Physical Review B - Condensed Matter and Materials Physics","date_published":"2018-07-15T00:00:00Z","article_number":"045402","ec_funded":1,"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2018","volume":98,"date_updated":"2023-09-08T13:22:57Z","date_created":"2018-12-11T11:45:08Z","author":[{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"month":"07","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.00308"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.98.045402"},{"scopus_import":"1","day":"26","article_processing_charge":"No","publication":"PNAS","citation":{"chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115"},"page":"6864-6869","date_published":"2018-06-26T00:00:00Z","type":"journal_article","abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"issue":"26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"203","title":"Auxin methylation is required for differential growth in Arabidopsis","status":"public","intvolume":" 115","oa_version":"None","month":"06","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"oa":1,"external_id":{"isi":["000436245000096"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.1073/pnas.1806565115","language":[{"iso":"eng"}],"publist_id":"7710","ec_funded":1,"year":"2018","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","author":[{"id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","first_name":"Mohamad","last_name":"Abbas","full_name":"Abbas, Mohamad"},{"full_name":"Hernández, García J","last_name":"Hernández","first_name":"García J"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"last_name":"Samodelov","first_name":"Sophia L","full_name":"Samodelov, Sophia L"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z","last_name":"Hammes"},{"first_name":"Matias D","last_name":"Zurbriggen","full_name":"Zurbriggen, Matias D"},{"first_name":"Miguel","last_name":"Blázquez","full_name":"Blázquez, Miguel"},{"first_name":"David","last_name":"Alabadí","full_name":"Alabadí, David"}],"date_updated":"2023-09-08T13:24:40Z","date_created":"2018-12-11T11:45:11Z","volume":115},{"date_updated":"2023-09-08T13:30:51Z","date_created":"2018-12-11T11:46:15Z","volume":121,"author":[{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robin","last_name":"Reuvers","full_name":"Reuvers, Robin"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","year":"2018","publist_id":"7432","article_number":"10007","language":[{"iso":"eng"}],"doi":"10.1209/0295-5075/121/10007","isi":1,"quality_controlled":"1","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.01822"}],"oa":1,"month":"01","oa_version":"Preprint","status":"public","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","intvolume":" 121","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"399","abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2018-01-01T00:00:00Z","article_type":"original","publication":"EPL","citation":{"short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5830","year":"2018","pmid":1,"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","publication_status":"epub_ahead","status":"public","publisher":"Wiley","department":[{"_id":"JiFr"}],"author":[{"last_name":"Zhang","first_name":"Luosha","full_name":"Zhang, Luosha"},{"first_name":"Xiong","last_name":"Shi","full_name":"Shi, Xiong"},{"full_name":"Zhang, Yutao","first_name":"Yutao","last_name":"Zhang"},{"full_name":"Wang, Jiajing","last_name":"Wang","first_name":"Jiajing"},{"full_name":"Yang, Jingwei","first_name":"Jingwei","last_name":"Yang"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"last_name":"Jiang","first_name":"Wenqian","full_name":"Jiang, Wenqian"},{"full_name":"Han, Xiangyu","last_name":"Han","first_name":"Xiangyu"},{"full_name":"Kang, Jingke","last_name":"Kang","first_name":"Jingke"},{"first_name":"Xuening","last_name":"Wang","full_name":"Wang, Xuening"},{"full_name":"Pan, Lixia","first_name":"Lixia","last_name":"Pan"},{"full_name":"Lv, Shuo","last_name":"Lv","first_name":"Shuo"},{"last_name":"Cao","first_name":"Bing","full_name":"Cao, Bing"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"full_name":"Wu, Jinbin","first_name":"Jinbin","last_name":"Wu"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"full_name":"Hu, Zhubing","first_name":"Zhubing","last_name":"Hu"},{"full_name":"Cui, Langjun","first_name":"Langjun","last_name":"Cui"},{"first_name":"Shinichiro","last_name":"Sawa","full_name":"Sawa, Shinichiro"},{"full_name":"He, Junmin","first_name":"Junmin","last_name":"He"},{"last_name":"Wang","first_name":"Guodong","full_name":"Wang, Guodong"}],"date_updated":"2023-09-11T12:43:31Z","date_created":"2019-01-13T22:59:11Z","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"publication":"Plant Cell and Environment","external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"citation":{"chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1111/pce.13475","date_published":"2018-10-31T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","month":"10","day":"31","publication_identifier":{"issn":["01407791"]},"article_processing_charge":"No"},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41556-018-0108-1","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"oa":1,"external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"publist_id":"7594","date_created":"2018-12-11T11:45:38Z","date_updated":"2023-09-11T12:44:08Z","volume":20,"author":[{"full_name":"Lilja, Anna","last_name":"Lilja","first_name":"Anna"},{"last_name":"Rodilla","first_name":"Veronica","full_name":"Rodilla, Veronica"},{"first_name":"Mathilde","last_name":"Huyghe","full_name":"Huyghe, Mathilde"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Landragin, Camille","last_name":"Landragin","first_name":"Camille"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"full_name":"Leroy, Olivier","first_name":"Olivier","last_name":"Leroy"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"last_name":"Fré","first_name":"Silvia","full_name":"Fré, Silvia"}],"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Nature Publishing Group","year":"2018","pmid":1,"day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-21T00:00:00Z","article_type":"original","page":"677 - 687","publication":"Nature Cell Biology","citation":{"ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1."},"abstract":[{"text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","status":"public","intvolume":" 20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"288"},{"citation":{"ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376."},"publication":"ACM Transactions on Graphics","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"304","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 37","ddc":["000","535","680"],"title":"Computational design of nanostructural color for additive manufacturing","status":"public","pubrep_id":"1028","oa_version":"Submitted 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Transactions on Graphics"],"issue":"4","abstract":[{"text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"oa":1,"external_id":{"isi":["000448185000120"]},"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3197517.3201376","language":[{"iso":"eng"}],"month":"08","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","year":"2018","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/"}]},"author":[{"full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger"},{"first_name":"Wolfgang","last_name":"Heidrich","full_name":"Heidrich, Wolfgang"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"volume":37,"date_updated":"2023-09-11T12:46:13Z","date_created":"2018-12-11T11:45:43Z","article_number":"159","ec_funded":1,"file_date_updated":"2020-07-14T12:45:59Z"},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"}],"oa":1,"external_id":{"isi":["000448185000096"]},"language":[{"iso":"eng"}],"doi":"10.1145/3197517.3201341","month":"08","publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"ACM","year":"2018","date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-11T12:48:09Z","volume":37,"author":[{"full_name":"Nakashima, Kazutaka","first_name":"Kazutaka","last_name":"Nakashima"},{"full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265"},{"last_name":"Iarussi","first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","full_name":"Iarussi, Emmanuel"},{"full_name":"Zhang, Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X","first_name":"Ran","last_name":"Zhang"},{"last_name":"Igarashi","first_name":"Takeo","full_name":"Igarashi, Takeo"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release","description":"News on IST Homepage"}]},"article_number":"135","file_date_updated":"2020-07-14T12:44:38Z","ec_funded":1,"publist_id":"8044","publication":"ACM Transaction on Graphics","citation":{"mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018."},"date_published":"2018-08-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","status":"public","ddc":["004","516","670"],"intvolume":" 37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12","oa_version":"Submitted Version","file":[{"creator":"system","file_size":104225664,"content_type":"application/pdf","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:18:38Z","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","file_id":"5360","relation":"main_file"},{"file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","access_level":"open_access","creator":"system","file_size":377743553,"content_type":"application/zip","file_id":"5361","relation":"main_file","date_created":"2018-12-12T10:18:39Z","date_updated":"2020-07-14T12:44:38Z","checksum":"3861e693ba47c51f3ec7b7867d573a61"},{"access_level":"open_access","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","creator":"system","content_type":"video/vnd.objectvideo","file_size":162634396,"file_id":"5362","relation":"main_file","checksum":"490040c685ed869536e2a18f5a906b94","date_created":"2018-12-12T10:18:41Z","date_updated":"2020-07-14T12:44:38Z"},{"date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:18:42Z","checksum":"be7fc8b229adda727419b6504b3b9352","file_id":"5363","relation":"main_file","creator":"system","content_type":"image/jpeg","file_size":527972,"file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","access_level":"open_access"}],"pubrep_id":"1037","type":"journal_article","abstract":[{"text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.","lang":"eng"}],"issue":"4"},{"acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","year":"2018","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Reiter, Johannes","last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"last_name":"Rand","first_name":"David","full_name":"Rand, David"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"volume":9,"date_updated":"2023-09-11T12:51:03Z","date_created":"2018-12-11T11:46:34Z","article_number":"555","ec_funded":1,"publist_id":"7368","file_date_updated":"2020-07-14T12:46:31Z","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":{"isi":["000424318200001"]},"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"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-017-02721-8","language":[{"iso":"eng"}],"month":"02","_id":"454","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 9","ddc":["004"],"title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","status":"public","pubrep_id":"964","oa_version":"Published Version","file":[{"file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":843646,"file_id":"4741","relation":"main_file","date_created":"2018-12-12T10:09:18Z","date_updated":"2020-07-14T12:46:31Z","checksum":"b6b90367545b4c615891c960ab0567f1"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"citation":{"chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8.","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8"},"publication":"Nature Communications","date_published":"2018-02-07T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"07"},{"doi":"10.1016/j.neuron.2018.02.024","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,"external_id":{"isi":["000429192100016"]},"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"isi":1,"quality_controlled":"1","month":"04","related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"last_name":"Hu","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua"},{"full_name":"Roth, Fabian","first_name":"Fabian","last_name":"Roth"},{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"volume":98,"date_updated":"2023-09-11T12:45:10Z","date_created":"2018-12-11T11:45:48Z","year":"2018","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"publist_id":"7545","file_date_updated":"2020-07-14T12:46:03Z","date_published":"2018-04-04T00:00:00Z","citation":{"ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","apa":"Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024."},"publication":"Neuron","page":"156 - 165","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":3180444,"content_type":"application/pdf","creator":"dernst","file_name":"2018_Neuron_Hu.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:03Z","date_created":"2018-12-17T10:37:50Z","checksum":"76070f3729f9c603e1080d0151aa2b11","relation":"main_file","file_id":"5690"}],"_id":"320","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 98","title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","ddc":["570"],"status":"public","issue":"1","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. "}],"type":"journal_article"},{"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3533881,"file_name":"2018_eLife_Payne.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T10:36:07Z","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","relation":"main_file"}],"oa_version":"Published Version","_id":"423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 7","ddc":["576"],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","date_published":"2018-03-09T00:00:00Z","citation":{"ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035."},"publication":"eLife","ec_funded":1,"publist_id":"7400","file_date_updated":"2020-07-14T12:46:25Z","article_number":"e32035","related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"volume":7,"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","year":"2018","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","publication_status":"published","month":"03","doi":"10.7554/eLife.32035","language":[{"iso":"eng"}],"external_id":{"isi":["000431035800001"]},"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,"project":[{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"quality_controlled":"1","isi":1},{"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"main_file_link":[{"url":"https://arxiv.org/abs/1808.07608","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-04414-5_16","conference":{"name":"Graph Drawing and Network Visualization","end_date":"2018-09-28","start_date":"2018-09-26","location":"Barcelona, Spain"},"publication_identifier":{"isbn":["9783030044138"]},"month":"12","department":[{"_id":"UlWa"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":"11282 ","date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T12:49:55Z","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"first_name":"Csaba D.","last_name":"Tóth","full_name":"Tóth, Csaba D."}],"page":"229-241","citation":{"mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16"},"date_published":"2018-12-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"18","status":"public","title":"Crossing minimization in perturbed drawings","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5791","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.","lang":"eng"}]},{"doi":"10.1103/PhysRevFluids.3.054401","language":[{"iso":"eng"}],"external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"quality_controlled":"1","isi":1,"month":"05","author":[{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"volume":3,"date_updated":"2023-09-11T12:45:44Z","date_created":"2018-12-11T11:45:39Z","year":"2018","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"publication_status":"published","publist_id":"7590","article_number":"054401","date_published":"2018-05-30T00:00:00Z","citation":{"ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018.","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401.","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018)."},"publication":"Physical Review Fluids","article_processing_charge":"No","day":"30","scopus_import":"1","oa_version":"Preprint","_id":"291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 3","title":"Complexity of the laminar-turbulent boundary in pipe flow","status":"public","issue":"5","abstract":[{"lang":"eng","text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions."}],"type":"journal_article"},{"citation":{"ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257."},"publication":"SIAM Journal on Discrete Mathematics","page":"2242 - 2257","date_published":"2018-09-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"06","_id":"58","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 32","status":"public","title":"Counting blanks in polygonal arrangements","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.00960"}],"oa":1,"external_id":{"isi":["000450810500036"],"arxiv":["1604.00960"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"doi":"10.1137/16M110407X","language":[{"iso":"eng"}],"month":"09","year":"2018","department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics ","publication_status":"published","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"last_name":"Segal Halevi","first_name":"Erel","full_name":"Segal Halevi, Erel"}],"volume":32,"date_created":"2018-12-11T11:44:24Z","date_updated":"2023-09-11T12:48:39Z","publist_id":"7996","ec_funded":1},{"status":"public","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"Dryad","year":"2018","_id":"9840","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"id":"423","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"citation":{"apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44."},"oa":1,"doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","day":"12","month":"03","article_processing_charge":"No"},{"day":"09","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2018-01-09T00:00:00Z","publication":"eLife","citation":{"chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073.","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073.","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073"},"abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4832","relation":"main_file","date_updated":"2020-07-14T12:47:20Z","date_created":"2018-12-12T10:10:43Z","checksum":"540f941e8d3530a9441e4affd94f07d7","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1435585}],"pubrep_id":"978","ddc":["570","590"],"title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","status":"public","intvolume":" 7","_id":"616","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"01","language":[{"iso":"eng"}],"doi":"10.7554/eLife.32073","quality_controlled":"1","isi":1,"project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"}],"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":{"isi":["000419601300001"]},"file_date_updated":"2020-07-14T12:47:20Z","publist_id":"7188","ec_funded":1,"article_number":"e32073","date_created":"2018-12-11T11:47:31Z","date_updated":"2023-09-11T12:54:26Z","volume":7,"author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"},{"full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Wiesenhofer","full_name":"Wiesenhofer, Florian"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon"},{"full_name":"Schmitt, Thomas","first_name":"Thomas","last_name":"Schmitt"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"id":"819","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"eLife Sciences Publications","year":"2018"},{"publist_id":"7791","file_date_updated":"2020-07-14T12:44:43Z","year":"2018","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","department":[{"_id":"EdHa"}],"publisher":"Cell Press","publication_status":"published","author":[{"full_name":"Sznurkowska, Magdalena","first_name":"Magdalena","last_name":"Sznurkowska"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Azzarelli, Roberta","first_name":"Roberta","last_name":"Azzarelli"},{"last_name":"Rulands","first_name":"Steffen","full_name":"Rulands, Steffen"},{"full_name":"Nestorowa, Sonia","first_name":"Sonia","last_name":"Nestorowa"},{"first_name":"Christopher","last_name":"Hindley","full_name":"Hindley, Christopher"},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"full_name":"Göttgens, Berthold","first_name":"Berthold","last_name":"Göttgens"},{"full_name":"Huch, Meritxell","first_name":"Meritxell","last_name":"Huch"},{"full_name":"Philpott, Anna","last_name":"Philpott","first_name":"Anna"},{"last_name":"Simons","first_name":"Benjamin","full_name":"Simons, Benjamin"}],"volume":46,"date_created":"2018-12-11T11:44:48Z","date_updated":"2023-09-11T12:52:41Z","month":"08","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,"external_id":{"isi":["000441327300012"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2018.06.028","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"132","intvolume":" 46","ddc":["570"],"status":"public","title":"Defining lineage potential and fate behavior of precursors during pancreas development","file":[{"file_id":"5694","relation":"main_file","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","date_updated":"2020-07-14T12:44:43Z","date_created":"2018-12-17T10:49:49Z","access_level":"open_access","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","creator":"dernst","file_size":8948384,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"06","citation":{"ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375."},"publication":"Developmental Cell","page":"360 - 375","article_type":"original","date_published":"2018-08-06T00:00:00Z"},{"ddc":["575"],"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","status":"public","intvolume":" 69","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"42","file":[{"content_type":"application/pdf","file_size":1292128,"creator":"dernst","file_name":"2018_JournalExperimBotany_Cucinotta.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T10:44:16Z","checksum":"ca3b6711040b1662488aeb3d1f961f13","relation":"main_file","file_id":"5691"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield.","lang":"eng"}],"issue":"21","page":"5169 - 5176","publication":"Journal of Experimental Botany","citation":{"ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281."},"date_published":"2018-07-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Oxford University Press","acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","year":"2018","date_updated":"2023-09-11T12:52:03Z","date_created":"2018-12-11T11:44:19Z","volume":69,"author":[{"full_name":"Cucinotta, Mara","last_name":"Cucinotta","first_name":"Mara"},{"last_name":"Manrique","first_name":"Silvia","full_name":"Manrique, Silvia"},{"full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Colombo, Lucia","first_name":"Lucia","last_name":"Colombo"}],"file_date_updated":"2020-07-14T12:46:25Z","publist_id":"8012","quality_controlled":"1","isi":1,"external_id":{"isi":["000448163900015"]},"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":"10.1093/jxb/ery281","month":"07"}]