[{"year":"2020","date_updated":"2023-09-05T15:10:02Z","day":"29","_id":"10865","date_published":"2020-04-29T00:00:00Z","month":"04","place":"Cham","citation":{"apa":"Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110, pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","ieee":"S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246.","chicago":"Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.","mla":"Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:10.1007/978-3-030-45374-9_8.","ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246.","ama":"Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8"},"volume":12110,"type":"book_chapter","status":"public","editor":[{"last_name":"Kiayias","first_name":"A","full_name":"Kiayias, A"}],"publication_status":"published","series_title":"LNCS","publication":"Public-Key Cryptography","acknowledgement":"We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project.","doi":"10.1007/978-3-030-45374-9_8","intvolume":" 12110","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030453732","9783030453749"]},"author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip"},{"full_name":"Prabhakaran, Manoj","first_name":"Manoj","last_name":"Prabhakaran"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"scopus_import":"1","page":"220-246","abstract":[{"lang":"eng","text":"We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) ."}],"article_processing_charge":"No","main_file_link":[{"url":"https://eprint.iacr.org/2020/090","open_access":"1"}],"title":"Witness maps and applications","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","quality_controlled":"1","oa":1,"date_created":"2022-03-18T11:35:51Z"},{"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"text":"We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem.","lang":"eng"}],"has_accepted_license":"1","page":"2143-2174","file":[{"file_name":"2020_LettersMathPhysics_Rademacher.pdf","date_created":"2020-11-20T12:04:26Z","success":1,"content_type":"application/pdf","file_id":"8784","date_updated":"2020-11-20T12:04:26Z","creator":"dernst","checksum":"3bdd41f10ad947b67a45b98f507a7d4a","file_size":478683,"access_level":"open_access","relation":"main_file"}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"isi":["000551556000006"]},"date_created":"2020-03-23T11:11:47Z","ec_funded":1,"ddc":["510"],"article_type":"original","oa":1,"oa_version":"Published Version","quality_controlled":"1","title":"Central limit theorem for Bose gases interacting through singular potentials","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2020-03-12T00:00:00Z","month":"03","department":[{"_id":"RoSe"}],"isi":1,"_id":"7611","day":"12","date_updated":"2023-09-05T15:14:50Z","year":"2020","file_date_updated":"2020-11-20T12:04:26Z","author":[{"orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"intvolume":" 110","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publication":"Letters in Mathematical Physics","doi":"10.1007/s11005-020-01286-w","acknowledgement":"Simone Rademacher acknowledges partial support from the NCCR SwissMAP. This project has received\r\nfunding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nS.R. would like to thank Benjamin Schlein for many fruitful discussions.","publication_status":"published","type":"journal_article","volume":110,"status":"public","citation":{"short":"S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174.","apa":"Rademacher, S. A. E. (2020). Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01286-w","ieee":"S. A. E. Rademacher, “Central limit theorem for Bose gases interacting through singular potentials,” Letters in Mathematical Physics, vol. 110. Springer Nature, pp. 2143–2174, 2020.","mla":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics, vol. 110, Springer Nature, 2020, pp. 2143–74, doi:10.1007/s11005-020-01286-w.","chicago":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01286-w.","ama":"Rademacher SAE. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 2020;110:2143-2174. doi:10.1007/s11005-020-01286-w","ista":"Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"isi":["000508511600001"]},"file":[{"relation":"main_file","access_level":"open_access","file_size":537941,"checksum":"ab8130c6e68101f5a091d05324c36f08","creator":"dernst","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-02-10T08:18:14Z","file_name":"2020_EcologMono_Baskett.pdf","content_type":"application/pdf","file_id":"7469"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study."}],"article_processing_charge":"Yes (via OA deal)","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","oa_version":"Published Version","quality_controlled":"1","issue":"1","date_created":"2020-01-07T12:47:07Z","ec_funded":1,"ddc":["570"],"article_type":"original","oa":1,"day":"01","year":"2020","date_updated":"2023-09-05T15:43:19Z","date_published":"2020-02-01T00:00:00Z","month":"02","article_number":"e01397","department":[{"_id":"NiBa"}],"isi":1,"_id":"7236","volume":90,"type":"journal_article","status":"public","publication_status":"published","citation":{"apa":"Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020.","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397.","chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397.","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"file_date_updated":"2020-07-14T12:47:54Z","author":[{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"full_name":"Schroeder, Lucy","first_name":"Lucy","last_name":"Schroeder"},{"first_name":"Marjorie G.","last_name":"Weber","full_name":"Weber, Marjorie G."},{"full_name":"Schemske, Douglas W.","first_name":"Douglas W.","last_name":"Schemske"}],"publication":"Ecological Monographs","doi":"10.1002/ecm.1397","intvolume":" 90","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-9615"],"eissn":["1557-7015"]}},{"pmid":1,"external_id":{"isi":["000534092400001"],"pmid":["32350870"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants."}],"has_accepted_license":"1","file":[{"file_name":"2020_09_NewPhytologist_Zhang.pdf","date_created":"2020-11-24T12:19:38Z","file_id":"8799","content_type":"application/pdf","success":1,"file_size":3643395,"relation":"main_file","access_level":"open_access","date_updated":"2020-11-24T12:19:38Z","creator":"dernst","checksum":"8e8150dbbba8cb65b72f81d1f0864b8b"}],"page":"1406-1416","article_processing_charge":"Yes (via OA deal)","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"issue":"5","title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","oa_version":"Published Version","quality_controlled":"1","article_type":"original","ddc":["580"],"oa":1,"date_created":"2020-04-30T08:43:29Z","ec_funded":1,"year":"2020","date_updated":"2023-09-05T15:46:04Z","day":"01","isi":1,"department":[{"_id":"JiFr"}],"_id":"7697","date_published":"2020-09-01T00:00:00Z","month":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16629.","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:10.1111/nph.16629.","ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629","apa":"Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629","short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” New Phytologist, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020."},"volume":227,"type":"journal_article","status":"public","publication_status":"published","publication":"New Phytologist","doi":"10.1111/nph.16629","intvolume":" 227","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"file_date_updated":"2020-11-24T12:19:38Z","author":[{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956"},{"full_name":"Hartinger, Corinna","orcid":"0000-0003-1618-2737","first_name":"Corinna","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4","last_name":"Hartinger"},{"full_name":"Wang, Xiaojuan","last_name":"Wang","first_name":"Xiaojuan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}]},{"day":"01","date_updated":"2023-09-05T16:00:13Z","year":"2020","date_published":"2020-05-01T00:00:00Z","month":"05","isi":1,"department":[{"_id":"ChWo"}],"_id":"8765","publication_status":"published","type":"journal_article","volume":39,"status":"public","citation":{"apa":"Schreck, C., & Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13914","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” Computer Graphics Forum, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.13914.","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:10.1111/cgf.13914.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 2020;39(2):89-99. doi:10.1111/cgf.13914"},"file_date_updated":"2020-11-23T09:05:13Z","author":[{"full_name":"Schreck, Camille","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"keyword":["Computer Networks and Communications"],"intvolume":" 39","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"publication":"Computer Graphics Forum","doi":"10.1111/cgf.13914","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","scopus_import":"1","external_id":{"isi":["000548709600008"]},"article_processing_charge":"No","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate."}],"has_accepted_license":"1","file":[{"success":1,"content_type":"application/pdf","file_id":"8796","date_created":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","date_updated":"2020-11-23T09:05:13Z","creator":"dernst","checksum":"7605f605acd84d0942b48bc7a1c2d72e","file_size":38969122,"relation":"main_file","access_level":"open_access"}],"page":"89-99","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","quality_controlled":"1","title":"A practical method for animating anisotropic elastoplastic materials","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","issue":"2","date_created":"2020-11-17T09:35:10Z","ec_funded":1,"ddc":["000"],"article_type":"original","oa":1},{"oa":1,"ddc":["540","541"],"article_type":"original","date_created":"2020-06-29T16:15:49Z","issue":"37","quality_controlled":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","article_processing_charge":"No","page":"16047-16051","has_accepted_license":"1","abstract":[{"text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.","lang":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","file_size":1904552,"checksum":"7dd0a56f6bd5de08ea75b1ec388c91bc","creator":"dernst","date_updated":"2020-09-17T08:59:43Z","date_created":"2020-09-17T08:59:43Z","file_name":"2020_AngChemieDE_Bouchal.pdf","content_type":"application/pdf","file_id":"8401","success":1}],"scopus_import":"1","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"intvolume":" 132","language":[{"iso":"eng"}],"doi":"10.1002/ange.202005378","publication":"Angewandte Chemie","author":[{"last_name":"Bouchal","first_name":"Roza","full_name":"Bouchal, Roza"},{"first_name":"Zhujie","last_name":"Li","full_name":"Li, Zhujie"},{"last_name":"Bongu","first_name":"Chandra","full_name":"Bongu, Chandra"},{"first_name":"Steven","last_name":"Le Vot","full_name":"Le Vot, Steven"},{"full_name":"Berthelot, Romain","last_name":"Berthelot","first_name":"Romain"},{"full_name":"Rotenberg, Benjamin","first_name":"Benjamin","last_name":"Rotenberg"},{"first_name":"Frederic","last_name":"Favier","full_name":"Favier, Frederic"},{"last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Mathieu","last_name":"Salanne","full_name":"Salanne, Mathieu"},{"full_name":"Fontaine, Olivier","first_name":"Olivier","last_name":"Fontaine"}],"file_date_updated":"2020-09-17T08:59:43Z","citation":{"mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie, vol. 132, no. 37, Wiley, 2020, pp. 16047–51, doi:10.1002/ange.202005378.","chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Frederic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie. Wiley, 2020. https://doi.org/10.1002/ange.202005378.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 2020;132(37):16047-16051. doi:10.1002/ange.202005378","ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 132(37), 16047–16051.","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202005378","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie 132 (2020) 16047–16051.","ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie, vol. 132, no. 37. Wiley, pp. 16047–16051, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","status":"public","volume":132,"type":"journal_article","_id":"8057","department":[{"_id":"StFr"}],"month":"09","date_published":"2020-09-07T00:00:00Z","date_updated":"2023-09-05T15:47:50Z","year":"2020","day":"07"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Social immunity modulates competition between coinfecting pathogens","oa_version":"Published Version","quality_controlled":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"issue":"3","ec_funded":1,"date_created":"2020-01-20T13:32:12Z","oa":1,"ddc":["570"],"article_type":"letter_note","scopus_import":"1","external_id":{"isi":["000507515900001"]},"page":"565-574","has_accepted_license":"1","abstract":[{"text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.","lang":"eng"}],"file":[{"date_created":"2020-11-19T11:27:10Z","file_name":"2020_EcologyLetters_Milutinovic.pdf","success":1,"content_type":"application/pdf","file_id":"8776","date_updated":"2020-11-19T11:27:10Z","checksum":"0cd8be386fa219db02845b7c3991ce04","creator":"dernst","file_size":561749,"access_level":"open_access","relation":"main_file"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","volume":23,"publication_status":"published","citation":{"ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 565–574, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574.","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13458","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 2020;23(3):565-574. doi:10.1111/ele.13458","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574.","mla":"Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:10.1111/ele.13458.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13458."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic"},{"full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"file_date_updated":"2020-11-19T11:27:10Z","doi":"10.1111/ele.13458","acknowledgement":"We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). ","publication":"Ecology Letters","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"language":[{"iso":"eng"}],"intvolume":" 23","day":"01","related_material":{"record":[{"relation":"research_data","id":"13060","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/","description":"News on IST Homepage","relation":"press_release"}]},"year":"2020","date_updated":"2023-09-05T16:04:49Z","month":"03","date_published":"2020-03-01T00:00:00Z","_id":"7343","isi":1,"department":[{"_id":"SyCr"},{"_id":"KrCh"}]},{"publication_status":"published","status":"public","volume":20,"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020."},"author":[{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Gammerdinger"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"file_date_updated":"2020-11-26T11:46:43Z","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"language":[{"iso":"eng"}],"intvolume":" 20","doi":"10.1111/1755-0998.13210","publication":"Molecular Ecology Resources","day":"01","date_updated":"2023-09-05T16:07:08Z","year":"2020","month":"11","date_published":"2020-11-01T00:00:00Z","_id":"8099","department":[{"_id":"BeVi"}],"isi":1,"oa_version":"Published Version","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Disagreement in FST estimators: A case study from sex chromosomes","issue":"6","ec_funded":1,"date_created":"2020-07-07T08:56:16Z","oa":1,"article_type":"original","ddc":["570"],"scopus_import":"1","external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"pmid":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"article_processing_charge":"Yes (via OA deal)","file":[{"file_size":820428,"relation":"main_file","access_level":"open_access","date_updated":"2020-11-26T11:46:43Z","creator":"dernst","checksum":"3d87ebb8757dcd504f20c618b72e6575","file_id":"8814","content_type":"application/pdf","success":1,"file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","date_created":"2020-11-26T11:46:43Z"}],"abstract":[{"text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.","lang":"eng"}],"page":"1517-1525","has_accepted_license":"1"},{"status":"public","volume":59,"type":"journal_article","publication_status":"published","citation":{"ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie International Edition, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020.","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition 59 (2020) 15913–1591.","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202005378","ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 59(37), 15913–1591.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 2020;59(37):15913-1591. doi:10.1002/anie.202005378","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition, vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:10.1002/anie.202005378.","chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202005378."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"first_name":"Roza","last_name":"Bouchal","full_name":"Bouchal, Roza"},{"first_name":"Zhujie","last_name":"Li","full_name":"Li, Zhujie"},{"first_name":"Chandra","last_name":"Bongu","full_name":"Bongu, Chandra"},{"full_name":"Le Vot, Steven","first_name":"Steven","last_name":"Le Vot"},{"last_name":"Berthelot","first_name":"Romain","full_name":"Berthelot, Romain"},{"last_name":"Rotenberg","first_name":"Benjamin","full_name":"Rotenberg, Benjamin"},{"full_name":"Favier, Fréderic","first_name":"Fréderic","last_name":"Favier"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Salanne, Mathieu","first_name":"Mathieu","last_name":"Salanne"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"}],"file_date_updated":"2020-09-17T08:57:16Z","doi":"10.1002/anie.202005378","publication":"Angewandte Chemie International Edition","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"language":[{"iso":"eng"}],"intvolume":" 59","day":"07","year":"2020","date_updated":"2023-09-05T16:02:53Z","month":"09","date_published":"2020-09-07T00:00:00Z","_id":"7847","isi":1,"department":[{"_id":"StFr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","quality_controlled":"1","oa_version":"Published Version","issue":"37","date_created":"2020-05-14T21:00:30Z","oa":1,"ddc":["540","546"],"article_type":"original","scopus_import":"1","external_id":{"pmid":["32390281"],"isi":["000541488700001"]},"pmid":1,"abstract":[{"lang":"eng","text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of 'free' and 'bound' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. "}],"has_accepted_license":"1","page":"15913-1591","file":[{"date_created":"2020-09-17T08:57:16Z","file_name":"2020_AngChemieINT_Buchal.pdf","success":1,"file_id":"8400","content_type":"application/pdf","date_updated":"2020-09-17T08:57:16Z","checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d","creator":"dernst","file_size":1966184,"relation":"main_file","access_level":"open_access"}],"article_processing_charge":"No"},{"scopus_import":"1","external_id":{"isi":["000503625200001"]},"file":[{"date_updated":"2020-07-14T12:47:54Z","creator":"dernst","checksum":"372f67f2744f4b6049e9778364766c22","file_size":3005474,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7486","date_created":"2020-02-14T12:02:50Z","file_name":"2020_EcologyLetters_Rybicki.pdf"}],"has_accepted_license":"1","page":"506-517","abstract":[{"lang":"eng","text":"Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity."}],"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"title":"Habitat fragmentation and species diversity in competitive communities","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa_version":"Published Version","issue":"3","date_created":"2020-01-04T11:04:30Z","ec_funded":1,"article_type":"original","ddc":["000"],"oa":1,"day":"01","year":"2020","date_updated":"2023-09-05T16:04:30Z","date_published":"2020-03-01T00:00:00Z","month":"03","department":[{"_id":"DaAl"}],"isi":1,"_id":"7224","volume":23,"type":"journal_article","status":"public","publication_status":"published","citation":{"chicago":"Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450.","mla":"Rybicki, Joel, et al. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 506–17, doi:10.1111/ele.13450.","ama":"Rybicki J, Abrego N, Ovaskainen O. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 2020;23(3):506-517. doi:10.1111/ele.13450","ista":"Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517.","apa":"Rybicki, J., Abrego, N., & Ovaskainen, O. (2020). Habitat fragmentation and species diversity in competitive communities. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13450","short":"J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517.","ieee":"J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:47:54Z","author":[{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"full_name":"Abrego, Nerea","last_name":"Abrego","first_name":"Nerea"},{"first_name":"Otso","last_name":"Ovaskainen","full_name":"Ovaskainen, Otso"}],"publication":"Ecology Letters","doi":"10.1111/ele.13450","language":[{"iso":"eng"}],"intvolume":" 23","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]}},{"year":"2020","date_updated":"2023-09-05T16:03:47Z","day":"14","related_material":{"record":[{"relation":"research_data","id":"9780","status":"public"}]},"_id":"8329","isi":1,"department":[{"_id":"StFr"}],"month":"12","date_published":"2020-12-14T00:00:00Z","citation":{"mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253.","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253","ieee":"W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020."},"status":"public","type":"journal_article","volume":59,"publication_status":"published","doi":"10.1002/anie.202008253","acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","publication":"Angewandte Chemie International Edition","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"intvolume":" 59","language":[{"iso":"eng"}],"author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"first_name":"Philipp","last_name":"Nothdurft","full_name":"Nothdurft, Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"full_name":"Frühwirt, Philipp","last_name":"Frühwirt","first_name":"Philipp"},{"first_name":"Max","last_name":"Schmallegger","full_name":"Schmallegger, Max"},{"last_name":"Gescheidt-Demner","first_name":"Georg","full_name":"Gescheidt-Demner, Georg"},{"first_name":"Roland","last_name":"Fischer","full_name":"Fischer, Roland"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger"},{"full_name":"Kern, Wolfgang","last_name":"Kern","first_name":"Wolfgang"},{"last_name":"Spirk","first_name":"Stefan","full_name":"Spirk, Stefan"}],"external_id":{"isi":["000576148700001"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles."}],"page":"22943-22946","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1002/anie.202008253","open_access":"1"}],"issue":"51","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","oa_version":"Published Version","quality_controlled":"1","oa":1,"article_type":"original","date_created":"2020-09-03T16:10:56Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.crjdfn318"}],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"citation":{"ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020)."},"publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Social immunity modulates competition between coinfecting pathogens","type":"research_data_reference","oa_version":"Published Version","doi":"10.5061/DRYAD.CRJDFN318","oa":1,"ddc":["570"],"date_created":"2023-05-23T16:11:22Z","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic"},{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","date_updated":"2023-09-05T16:04:48Z","day":"19","related_material":{"record":[{"relation":"used_in_publication","id":"7343","status":"public"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"_id":"13060","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"article_processing_charge":"No","month":"12","date_published":"2020-12-19T00:00:00Z"},{"oa":1,"doi":"10.5517/ccdc.csd.cc24vsrk","author":[{"full_name":"Schlemmer, Werner","first_name":"Werner","last_name":"Schlemmer"},{"full_name":"Nothdurft, Philipp","last_name":"Nothdurft","first_name":"Philipp"},{"last_name":"Petzold","first_name":"Alina","full_name":"Petzold, Alina"},{"full_name":"Riess, Gisbert","first_name":"Gisbert","last_name":"Riess"},{"full_name":"Frühwirt, Philipp","first_name":"Philipp","last_name":"Frühwirt"},{"first_name":"Max","last_name":"Schmallegger","full_name":"Schmallegger, Max"},{"last_name":"Gescheidt-Demner","first_name":"Georg","full_name":"Gescheidt-Demner, Georg"},{"full_name":"Fischer, Roland","last_name":"Fischer","first_name":"Roland"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger"},{"first_name":"Wolfgang","last_name":"Kern","full_name":"Kern, Wolfgang"},{"full_name":"Spirk, Stefan","first_name":"Stefan","last_name":"Spirk"}],"date_created":"2021-08-06T07:41:07Z","citation":{"ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.","mla":"Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.","ieee":"W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk"},"main_file_link":[{"open_access":"1","url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk"}],"oa_version":"Published Version","type":"research_data_reference","title":"CCDC 1991959: Experimental Crystal Structure Determination","status":"public","publisher":"CCDC","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","department":[{"_id":"StFr"}],"_id":"9780","abstract":[{"lang":"eng","text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"}],"date_published":"2020-03-22T00:00:00Z","month":"03","date_updated":"2023-09-05T16:03:47Z","year":"2020","related_material":{"record":[{"relation":"used_in_publication","id":"8329","status":"public"}]},"day":"22"},{"year":"2020","date_updated":"2023-09-06T14:48:01Z","day":"01","department":[{"_id":"RySh"}],"isi":1,"_id":"7207","date_published":"2020-05-01T00:00:00Z","month":"05","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802","ieee":"A. Martín-Belmonte et al., “Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease,” Brain Pathology, vol. 30, no. 3. Wiley, pp. 554–575, 2020.","mla":"Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:10.1111/bpa.12802.","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802.","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802"},"volume":30,"type":"journal_article","status":"public","publication_status":"published","publication":"Brain Pathology","doi":"10.1111/bpa.12802","language":[{"iso":"eng"}],"intvolume":" 30","publication_identifier":{"eissn":["17503639"],"issn":["10156305"]},"file_date_updated":"2020-09-22T09:47:19Z","author":[{"first_name":"Alejandro","last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro"},{"last_name":"Aguado","first_name":"Carolina","full_name":"Aguado, Carolina"},{"full_name":"Alfaro-Ruíz, Rocío","first_name":"Rocío","last_name":"Alfaro-Ruíz"},{"full_name":"Moreno-Martínez, Ana Esther","last_name":"Moreno-Martínez","first_name":"Ana Esther"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"full_name":"Martínez-Hernández, José","last_name":"Martínez-Hernández","first_name":"José"},{"full_name":"Buisson, Alain","first_name":"Alain","last_name":"Buisson"},{"first_name":"Simon","last_name":"Früh","full_name":"Früh, Simon"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"}],"pmid":1,"external_id":{"pmid":["31729777"],"isi":["000502270900001"]},"scopus_import":"1","has_accepted_license":"1","file":[{"date_created":"2020-09-22T09:47:19Z","file_name":"2020_BrainPathology_MartinBelmonte.pdf","success":1,"file_id":"8554","content_type":"application/pdf","date_updated":"2020-09-22T09:47:19Z","checksum":"549cc1b18f638a21d17a939ba5563fa9","creator":"dernst","file_size":4220935,"access_level":"open_access","relation":"main_file"}],"page":"554-575","abstract":[{"text":"The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.","lang":"eng"}],"article_processing_charge":"No","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907"}],"issue":"3","title":"Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","oa_version":"Published Version","quality_controlled":"1","article_type":"original","ddc":["570"],"oa":1,"date_created":"2019-12-22T23:00:43Z","ec_funded":1},{"date_updated":"2023-09-06T14:48:57Z","year":"2020","related_material":{"record":[{"status":"public","id":"13067","relation":"research_data"}]},"day":"01","_id":"7205","isi":1,"department":[{"_id":"NiBa"}],"month":"03","date_published":"2020-03-01T00:00:00Z","citation":{"ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570.","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","status":"public","volume":33,"type":"journal_article","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"language":[{"iso":"eng"}],"intvolume":" 33","doi":"10.1111/jeb.13570","publication":"Journal of Evolutionary Biology","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"file_date_updated":"2020-09-22T09:42:18Z","external_id":{"isi":["000500954800001"],"pmid":["31724256"]},"pmid":1,"scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"file":[{"file_size":885611,"relation":"main_file","access_level":"open_access","date_updated":"2020-09-22T09:42:18Z","checksum":"7534ff0839709c0c5265c12d29432f03","creator":"dernst","file_name":"2020_EvolBiology_Johannesson.pdf","date_created":"2020-09-22T09:42:18Z","file_id":"8553","content_type":"application/pdf","success":1}],"page":"342-351","has_accepted_license":"1","issue":"3","oa_version":"Published Version","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","oa":1,"article_type":"original","ddc":["570"],"date_created":"2019-12-22T23:00:43Z"},{"oa_version":"None","quality_controlled":"1","title":"Zebrafish gastrulation: Putting fate in motion","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-01-05T23:00:46Z","ec_funded":1,"scopus_import":"1","pmid":1,"external_id":{"pmid":["31959295"],"isi":["000611830600013"]},"article_processing_charge":"No","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601","_id":"2646861A-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03196","_id":"2608FC64-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of epithelial cell layer spreading in zebrafish"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"}],"page":"343-375","abstract":[{"lang":"eng","text":"Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation."}],"publication_status":"published","volume":136,"type":"book_chapter","status":"public","citation":{"ieee":"D. C. Nunes Pinheiro and C.-P. J. Heisenberg, “Zebrafish gastrulation: Putting fate in motion,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–375.","short":"D.C. Nunes Pinheiro, C.-P.J. Heisenberg, in:, Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 343–375.","apa":"Nunes Pinheiro, D. C., & Heisenberg, C.-P. J. (2020). Zebrafish gastrulation: Putting fate in motion. In Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 343–375). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.10.009","ama":"Nunes Pinheiro DC, Heisenberg C-PJ. Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Vol 136. Elsevier; 2020:343-375. doi:10.1016/bs.ctdb.2019.10.009","ista":"Nunes Pinheiro DC, Heisenberg C-PJ. 2020.Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Current Topics in Developmental Biology, vol. 136, 343–375.","mla":"Nunes Pinheiro, Diana C., and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–75, doi:10.1016/bs.ctdb.2019.10.009.","chicago":"Nunes Pinheiro, Diana C, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” In Gastrulation: From Embryonic Pattern to Form, 136:343–75. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.10.009."},"author":[{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"intvolume":" 136","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00702153"]},"publication":"Gastrulation: From Embryonic Pattern to Form","acknowledgement":"We thank Alexandra Schauer, Nicoletta Petridou and Feyza Nur Arslan for comments on the manuscript. Research in the Heisenberg laboratory is supported by an ERC Advanced Grant (MECSPEC 742573), ANR/FWF (I03601) and FWF/DFG (I03196) International Cooperation Grants. D. Pinheiro acknowledges a fellowship from EMBO ALTF (850-2017) and is currently supported by HFSP LTF (LT000429/2018-L2).","doi":"10.1016/bs.ctdb.2019.10.009","day":"01","date_updated":"2023-09-06T14:54:36Z","year":"2020","alternative_title":["Current Topics in Developmental Biology"],"date_published":"2020-06-01T00:00:00Z","month":"06","isi":1,"department":[{"_id":"CaHe"}],"_id":"7227"},{"_id":"7417","isi":1,"department":[{"_id":"JiFr"}],"month":"01","date_published":"2020-01-01T00:00:00Z","article_number":"e1687185","year":"2020","date_updated":"2023-09-06T15:23:04Z","day":"01","doi":"10.1080/15592324.2019.1687185","publication":"Plant Signaling & Behavior","publication_identifier":{"issn":["1559-2324"]},"language":[{"iso":"eng"}],"intvolume":" 15","author":[{"first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593"},{"first_name":"S.","last_name":"Gille","full_name":"Gille, S."},{"full_name":"Pauly, M.","first_name":"M.","last_name":"Pauly"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"citation":{"chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185.","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020).","apa":"Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020."},"status":"public","type":"journal_article","volume":15,"publication_status":"published","abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}],"article_processing_charge":"No","external_id":{"pmid":["31696770"],"isi":["000494907500001"]},"pmid":1,"scopus_import":"1","oa":1,"article_type":"original","date_created":"2020-01-30T10:14:14Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Informa UK Limited","title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","oa_version":"Submitted Version","quality_controlled":"1"},{"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","oa_version":"Published Version","date_created":"2019-03-28T10:21:15Z","ec_funded":1,"ddc":["530","510"],"article_type":"original","oa":1,"scopus_import":"1","external_id":{"arxiv":["1809.03971"],"isi":["000529483000001"]},"has_accepted_license":"1","file":[{"date_created":"2020-11-18T11:14:37Z","file_name":"2020_CommMathPhysics_Erdoes.pdf","success":1,"file_id":"8771","content_type":"application/pdf","date_updated":"2020-11-18T11:14:37Z","checksum":"c3a683e2afdcea27afa6880b01e53dc2","creator":"dernst","file_size":2904574,"relation":"main_file","access_level":"open_access"}],"page":"1203-1278","abstract":[{"lang":"eng","text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969)."}],"article_processing_charge":"Yes (via OA deal)","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"volume":378,"type":"journal_article","status":"public","publication_status":"published","citation":{"ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020.","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278.","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.","mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4.","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file_date_updated":"2020-11-18T11:14:37Z","author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder"}],"publication":"Communications in Mathematical Physics","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","doi":"10.1007/s00220-019-03657-4","language":[{"iso":"eng"}],"intvolume":" 378","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6179"}]},"year":"2020","date_updated":"2023-09-07T12:54:12Z","date_published":"2020-09-01T00:00:00Z","month":"09","isi":1,"department":[{"_id":"LaEr"}],"_id":"6185"},{"publication_status":"published","type":"dissertation","status":"public","citation":{"short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629"},"file_date_updated":"2020-07-14T12:48:01Z","author":[{"last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7629","degree_awarded":"PhD","day":"31","date_updated":"2023-09-07T13:03:12Z","year":"2020","alternative_title":["ISTA Thesis"],"date_published":"2020-03-31T00:00:00Z","month":"03","department":[{"_id":"JaMa"}],"_id":"7629","oa_version":"Published Version","title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"}],"date_created":"2020-04-02T06:40:23Z","ec_funded":1,"ddc":["510"],"oa":1,"article_processing_charge":"No","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"file":[{"content_type":"application/pdf","file_id":"7657","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf","relation":"main_file","access_level":"open_access","file_size":3297129,"checksum":"c814a1a6195269ca6fe48b0dca45ae8a","creator":"dernst","date_updated":"2020-07-14T12:48:01Z"},{"access_level":"closed","relation":"source_file","file_size":1063908,"checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","content_type":"application/x-zip-compressed","file_id":"7658","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z"}],"abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"page":"154","has_accepted_license":"1"},{"file":[{"success":1,"content_type":"application/pdf","file_id":"8575","date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","checksum":"20e71f015fbbd78fea708893ad634ed0","creator":"dernst","date_updated":"2020-09-28T07:25:35Z","relation":"main_file","access_level":"open_access","file_size":6354833},{"date_created":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip","content_type":"application/x-zip-compressed","file_id":"8576","file_size":23020401,"access_level":"closed","relation":"source_file","date_updated":"2020-09-28T07:25:37Z","checksum":"a8de2c14a1bb4e53c857787efbb289e1","creator":"dernst"}],"has_accepted_license":"1","page":"158","abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","title":"Local adaptation in metapopulations","oa_version":"Published Version","oa":1,"ddc":["570"],"date_created":"2020-09-28T07:33:38Z","year":"2020","date_updated":"2023-09-07T13:11:39Z","day":"20","degree_awarded":"PhD","_id":"8574","department":[{"_id":"NiBa"}],"month":"09","date_published":"2020-09-20T00:00:00Z","alternative_title":["ISTA Thesis"],"citation":{"ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020."},"status":"public","type":"dissertation","publication_status":"published","doi":"10.15479/AT:ISTA:8574","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","full_name":"Szep, Eniko"}],"file_date_updated":"2020-09-28T07:25:37Z"},{"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","title":"The free energy of a dilute two-dimensional Bose gas","supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"ec_funded":1,"date_created":"2020-02-24T09:17:27Z","oa":1,"ddc":["510"],"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"article_processing_charge":"No","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"file":[{"date_created":"2020-02-24T09:15:06Z","file_name":"thesis.pdf","file_id":"7515","content_type":"application/pdf","file_size":1563429,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:59Z","creator":"dernst","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6"},{"date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","file_id":"7516","creator":"dernst","checksum":"ad7425867b52d7d9e72296e87bc9cb67","date_updated":"2020-07-14T12:47:59Z","access_level":"closed","relation":"source_file","file_size":2028038}],"page":"148","has_accepted_license":"1","publication_status":"published","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514."},"author":[{"full_name":"Mayer, Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"file_date_updated":"2020-07-14T12:47:59Z","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7514","related_material":{"record":[{"relation":"part_of_dissertation","id":"7524","status":"public"}]},"degree_awarded":"PhD","day":"24","date_updated":"2023-09-07T13:12:42Z","year":"2020","alternative_title":["ISTA Thesis"],"month":"02","date_published":"2020-02-24T00:00:00Z","_id":"7514","department":[{"_id":"RoSe"},{"_id":"GradSch"}]},{"department":[{"_id":"LeSa"}],"_id":"8353","date_published":"2020-09-09T00:00:00Z","month":"09","alternative_title":["ISTA Thesis"],"year":"2020","date_updated":"2023-09-07T13:14:09Z","day":"09","related_material":{"record":[{"relation":"part_of_dissertation","id":"8284","status":"public"}]},"degree_awarded":"PhD","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","doi":"10.15479/AT:ISTA:8353","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-09-16T12:40:56Z","author":[{"last_name":"Steiner","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia"}],"citation":{"mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020."},"type":"dissertation","status":"public","publication_status":"published","file":[{"content_type":"application/pdf","file_id":"8354","date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf","creator":"jsteiner","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","access_level":"open_access","relation":"main_file","file_size":117547589},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8355","file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z","file_size":223328668,"relation":"source_file","access_level":"closed","date_updated":"2020-09-15T08:48:37Z","checksum":"ba112f957b7145462d0ab79044873ee9","creator":"jsteiner"}],"has_accepted_license":"1","abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"page":"191","article_processing_charge":"No","project":[{"name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741"}],"ddc":["572"],"oa":1,"date_created":"2020-09-09T14:27:01Z","supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa_version":"None"},{"date_updated":"2023-09-07T13:13:05Z","year":"2020","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7643"}]},"degree_awarded":"PhD","day":"30","_id":"8589","department":[{"_id":"JiFr"}],"alternative_title":["ISTA Thesis"],"month":"09","date_published":"2020-09-30T00:00:00Z","citation":{"chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020."},"publication_status":"published","status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","doi":"10.15479/AT:ISTA:8589","author":[{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han"}],"file_date_updated":"2021-10-01T13:33:02Z","article_processing_charge":"No","file":[{"file_name":"2020_Han_Thesis.docx","date_created":"2020-09-30T14:50:20Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8590","file_size":49198118,"relation":"source_file","access_level":"closed","date_updated":"2020-09-30T14:50:20Z","checksum":"c4bda1947d4c09c428ac9ce667b02327","creator":"dernst"},{"access_level":"open_access","relation":"main_file","file_size":15513963,"checksum":"3f4f5d1718c2230adf30639ecaf8a00b","creator":"dernst","date_updated":"2021-10-01T13:33:02Z","file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z","content_type":"application/pdf","file_id":"8591"}],"page":"164","has_accepted_license":"1","abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Novel insights into PIN polarity regulation during Arabidopsis development","oa":1,"ddc":["580"],"date_created":"2020-09-30T14:50:51Z"},{"article_number":"e59407","month":"07","date_published":"2020-07-31T00:00:00Z","_id":"8284","isi":1,"department":[{"_id":"LeSa"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8353"}]},"day":"31","date_updated":"2023-09-07T13:14:08Z","year":"2020","author":[{"last_name":"Steiner","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia"},{"last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"file_date_updated":"2020-08-24T13:31:53Z","publication_identifier":{"eissn":["2050084X"]},"intvolume":" 9","language":[{"iso":"eng"}],"doi":"10.7554/eLife.59407","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","publication":"eLife","publication_status":"published","status":"public","type":"journal_article","volume":9,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407."},"project":[{"grant_number":"24741","_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"article_processing_charge":"No","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"8289","success":1,"date_created":"2020-08-24T13:31:53Z","file_name":"2020_eLife_Steiner.pdf","file_size":7320493,"access_level":"open_access","relation":"main_file","date_updated":"2020-08-24T13:31:53Z","creator":"cziletti","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15"}],"abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"scopus_import":"1","external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"pmid":1,"date_created":"2020-08-24T06:24:04Z","oa":1,"ddc":["570"],"article_type":"original","oa_version":"Published Version","quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter"},{"oa":1,"ddc":["530","570"],"date_created":"2020-07-23T09:51:28Z","supervisor":[{"last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Gene regulation across scales – how biophysical constraints shape evolution","oa_version":"Published Version","file":[{"date_updated":"2020-07-27T12:00:07Z","creator":"rgrah","file_size":16638998,"relation":"main_file","access_level":"open_access","success":1,"file_id":"8176","content_type":"application/pdf","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf"},{"access_level":"closed","relation":"main_file","file_size":347459978,"creator":"rgrah","date_updated":"2020-07-30T13:04:55Z","file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","file_id":"8177","content_type":"application/zip"}],"abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"page":"310","has_accepted_license":"1","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","doi":"10.15479/AT:ISTA:8155","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"file_date_updated":"2020-07-30T13:04:55Z","citation":{"ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155"},"status":"public","type":"dissertation","publication_status":"published","_id":"8155","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"month":"07","date_published":"2020-07-24T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2020","date_updated":"2023-09-07T13:13:27Z","day":"24","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"7675","relation":"part_of_dissertation"},{"status":"public","id":"7569","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7652","status":"public"}]}},{"publication":"Plant Physiology","doi":"10.1104/pp.20.00212","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","intvolume":" 183","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"},{"full_name":"Rakusova, Hana","first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova"},{"last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"citation":{"short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212.","chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40."},"type":"journal_article","volume":183,"status":"public","publication_status":"published","isi":1,"department":[{"_id":"JiFr"}],"_id":"7643","date_published":"2020-05-08T00:00:00Z","month":"05","year":"2020","date_updated":"2023-09-07T13:13:04Z","day":"08","related_material":{"record":[{"id":"8589","relation":"dissertation_contains","status":"public"}]},"article_type":"letter_note","oa":1,"date_created":"2020-04-06T10:06:40Z","ec_funded":1,"issue":"5","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa_version":"Published Version","page":"37-40","article_processing_charge":"No","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"pmid":1,"external_id":{"pmid":["32107280"],"isi":["000536641800018"]},"scopus_import":"1"},{"status":"public","publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Normative models of enhancer function","type":"preprint","oa_version":"Preprint","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"citation":{"short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405."},"date_created":"2020-04-23T10:12:51Z","author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"doi":"10.1101/2020.04.08.029405","publication":"bioRxiv","oa":1,"language":[{"iso":"eng"}],"day":"09","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8155"}]},"year":"2020","date_updated":"2023-09-07T13:13:26Z","month":"04","date_published":"2020-04-09T00:00:00Z","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology."}],"project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"_id":"7675","article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"title":"The hole system of triangulated shapes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ddc":["514"],"oa":1,"date_created":"2020-02-06T14:56:53Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"relation":"main_file","access_level":"open_access","file_size":76195184,"creator":"koelsboe","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","date_updated":"2020-07-14T12:47:58Z","file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","content_type":"application/pdf","file_id":"7461"},{"file_size":122103715,"access_level":"closed","relation":"source_file","date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","checksum":"7a52383c812b0be64d3826546509e5a4","file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","file_id":"7462","description":"latex source files, figures","content_type":"application/x-zip-compressed"}],"page":"155","has_accepted_license":"1","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"citation":{"mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020."},"type":"dissertation","status":"public","publication_status":"published","doi":"10.15479/AT:ISTA:7460","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"file_date_updated":"2020-07-14T12:47:58Z","author":[{"orcid":"0000-0002-4672-8297","full_name":"Ölsböck, Katharina","last_name":"Ölsböck","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","date_updated":"2023-09-07T13:15:30Z","day":"10","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6608"}]},"degree_awarded":"PhD","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"_id":"7460","date_published":"2020-02-10T00:00:00Z","month":"02","alternative_title":["ISTA Thesis"]},{"supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"On the average-case hardness of total search problems","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","ddc":["000"],"oa":1,"date_created":"2020-05-26T14:08:55Z","ec_funded":1,"abstract":[{"lang":"eng","text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. "}],"file":[{"relation":"main_file","access_level":"open_access","file_size":1622742,"checksum":"b39e2e1c376f5819b823fb7077491c64","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","file_id":"7897","file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z"},{"file_name":"Thesis_Kamath.zip","date_created":"2020-05-26T14:08:23Z","file_id":"7898","content_type":"application/x-zip-compressed","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","relation":"source_file","access_level":"closed","file_size":15301529}],"page":"126","has_accepted_license":"1","article_processing_charge":"No","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896."},"type":"dissertation","status":"public","publication_status":"published","doi":"10.15479/AT:ISTA:7896","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-07-14T12:48:04Z","author":[{"full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg"}],"year":"2020","date_updated":"2023-09-07T13:15:55Z","day":"25","related_material":{"record":[{"relation":"part_of_dissertation","id":"6677","status":"public"}]},"degree_awarded":"PhD","department":[{"_id":"KrPi"}],"_id":"7896","date_published":"2020-05-25T00:00:00Z","month":"05","alternative_title":["ISTA Thesis"]},{"publication_status":"published","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","location":" Snowmass Village, CO, United States","end_date":"2020-03-05"},"status":"public","type":"conference","citation":{"ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288.","chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","apa":"Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288"},"author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"publication_identifier":{"isbn":["9781728165530"]},"language":[{"iso":"eng"}],"doi":"10.1109/WACV45572.2020.9093288","publication":"IEEE Winter Conference on Applications of Computer Vision","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"id":"8390","relation":"dissertation_contains","status":"public"}]},"day":"01","date_updated":"2023-09-07T13:16:17Z","year":"2020","article_number":"1716-1725","month":"03","date_published":"2020-03-01T00:00:00Z","_id":"7936","department":[{"_id":"ChLa"}],"oa_version":"Preprint","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","title":"Localizing grouped instances for efficient detection in low-resource scenarios","main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"date_created":"2020-06-07T22:00:53Z","oa":1,"scopus_import":1,"external_id":{"arxiv":["2004.12623"]},"article_processing_charge":"No","abstract":[{"text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures.","lang":"eng"}]},{"abstract":[{"text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning.","lang":"eng"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.11995"]},"scopus_import":"1","oa":1,"date_created":"2020-06-07T22:00:53Z","main_file_link":[{"url":"http://arxiv.org/abs/2008.11995","open_access":"1"}],"title":"A flexible selection scheme for minimum-effort transfer learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"ChLa"}],"_id":"7937","date_published":"2020-03-01T00:00:00Z","month":"03","article_number":"2180-2189","year":"2020","date_updated":"2023-09-07T13:16:17Z","day":"01","related_material":{"record":[{"status":"deleted","relation":"dissertation_contains","id":"8331"},{"status":"public","relation":"dissertation_contains","id":"8390"}]},"publication":"2020 IEEE Winter Conference on Applications of Computer Vision","doi":"10.1109/WACV45572.2020.9093635","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728165530"]},"author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"citation":{"short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635.","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635.","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635"},"type":"conference","status":"public","publication_status":"published","conference":{"end_date":"2020-03-05","name":"WACV: Winter Conference on Applications of Computer Vision","location":"Snowmass Village, CO, United States","start_date":"2020-03-01"}},{"abstract":[{"text":"Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach.","lang":"eng"}],"page":"48-56","article_processing_charge":"No","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"scopus_import":"1","date_created":"2020-08-02T22:00:58Z","title":"Multiple-environment Markov decision processes: Efficient analysis and applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for the Advancement of Artificial Intelligence","oa_version":"None","quality_controlled":"1","date_published":"2020-06-01T00:00:00Z","month":"06","department":[{"_id":"KrCh"}],"_id":"8193","day":"01","related_material":{"record":[{"relation":"dissertation_contains","id":"8390","status":"public"}]},"year":"2020","date_updated":"2023-09-07T13:16:18Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin"},{"full_name":"Karkhanis, Deep","last_name":"Karkhanis","first_name":"Deep"},{"last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"}],"publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y.","intvolume":" 30","language":[{"iso":"eng"}],"publication_identifier":{"issn":["23340835"],"eissn":["23340843"]},"type":"conference","volume":30,"status":"public","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"Nancy, France","start_date":"2020-10-26","end_date":"2020-10-30"},"publication_status":"published","citation":{"apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., & Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In Proceedings of the 30th International Conference on Automated Planning and Scheduling (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","short":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","ieee":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in Proceedings of the 30th International Conference on Automated Planning and Scheduling, Nancy, France, 2020, vol. 30, pp. 48–56.","mla":"Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” Proceedings of the 30th International Conference on Automated Planning and Scheduling, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In Proceedings of the 30th International Conference on Automated Planning and Scheduling, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020.","ista":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56.","ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: Proceedings of the 30th International Conference on Automated Planning and Scheduling. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56."}},{"year":"2020","date_updated":"2023-09-07T13:16:18Z","day":"08","related_material":{"record":[{"status":"deleted","relation":"dissertation_contains","id":"8331"},{"relation":"dissertation_contains","id":"8390","status":"public"}]},"_id":"8092","department":[{"_id":"ChLa"}],"month":"01","date_published":"2020-01-08T00:00:00Z","citation":{"chicago":"Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.","mla":"Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3.","ista":"Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49.","ama":"Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3","short":"A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49.","apa":"Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3","ieee":"A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49."},"status":"public","editor":[{"last_name":"Singh","first_name":"Richa","full_name":"Singh, Richa"},{"full_name":"Vatsa, Mayank","first_name":"Mayank","last_name":"Vatsa"},{"last_name":"Patel","first_name":"Vishal M.","full_name":"Patel, Vishal M."},{"full_name":"Ratha, Nalini","last_name":"Ratha","first_name":"Nalini"}],"type":"book_chapter","publication_status":"published","doi":"10.1007/978-3-030-30671-7_3","publication":"Domain Adaptation for Visual Understanding","publication_identifier":{"isbn":["9783030306717"]},"language":[{"iso":"eng"}],"author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705"},{"last_name":"Bousmalis","first_name":"Konstantinos","full_name":"Bousmalis, Konstantinos"},{"full_name":"Gouws, Stephan","last_name":"Gouws","first_name":"Stephan"},{"full_name":"Bertsch, Fred","first_name":"Fred","last_name":"Bertsch"},{"full_name":"Mosseri, Inbar","first_name":"Inbar","last_name":"Mosseri"},{"last_name":"Cole","first_name":"Forrester","full_name":"Cole, Forrester"},{"last_name":"Murphy","first_name":"Kevin","full_name":"Murphy, Kevin"}],"external_id":{"arxiv":["1711.05139"]},"scopus_import":"1","page":"33-49","abstract":[{"text":"Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.","lang":"eng"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.05139"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","oa_version":"Preprint","quality_controlled":"1","oa":1,"date_created":"2020-07-05T22:00:46Z"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"7950","status":"public"},{"id":"5986","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","day":"09","date_updated":"2023-09-07T13:17:37Z","year":"2020","alternative_title":["ISTA Thesis"],"date_published":"2020-06-09T00:00:00Z","month":"06","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"_id":"7944","publication_status":"published","type":"dissertation","status":"public","citation":{"ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944."},"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"file_date_updated":"2020-07-14T12:48:05Z","author":[{"last_name":"Masárová","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"}],"keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-005-3"]},"doi":"10.15479/AT:ISTA:7944","license":"https://creativecommons.org/licenses/by-sa/4.0/","article_processing_charge":"No","file":[{"checksum":"df688bc5a82b50baee0b99d25fc7b7f0","creator":"zmasarov","date_updated":"2020-07-14T12:48:05Z","relation":"main_file","access_level":"open_access","file_size":13661779,"content_type":"application/pdf","file_id":"7945","file_name":"THESIS_Zuzka_Masarova.pdf","date_created":"2020-06-08T00:34:00Z"},{"date_updated":"2020-07-14T12:48:05Z","checksum":"45341a35b8f5529c74010b7af43ac188","creator":"zmasarov","file_size":32184006,"access_level":"closed","relation":"source_file","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","date_created":"2020-06-08T00:35:30Z","content_type":"application/zip","file_id":"7946"}],"abstract":[{"lang":"eng","text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars."}],"has_accepted_license":"1","page":"160","oa_version":"Published Version","title":"Reconfiguration problems","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-06-08T00:49:46Z","ddc":["516","514"],"oa":1},{"abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"article_processing_charge":"No","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"external_id":{"isi":["000530448300001"],"arxiv":["1912.02658"]},"date_created":"2020-09-30T10:33:17Z","ec_funded":1,"article_type":"original","oa":1,"title":"Intermolecular forces and correlations mediated by a phonon bath","publisher":"AIP Publishing","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa_version":"Preprint","issue":"16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"date_published":"2020-04-27T00:00:00Z","month":"04","article_number":"164302","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"isi":1,"_id":"8587","day":"27","related_material":{"record":[{"status":"public","id":"8958","relation":"dissertation_contains"}]},"year":"2020","date_updated":"2023-09-07T13:16:42Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"author":[{"full_name":"Li, Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang"},{"last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert"}],"publication":"The Journal of Chemical Physics","doi":"10.1063/1.5144759","acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868.","language":[{"iso":"eng"}],"intvolume":" 152","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"type":"journal_article","volume":152,"status":"public","publication_status":"published","citation":{"ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 2020;152(16). doi:10.1063/1.5144759","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:10.1063/1.5144759.","chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5144759.","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” The Journal of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020)."}},{"author":[{"full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","last_name":"Bezeljak"}],"file_date_updated":"2021-09-16T12:49:12Z","doi":"10.15479/AT:ISTA:8341","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"status":"public","type":"dissertation","publication_status":"published","citation":{"short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"month":"09","date_published":"2020-09-08T00:00:00Z","alternative_title":["ISTA Thesis"],"_id":"8341","department":[{"_id":"MaLo"}],"day":"08","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7580"}]},"degree_awarded":"PhD","year":"2020","date_updated":"2023-09-07T13:17:06Z","date_created":"2020-09-08T08:53:53Z","oa":1,"ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","title":"In vitro reconstitution of a Rab activation switch","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"page":"215","has_accepted_license":"1","file":[{"date_created":"2020-09-08T09:00:29Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","content_type":"application/x-zip-compressed","file_id":"8342","relation":"source_file","access_level":"closed","file_size":65246782,"creator":"dernst","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z"},{"date_created":"2020-09-08T09:00:27Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","content_type":"application/pdf","file_id":"8343","access_level":"open_access","relation":"main_file","file_size":31259058,"checksum":"59a62275088b00b7241e6ff4136434c7","creator":"dernst","date_updated":"2021-09-16T12:49:12Z"}],"abstract":[{"lang":"eng","text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level."}],"article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"issue":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Proceedings of the National Academy of Sciences","title":"Stochastic activation and bistability in a Rab GTPase regulatory network","oa_version":"Preprint","quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"article_type":"original","date_created":"2020-03-12T05:32:26Z","external_id":{"isi":["000521821800040"]},"scopus_import":"1","abstract":[{"text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell.","lang":"eng"}],"page":"6504-6549","project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"article_processing_charge":"No","citation":{"mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020."},"status":"public","type":"journal_article","volume":117,"publication_status":"published","doi":"10.1073/pnas.1921027117","publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"intvolume":" 117","author":[{"orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban"},{"full_name":"Loya, Hrushikesh","last_name":"Loya","first_name":"Hrushikesh"},{"full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saunders","first_name":"Timothy E.","full_name":"Saunders, Timothy E."},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"year":"2020","date_updated":"2023-09-07T13:17:06Z","day":"24","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8341"}]},"_id":"7580","isi":1,"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"month":"03","date_published":"2020-03-24T00:00:00Z"},{"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"oa_version":"Published Version","title":"Combinatorial width parameters for 3-dimensional manifolds","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"}],"date_created":"2020-06-26T10:00:36Z","ddc":["514"],"oa":1,"article_processing_charge":"No","page":"xviii+120","abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_id":"8034","file_name":"Kristof_Huszar-Thesis.pdf","date_created":"2020-06-26T10:03:58Z","file_size":2637562,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:08Z","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","creator":"khuszar"},{"file_name":"Kristof_Huszar-Thesis-source.zip","date_created":"2020-06-26T10:10:06Z","content_type":"application/x-zip-compressed","file_id":"8035","relation":"source_file","access_level":"closed","file_size":7163491,"creator":"khuszar","checksum":"d5f8456202b32f4a77552ef47a2837d1","date_updated":"2020-07-14T12:48:08Z"}],"has_accepted_license":"1","publication_status":"published","type":"dissertation","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032"},"file_date_updated":"2020-07-14T12:48:08Z","author":[{"last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8032","degree_awarded":"PhD","related_material":{"record":[{"relation":"dissertation_contains","id":"6556","status":"public"},{"relation":"dissertation_contains","id":"7093","status":"public"}]},"day":"26","date_updated":"2023-09-07T13:18:27Z","year":"2020","alternative_title":["ISTA Thesis"],"date_published":"2020-06-26T00:00:00Z","month":"06","department":[{"_id":"UlWa"}],"_id":"8032"},{"type":"conference","volume":12224,"status":"public","publication_status":"published","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: Computer Aided Verification. Vol 12224. Springer Nature; 2020:275-298. doi:10.1007/978-3-030-53288-8_14","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In Computer Aided Verification, 12224:275–98. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53288-8_14.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2020). Refinement for structured concurrent programs. In Computer Aided Verification (Vol. 12224, pp. 275–298). Springer Nature. https://doi.org/10.1007/978-3-030-53288-8_14"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file_date_updated":"2020-08-06T08:14:54Z","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"publication":"Computer Aided Verification","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","doi":"10.1007/978-3-030-53288-8_14","intvolume":" 12224","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783030532888"],"isbn":["9783030532871"],"eissn":["1611-3349"]},"day":"14","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"year":"2020","date_updated":"2023-09-07T13:18:00Z","date_published":"2020-07-14T00:00:00Z","month":"07","alternative_title":["LNCS"],"isi":1,"department":[{"_id":"ToHe"}],"_id":"8195","title":"Refinement for structured concurrent programs","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version","date_created":"2020-08-03T11:45:35Z","ddc":["000"],"oa":1,"scopus_import":"1","external_id":{"isi":["000695276000014"]},"page":"275-298","file":[{"date_created":"2020-08-06T08:14:54Z","file_name":"2020_LNCS_Kragl.pdf","content_type":"application/pdf","file_id":"8201","success":1,"file_size":804237,"relation":"main_file","access_level":"open_access","date_updated":"2020-08-06T08:14:54Z","creator":"dernst"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier."}],"article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}]},{"month":"06","date_published":"2020-06-01T00:00:00Z","_id":"8012","department":[{"_id":"ToHe"}],"isi":1,"day":"01","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"year":"2020","date_updated":"2023-09-07T13:18:00Z","author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl"},{"full_name":"Enea, Constantin","last_name":"Enea","first_name":"Constantin"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Suha Orhun","last_name":"Mutluergil","full_name":"Mutluergil, Suha Orhun"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"doi":"10.1145/3385412.3385980","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","publication_identifier":{"isbn":["9781450376136"]},"language":[{"iso":"eng"}],"status":"public","type":"conference","publication_status":"published","conference":{"end_date":"2020-06-20","name":"PLDI: Programming Language Design and Implementation","location":"London, United Kingdom","start_date":"2020-06-15"},"citation":{"ama":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980","ista":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. 2020. Inductive sequentialization of asynchronous programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 227–242.","chicago":"Kragl, Bernhard, Constantin Enea, Thomas A Henzinger, Suha Orhun Mutluergil, and Shaz Qadeer. “Inductive Sequentialization of Asynchronous Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 227–42. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385980.","mla":"Kragl, Bernhard, et al. “Inductive Sequentialization of Asynchronous Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–42, doi:10.1145/3385412.3385980.","ieee":"B. Kragl, C. Enea, T. A. Henzinger, S. O. Mutluergil, and S. Qadeer, “Inductive sequentialization of asynchronous programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 227–242.","apa":"Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980","short":"B. Kragl, C. Enea, T.A. Henzinger, S.O. Mutluergil, S. Qadeer, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–242."},"page":"227-242","abstract":[{"lang":"eng","text":"Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos."}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"article_processing_charge":"No","scopus_import":"1","external_id":{"isi":["000614622300016"]},"date_created":"2020-06-25T11:40:16Z","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","title":"Inductive sequentialization of asynchronous programs","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}]},{"date_created":"2020-09-10T09:26:49Z","oa":1,"ddc":["572"],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"page":"135","file":[{"checksum":"882f93fe9c351962120e2669b84bf088","creator":"pcaldas","date_updated":"2020-09-10T12:11:29Z","relation":"main_file","access_level":"open_access","file_size":141602462,"success":1,"file_id":"8364","content_type":"application/pdf","file_name":"phd_thesis_pcaldas.pdf","date_created":"2020-09-10T12:11:29Z"},{"content_type":"application/x-zip-compressed","file_id":"8365","file_name":"phd_thesis_latex_pcaldas.zip","date_created":"2020-09-10T12:18:17Z","creator":"pcaldas","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","date_updated":"2020-09-11T07:48:10Z","relation":"source_file","access_level":"closed","file_size":450437458}],"article_processing_charge":"No","author":[{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461"}],"file_date_updated":"2020-09-11T07:48:10Z","doi":"10.15479/AT:ISTA:8358","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"status":"public","type":"dissertation","publication_status":"published","citation":{"mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"09","date_published":"2020-09-10T00:00:00Z","alternative_title":["ISTA Thesis"],"_id":"8358","department":[{"_id":"MaLo"}],"day":"10","related_material":{"record":[{"relation":"dissertation_contains","id":"7572","status":"public"},{"relation":"part_of_dissertation","id":"7197","status":"public"}]},"degree_awarded":"PhD","year":"2020","date_updated":"2023-09-07T13:18:51Z"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"9056","status":"public"}]},"day":"26","date_updated":"2023-09-07T13:29:00Z","year":"2020","article_number":"75","alternative_title":["LIPIcs"],"month":"08","date_published":"2020-08-26T00:00:00Z","_id":"8703","department":[{"_id":"HeEd"}],"publication_status":"published","conference":{"end_date":"2020-09-09","start_date":"2020-09-07","location":"Virtual, Online; Pisa, Italy","name":"ESA: Annual European Symposium on Algorithms"},"status":"public","volume":173,"type":"conference","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"citation":{"apa":"Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in 28th Annual European Symposium on Algorithms, Virtual, Online; Pisa, Italy, 2020, vol. 173.","mla":"Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” 28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75.","chicago":"Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.75.","ista":"Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75.","ama":"Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75"},"author":[{"orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"},{"first_name":"Mael","last_name":"Rouxel-Labbé","full_name":"Rouxel-Labbé, Mael"},{"full_name":"Teillaud, Monique","first_name":"Monique","last_name":"Teillaud"}],"file_date_updated":"2020-10-27T14:31:52Z","publication_identifier":{"isbn":["9783959771627"],"issn":["18688969"]},"language":[{"iso":"eng"}],"intvolume":" 173","doi":"10.4230/LIPIcs.ESA.2020.75","publication":"28th Annual European Symposium on Algorithms","scopus_import":"1","license":"https://creativecommons.org/licenses/by/3.0/","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","has_accepted_license":"1","file":[{"checksum":"fe0f7c49a99ed870c671b911e10d5496","creator":"cziletti","date_updated":"2020-10-27T14:31:52Z","relation":"main_file","access_level":"open_access","file_size":733291,"success":1,"file_id":"8712","content_type":"application/pdf","date_created":"2020-10-27T14:31:52Z","file_name":"2020_LIPIcs_Osang.pdf"}],"abstract":[{"lang":"eng","text":"Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. "}],"quality_controlled":"1","oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Generalizing CGAL periodic Delaunay triangulations","ec_funded":1,"date_created":"2020-10-25T23:01:18Z","oa":1,"ddc":["000"]},{"related_material":{"link":[{"url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html","relation":"supplementary_material"}],"record":[{"id":"9418","relation":"dissertation_contains","status":"public"}]},"day":"26","date_updated":"2023-09-07T13:29:50Z","year":"2020","month":"04","date_published":"2020-04-26T00:00:00Z","_id":"7481","article_processing_charge":"No","department":[{"_id":"ChLa"}],"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:59Z","creator":"bphuong","checksum":"8d372ea5defd8cb8fdc430111ed754a9","file_size":405469,"relation":"main_file","access_level":"open_access","file_name":"main.pdf","date_created":"2020-02-11T09:07:27Z","content_type":"application/pdf","file_id":"7482"}],"abstract":[{"text":"We address the following question: How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact. Two such transformations are known for feed-forward architectures: permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations. For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling. The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest.","lang":"eng"}],"quality_controlled":"1","conference":{"end_date":"2020-04-30","start_date":"2020-04-27","location":"Online","name":"ICLR: International Conference on Learning Representations"},"oa_version":"Published Version","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"conference","title":"Functional vs. parametric equivalence of ReLU networks","citation":{"ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020."},"author":[{"last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"file_date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-11T09:07:37Z","oa":1,"ddc":["000"],"language":[{"iso":"eng"}],"publication":"8th International Conference on Learning Representations"},{"author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"language":[{"iso":"eng"}],"intvolume":" 52","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","doi":"10.1137/19m126284x","publication":"SIAM Journal on Mathematical Analysis","publication_status":"published","status":"public","volume":52,"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622, 2020.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","apa":"Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics , 2020, pp. 605–22, doi:10.1137/19m126284x.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x."},"month":"02","date_published":"2020-02-12T00:00:00Z","_id":"9781","isi":1,"department":[{"_id":"RoSe"}],"related_material":{"record":[{"id":"9733","relation":"dissertation_contains","status":"public"}]},"day":"12","date_updated":"2023-09-07T13:30:11Z","year":"2020","ec_funded":1,"date_created":"2021-08-06T07:34:16Z","oa":1,"article_type":"original","ddc":["510"],"quality_controlled":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Society for Industrial & Applied Mathematics ","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","main_file_link":[{"url":"https://arxiv.org/abs/1904.08647","open_access":"1"}],"issue":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"article_processing_charge":"No","page":"605-622","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum."}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]}},{"external_id":{"isi":["000511060200001"]},"scopus_import":"1","file":[{"file_size":1897571,"relation":"main_file","access_level":"open_access","date_updated":"2020-11-20T09:14:22Z","checksum":"f107e21b58f5930876f47144be37cf6c","creator":"dernst","date_created":"2020-11-20T09:14:22Z","file_name":"2020_ArchRatMechAn_Fischer.pdf","file_id":"8779","content_type":"application/pdf","success":1}],"page":"967-1087","has_accepted_license":"1","abstract":[{"text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","quality_controlled":"1","oa_version":"Published Version","oa":1,"article_type":"original","ddc":["530","532"],"ec_funded":1,"date_created":"2020-02-16T23:00:50Z","year":"2020","date_updated":"2023-09-07T13:30:45Z","day":"01","related_material":{"record":[{"status":"public","id":"10007","relation":"dissertation_contains"}]},"_id":"7489","department":[{"_id":"JuFi"}],"isi":1,"month":"05","date_published":"2020-05-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2.","mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2.","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087.","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 2020;236:967-1087. doi:10.1007/s00205-019-01486-2","apa":"Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” Archive for Rational Mechanics and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020."},"status":"public","type":"journal_article","volume":236,"publication_status":"published","doi":"10.1007/s00205-019-01486-2","publication":"Archive for Rational Mechanics and Analysis","publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"intvolume":" 236","language":[{"iso":"eng"}],"author":[{"last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"},{"last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"}],"file_date_updated":"2020-11-20T09:14:22Z"},{"article_processing_charge":"No","department":[{"_id":"JuFi"}],"_id":"10012","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable."}],"article_number":"2003.05478","date_published":"2020-03-11T00:00:00Z","month":"03","date_updated":"2023-09-07T13:30:45Z","year":"2020","external_id":{"arxiv":["2003.05478"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10007"}]},"day":"11","language":[{"iso":"eng"}],"oa":1,"publication":"arXiv","acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072"},{"last_name":"Laux","first_name":"Tim","full_name":"Laux, Tim"},{"first_name":"Thilo","last_name":"Simon","full_name":"Simon, Thilo"}],"date_created":"2021-09-13T12:17:11Z","ec_funded":1,"citation":{"short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","apa":"Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.","ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.","chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d.","ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv."},"main_file_link":[{"url":"https://arxiv.org/abs/2003.05478","open_access":"1"}],"oa_version":"Preprint","publication_status":"submitted","type":"preprint","title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"date_created":"2020-11-15T23:01:17Z","ec_funded":1,"article_type":"original","ddc":["530"],"oa":1,"title":"Surpassing the resistance quantum with a geometric superinductor","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","quality_controlled":"1","issue":"4","has_accepted_license":"1","abstract":[{"text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. ","lang":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","file_size":2607823,"checksum":"2a634abe75251ae7628cd54c8a4ce2e8","creator":"dernst","date_updated":"2021-03-29T11:43:20Z","date_created":"2021-03-29T11:43:20Z","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","file_id":"9300","content_type":"application/pdf","success":1}],"article_processing_charge":"No","project":[{"name":"Integrating superconducting quantum circuits","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"name":"Quantum readout techniques and technologies","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","external_id":{"isi":["000582797300003"],"arxiv":["2007.01644"]},"file_date_updated":"2021-03-29T11:43:20Z","author":[{"last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"publication":"Physical Review Applied","acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","doi":"10.1103/PhysRevApplied.14.044055","intvolume":" 14","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23317019"]},"volume":14,"type":"journal_article","status":"public","publication_status":"published","citation":{"ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” Physical Review Applied, vol. 14, no. 4. American Physical Society, 2020.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 2020;14(4). doi:10.1103/PhysRevApplied.14.044055","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055.","mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055."},"date_published":"2020-10-29T00:00:00Z","month":"10","article_number":"044055","department":[{"_id":"JoFi"}],"isi":1,"_id":"8755","day":"29","related_material":{"record":[{"relation":"research_data","id":"13070","status":"public"},{"status":"public","id":"9920","relation":"dissertation_contains"}]},"year":"2020","date_updated":"2023-09-07T13:31:22Z"},{"issue":"7","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"title":"Homogenisation of one-dimensional discrete optimal transport","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","quality_controlled":"1","article_type":"original","oa":1,"date_created":"2020-03-08T23:00:47Z","ec_funded":1,"external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport."}],"page":"204-234","article_processing_charge":"No","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"},{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"citation":{"ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008.","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008"},"volume":139,"type":"journal_article","status":"public","publication_status":"published","publication":"Journal de Mathematiques Pures et Appliquees","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","doi":"10.1016/j.matpur.2020.02.008","language":[{"iso":"eng"}],"intvolume":" 139","publication_identifier":{"issn":["00217824"]},"author":[{"last_name":"Gladbach","first_name":"Peter","full_name":"Gladbach, Peter"},{"last_name":"Kopfer","first_name":"Eva","full_name":"Kopfer, Eva"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale"}],"year":"2020","date_updated":"2023-09-07T13:31:05Z","day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10030"}]},"isi":1,"department":[{"_id":"JaMa"}],"_id":"7573","date_published":"2020-07-01T00:00:00Z","month":"07"},{"article_number":"2008.10962","date_published":"2020-08-25T00:00:00Z","month":"08","department":[{"_id":"JaMa"}],"article_processing_charge":"No","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"_id":"10022","abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}],"page":"33","related_material":{"record":[{"status":"public","relation":"later_version","id":"11739"},{"status":"public","relation":"dissertation_contains","id":"10030"}]},"day":"25","date_updated":"2023-09-07T13:31:05Z","year":"2020","external_id":{"arxiv":["2008.10962"]},"author":[{"last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale"}],"date_created":"2021-09-17T10:57:27Z","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"publication":"arXiv","acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","oa_version":"Preprint","publication_status":"submitted","type":"preprint","title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","citation":{"short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","apa":"Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. .","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d.","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962.","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10962"}]},{"scopus_import":"1","external_id":{"arxiv":["2002.10384"]},"page":"5416-5425","abstract":[{"lang":"eng","text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. "}],"has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"9120","success":1,"date_created":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf","relation":"main_file","access_level":"open_access","file_size":281286,"creator":"dernst","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","date_updated":"2021-02-15T09:00:01Z"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"article_processing_charge":"No","publisher":"ML Research Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"On the sample complexity of adversarial multi-source PAC learning","oa_version":"Published Version","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"date_created":"2020-11-05T15:25:58Z","oa":1,"ddc":["000"],"day":"12","related_material":{"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}],"record":[{"relation":"dissertation_contains","id":"10799","status":"public"}]},"year":"2020","date_updated":"2023-09-07T13:42:08Z","month":"07","date_published":"2020-07-12T00:00:00Z","_id":"8724","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"status":"public","type":"conference","volume":119,"conference":{"location":"Online","start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning","end_date":"2020-07-18"},"publication_status":"published","citation":{"ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.","short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425.","ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.","ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25.","chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020."},"author":[{"last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"},{"last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias","full_name":"Frantar, Elias"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"file_date_updated":"2021-02-15T09:00:01Z","acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","publication":"Proceedings of the 37th International Conference on Machine Learning","publication_identifier":{"issn":["2640-3498"]},"language":[{"iso":"eng"}],"intvolume":" 119"},{"external_id":{"isi":["000573298000001"]},"scopus_import":"1","article_processing_charge":"No","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Analytic and machine learning approaches to composite quantum impurities","grant_number":"25681","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"}],"file":[{"file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","date_created":"2020-10-12T12:18:47Z","success":1,"content_type":"application/pdf","file_id":"8650","creator":"dernst","checksum":"c9238fff422e7a957c3a0d559f756b3a","date_updated":"2020-10-12T12:18:47Z","relation":"main_file","access_level":"open_access","file_size":2725143}],"abstract":[{"lang":"eng","text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures."}],"has_accepted_license":"1","issue":"9","quality_controlled":"1","oa_version":"Published Version","title":"Detecting composite orders in layered models via machine learning","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IOP Publishing","article_type":"original","ddc":["530"],"oa":1,"date_created":"2020-10-11T22:01:14Z","ec_funded":1,"date_updated":"2023-09-07T13:44:16Z","year":"2020","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10759"}]},"day":"01","department":[{"_id":"MiLe"}],"isi":1,"_id":"8644","article_number":"093026","date_published":"2020-09-01T00:00:00Z","month":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020.","apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44.","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44."},"publication_status":"published","type":"journal_article","volume":22,"status":"public","intvolume":" 22","language":[{"iso":"eng"}],"publication_identifier":{"issn":["13672630"]},"publication":"New Journal of Physics","doi":"10.1088/1367-2630/abae44","acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","file_date_updated":"2020-10-12T12:18:47Z","author":[{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","last_name":"Defenu","full_name":"Defenu, N"},{"full_name":"Chiacchiera, S","last_name":"Chiacchiera","first_name":"S"},{"first_name":"A","last_name":"Trombettoni","full_name":"Trombettoni, A"},{"last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"}]},{"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","oa_version":"Published Version","quality_controlled":"1","issue":"12","ec_funded":1,"date_created":"2020-10-25T23:01:19Z","oa":1,"article_type":"original","ddc":["530"],"scopus_import":"1","external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"abstract":[{"lang":"eng","text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model."}],"has_accepted_license":"1","page":"4003-4025","file":[{"access_level":"open_access","relation":"main_file","file_size":469831,"checksum":"c12c9c1e6f08def245e42f3cb1d83827","creator":"cziletti","date_updated":"2020-10-27T12:49:04Z","file_id":"8711","content_type":"application/pdf","success":1,"date_created":"2020-10-27T12:49:04Z","file_name":"2020_Annales_Mysliwy.pdf"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","volume":21,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3.","mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3.","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3","ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025.","short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","apa":"Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3","ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020."},"author":[{"last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"file_date_updated":"2020-10-27T12:49:04Z","doi":"10.1007/s00023-020-00969-3","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","publication":"Annales Henri Poincare","publication_identifier":{"issn":["1424-0637"]},"intvolume":" 21","language":[{"iso":"eng"}],"day":"01","related_material":{"record":[{"id":"11473","relation":"dissertation_contains","status":"public"}]},"year":"2020","date_updated":"2023-09-07T13:43:51Z","month":"12","date_published":"2020-12-01T00:00:00Z","_id":"8705","department":[{"_id":"RoSe"}],"isi":1},{"issue":"6","quality_controlled":"1","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","article_type":"original","date_created":"2022-03-18T10:10:53Z","external_id":{"isi":["000555398600001"]},"scopus_import":"1","article_processing_charge":"No","page":"741-758","abstract":[{"lang":"eng","text":"We introduce in this paper AMT2.0, 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, which integrates timed regular expressions within signal temporal logic. 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. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance."}],"citation":{"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,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z","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.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z."},"publication_status":"published","status":"public","volume":22,"type":"journal_article","publication_identifier":{"eissn":["1433-2787"],"issn":["1433-2779"]},"language":[{"iso":"eng"}],"intvolume":" 22","doi":"10.1007/s10009-020-00582-z","publication":"International Journal on Software Tools for Technology Transfer","author":[{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Lebeltel, Olivier","first_name":"Olivier","last_name":"Lebeltel"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Ulus","first_name":"Dogan","full_name":"Ulus, Dogan"}],"keyword":["Information Systems","Software"],"date_updated":"2023-09-08T11:52:02Z","year":"2020","related_material":{"record":[{"relation":"earlier_version","id":"299","status":"public"}]},"day":"03","_id":"10861","isi":1,"department":[{"_id":"ToHe"}],"month":"08","date_published":"2020-08-03T00:00:00Z"},{"day":"01","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"year":"2020","date_updated":"2023-09-11T10:21:00Z","month":"12","date_published":"2020-12-01T00:00:00Z","_id":"14125","department":[{"_id":"FrLo"}],"status":"public","type":"journal_article","volume":36,"publication_status":"published","citation":{"mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. 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Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020."},"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"author":[{"full_name":"Stark, Stefan G","last_name":"Stark","first_name":"Stefan G"},{"last_name":"Ficek","first_name":"Joanna","full_name":"Ficek, Joanna"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"last_name":"Chevrier","first_name":"Stéphane","full_name":"Chevrier, Stéphane"},{"full_name":"Singer, Franziska","first_name":"Franziska","last_name":"Singer"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"full_name":"Al-Quaddoomi, Faisal S","first_name":"Faisal 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A","last_name":"Tuncel","full_name":"Tuncel, Mustafa A"},{"first_name":"Marina","last_name":"Tusup","full_name":"Tusup, Marina"},{"first_name":"Audrey Van","last_name":"Drogen","full_name":"Drogen, Audrey Van"},{"last_name":"Vetter","first_name":"Marcus","full_name":"Vetter, Marcus"},{"full_name":"Vlajnic, Tatjana","first_name":"Tatjana","last_name":"Vlajnic"},{"full_name":"Weber, Sandra","last_name":"Weber","first_name":"Sandra"},{"full_name":"Weber, Walter P","first_name":"Walter P","last_name":"Weber"},{"first_name":"Rebekka","last_name":"Wegmann","full_name":"Wegmann, Rebekka"},{"full_name":"Weller, Michael","first_name":"Michael","last_name":"Weller"},{"full_name":"Wendt, Fabian","first_name":"Fabian","last_name":"Wendt"},{"full_name":"Wey, Norbert","first_name":"Norbert","last_name":"Wey"},{"full_name":"Wicki, Andreas","last_name":"Wicki","first_name":"Andreas"},{"full_name":"Wollscheid, Bernd","last_name":"Wollscheid","first_name":"Bernd"},{"last_name":"Yu","first_name":"Shuqing","full_name":"Yu, Shuqing"},{"first_name":"Johanna","last_name":"Ziegler","full_name":"Ziegler, Johanna"},{"last_name":"Zimmermann","first_name":"Marc","full_name":"Zimmermann, Marc"},{"full_name":"Zoche, Martin","last_name":"Zoche","first_name":"Martin"},{"last_name":"Zuend","first_name":"Gregor","full_name":"Zuend, Gregor"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Lehmann, Kjong-Van","last_name":"Lehmann","first_name":"Kjong-Van"}],"doi":"10.1093/bioinformatics/btaa843","publication":"Bioinformatics","publication_identifier":{"eissn":["1367-4811"]},"intvolume":" 36","language":[{"iso":"eng"}],"extern":"1","scopus_import":"1","external_id":{"pmid":["33381818"]},"pmid":1,"abstract":[{"lang":"eng","text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively."}],"page":"i919-i927","article_processing_charge":"No","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"SCIM: Universal single-cell matching with unpaired feature sets","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"issue":"Supplement_2","date_created":"2023-08-21T12:28:20Z","oa":1,"article_type":"original"},{"status":"public","type":"conference","volume":34,"conference":{"end_date":"2020-02-12","location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"publication_status":"published","citation":{"ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684.","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120."},"author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"doi":"10.1609/aaai.v34i09.7120","publication":"The 34th AAAI Conference on Artificial Intelligence","publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"]},"intvolume":" 34","extern":"1","language":[{"iso":"eng"}],"day":"28","year":"2020","date_updated":"2023-09-12T07:44:48Z","month":"07","date_published":"2020-07-28T00:00:00Z","_id":"14186","department":[{"_id":"FrLo"}],"publisher":"Association for the Advancement of Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A commentary on the unsupervised learning of disentangled representations","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"issue":"9","date_created":"2023-08-22T14:07:26Z","oa":1,"scopus_import":"1","external_id":{"arxiv":["2007.14184"]},"abstract":[{"text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research.","lang":"eng"}],"page":"13681-13684","article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02886"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Weakly-supervised disentanglement without compromises","oa_version":"Preprint","quality_controlled":"1","oa":1,"date_created":"2023-08-22T14:08:14Z","external_id":{"arxiv":["2002.02886"]},"scopus_import":"1","page":"6348–6359","abstract":[{"text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios.","lang":"eng"}],"article_processing_charge":"No","citation":{"apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359.","chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359.","ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359."},"status":"public","type":"conference","volume":119,"publication_status":"published","conference":{"end_date":"2020-07-18","name":"International Conference on Machine Learning","start_date":"2020-07-13","location":"Virtual"},"publication":"Proceedings of the 37th International Conference on Machine Learning","intvolume":" 119","extern":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Ben","last_name":"Poole","full_name":"Poole, Ben"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"}],"year":"2020","date_updated":"2023-09-12T07:59:29Z","day":"07","_id":"14188","department":[{"_id":"FrLo"}],"month":"07","date_published":"2020-07-07T00:00:00Z","alternative_title":["PMLR"]},{"date_published":"2020-07-27T00:00:00Z","month":"07","alternative_title":["PMLR"],"abstract":[{"text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package.","lang":"eng"}],"page":"7253-7262","article_processing_charge":"No","department":[{"_id":"FrLo"}],"_id":"14187","day":"27","year":"2020","external_id":{"arxiv":["2002.11860"]},"date_updated":"2023-09-12T08:03:40Z","date_created":"2023-08-22T14:07:52Z","author":[{"first_name":"Geoffrey","last_name":"Négiar","full_name":"Négiar, Geoffrey"},{"full_name":"Dresdner, Gideon","first_name":"Gideon","last_name":"Dresdner"},{"full_name":"Tsai, Alicia","first_name":"Alicia","last_name":"Tsai"},{"full_name":"Ghaoui, Laurent El","last_name":"Ghaoui","first_name":"Laurent El"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello"},{"last_name":"Freund","first_name":"Robert M.","full_name":"Freund, Robert M."},{"full_name":"Pedregosa, Fabian","last_name":"Pedregosa","first_name":"Fabian"}],"publication":"Proceedings of the 37th International Conference on Machine Learning","extern":"1","intvolume":" 119","language":[{"iso":"eng"}],"oa":1,"title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","volume":119,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","conference":{"end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13","name":"International Conference on Machine Learning"},"quality_controlled":"1","oa_version":"Preprint","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2002.11860","open_access":"1"}],"citation":{"short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual.","ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262."}},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets."}],"has_accepted_license":"1","scopus_import":"1","external_id":{"arxiv":["2010.14766"]},"date_created":"2023-08-22T14:10:34Z","oa":1,"article_type":"original","ddc":["000"],"quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MIT Press","title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"article_number":"209","month":"09","date_published":"2020-09-01T00:00:00Z","_id":"14195","department":[{"_id":"FrLo"}],"day":"01","date_updated":"2023-09-12T09:23:56Z","year":"2020","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"},{"last_name":"Lucic","first_name":"Mario","full_name":"Lucic, Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"extern":"1","language":[{"iso":"eng"}],"intvolume":" 21","publication":"Journal of Machine Learning Research","publication_status":"published","status":"public","volume":21,"type":"journal_article","citation":{"mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020.","ama":"Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020).","ieee":"F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"quality_controlled":"1","oa_version":"Published Version","title":"The relation between crosstalk and gene regulation form revisited","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Public Library of Science","issue":"2","date_created":"2020-03-06T07:39:38Z","article_type":"original","ddc":["000","570"],"oa":1,"scopus_import":"1","external_id":{"isi":["000526725200019"]},"article_processing_charge":"No","file":[{"content_type":"application/pdf","file_id":"7579","date_created":"2020-03-09T15:12:21Z","file_name":"2020_PlosCompBio_Grah.pdf","creator":"dernst","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","date_updated":"2020-07-14T12:48:00Z","access_level":"open_access","relation":"main_file","file_size":2209325}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models."}],"publication_status":"published","volume":16,"type":"journal_article","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642."},"file_date_updated":"2020-07-14T12:48:00Z","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"intvolume":" 16","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication":"PLOS Computational Biology","doi":"10.1371/journal.pcbi.1007642","related_material":{"record":[{"id":"9716","relation":"research_data","status":"deleted"},{"relation":"research_data","id":"9776","status":"public"},{"status":"public","id":"9779","relation":"used_in_publication"},{"status":"public","id":"8155","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"9777"}]},"day":"25","date_updated":"2023-09-12T11:02:24Z","year":"2020","article_number":"e1007642","date_published":"2020-02-25T00:00:00Z","month":"02","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"isi":1,"_id":"7569"},{"day":"05","date_updated":"2023-09-12T11:05:28Z","external_id":{"pmid":["PPR234457 "]},"year":"2020","pmid":1,"month":"11","date_published":"2020-11-05T00:00:00Z","_id":"8813","article_processing_charge":"No","department":[{"_id":"SiHi"}],"abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"oa_version":"Preprint","publication_status":"submitted","publisher":"Cold Spring Harbor Laboratory","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","citation":{"short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948."},"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"last_name":"Titz-Teixeira","first_name":"Fabian","full_name":"Titz-Teixeira, Fabian"},{"last_name":"Suzuki","first_name":"Toru","full_name":"Suzuki, Toru"},{"full_name":"Asami, Maki","last_name":"Asami","first_name":"Maki"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"first_name":"Matthias","last_name":"Farlik","full_name":"Farlik, Matthias"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Andreas","last_name":"Beyer","full_name":"Beyer, Andreas"},{"full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F.","last_name":"Perry"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"date_created":"2020-11-26T07:17:19Z","oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/2020.11.03.366948","publication":"bioRxiv"},{"_id":"9777","department":[{"_id":"GaTk"}],"article_processing_charge":"No","month":"02","date_published":"2020-02-25T00:00:00Z","year":"2020","date_updated":"2023-09-12T11:02:25Z","day":"25","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7569"}]},"doi":"10.1371/journal.pcbi.1007642.s002","oa":1,"date_created":"2021-08-06T07:21:51Z","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"}],"main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}],"citation":{"apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.","ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002.","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002"},"publisher":"Public Library of Science","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Maximizing crosstalk","type":"research_data_reference","oa_version":"None"},{"page":"120","file":[{"date_updated":"2020-09-04T12:17:47Z","creator":"bkragl","checksum":"26fe261550f691280bda4c454bf015c7","file_size":1348815,"relation":"main_file","access_level":"open_access","file_name":"kragl-thesis.pdf","date_created":"2020-09-04T12:17:47Z","content_type":"application/pdf","file_id":"8333"},{"file_size":372312,"access_level":"closed","relation":"source_file","date_updated":"2020-09-04T13:00:17Z","checksum":"b9694ce092b7c55557122adba8337ebc","creator":"bkragl","file_name":"kragl-thesis.zip","date_created":"2020-09-04T13:00:17Z","file_id":"8335","content_type":"application/zip"}],"abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization 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. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","ddc":["000"],"oa":1,"date_created":"2020-09-04T12:24:12Z","supervisor":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","department":[{"_id":"ToHe"}],"_id":"8332","date_published":"2020-09-03T00:00:00Z","month":"09","alternative_title":["ISTA Thesis"],"year":"2020","date_updated":"2023-09-13T08:45:08Z","day":"03","related_material":{"record":[{"relation":"part_of_dissertation","id":"133","status":"public"},{"id":"8012","relation":"part_of_dissertation","status":"public"},{"id":"8195","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"160","status":"public"}]},"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8332","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-09-04T13:00:17Z","author":[{"last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"}],"citation":{"mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020."},"type":"dissertation","status":"public","publication_status":"published"},{"date_published":"2020-01-01T00:00:00Z","article_processing_charge":"No","department":[{"_id":"FrLo"}],"_id":"14326","page":"11525-11538","abstract":[{"lang":"eng","text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n"}],"date_updated":"2023-09-13T12:19:19Z","year":"2020","external_id":{"arxiv":["2006.15055"]},"author":[{"last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Weissenborn, Dirk","first_name":"Dirk","last_name":"Weissenborn"},{"first_name":"Thomas","last_name":"Unterthiner","full_name":"Unterthiner, Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"last_name":"Heigold","first_name":"Georg","full_name":"Heigold, Georg"},{"full_name":"Uszkoreit, Jakob","first_name":"Jakob","last_name":"Uszkoreit"},{"first_name":"Alexey","last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey"},{"last_name":"Kipf","first_name":"Thomas","full_name":"Kipf, Thomas"}],"date_created":"2023-09-13T12:03:46Z","language":[{"iso":"eng"}],"extern":"1","intvolume":" 33","publication_identifier":{"isbn":["9781713829546"]},"oa":1,"publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Virtual","start_date":"2020-12-06","end_date":"2020-12-12"},"oa_version":"Preprint","publication_status":"published","volume":33,"title":"Object-centric learning with slot attention","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Curran Associates","status":"public","citation":{"ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538.","ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.","chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38.","ieee":"F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538.","apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.","short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}]},{"_id":"71","department":[{"_id":"JaMa"}],"isi":1,"month":"10","date_published":"2020-10-01T00:00:00Z","date_updated":"2023-09-18T08:13:15Z","year":"2020","day":"01","publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"language":[{"iso":"eng"}],"intvolume":" 52","doi":"10.1137/19M1243440","publication":"SIAM Journal on Mathematical Analysis","author":[{"full_name":"Gladbach, Peter","first_name":"Peter","last_name":"Gladbach"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"}],"publist_id":"7983","citation":{"ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802."},"publication_status":"published","status":"public","type":"journal_article","volume":52,"article_processing_charge":"No","page":"2759-2802","abstract":[{"lang":"eng","text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric."}],"external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"scopus_import":"1","oa":1,"article_type":"original","date_created":"2018-12-11T11:44:28Z","main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"issue":"3","quality_controlled":"1","oa_version":"Preprint","publisher":"Society for Industrial and Applied Mathematics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Scaling limits of discrete optimal transport"},{"issue":"6","title":"Simulating liquids on dynamically warping grids","publisher":"IEEE","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","quality_controlled":"1","article_type":"original","ddc":["006"],"oa":1,"date_created":"2018-12-16T22:59:21Z","pmid":1,"external_id":{"pmid":["30507534"],"isi":["000532295600014"]},"scopus_import":"1","has_accepted_license":"1","page":"2288-2302","file":[{"date_updated":"2020-10-08T08:34:53Z","creator":"wojtan","checksum":"8d4c55443a0ee335bb5bb652de503042","file_size":21910098,"relation":"main_file","access_level":"open_access","success":1,"file_id":"8626","content_type":"application/pdf","date_created":"2020-10-08T08:34:53Z","file_name":"preprint.pdf"}],"abstract":[{"text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.","lang":"eng"}],"article_processing_charge":"No","citation":{"ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.","mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628."},"volume":26,"type":"journal_article","status":"public","publication_status":"published","publication":"IEEE Transactions on Visualization and Computer Graphics","doi":"10.1109/TVCG.2018.2883628","acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","language":[{"iso":"eng"}],"intvolume":" 26","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"file_date_updated":"2020-10-08T08:34:53Z","author":[{"full_name":"Hikaru, Ibayashi","last_name":"Hikaru","first_name":"Ibayashi"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"year":"2020","date_updated":"2023-09-18T09:30:01Z","day":"01","department":[{"_id":"ChWo"}],"isi":1,"_id":"5681","date_published":"2020-06-01T00:00:00Z","month":"06"},{"file":[{"relation":"main_file","access_level":"open_access","file_size":3622305,"checksum":"3994c54a1241451d561db1d4f43bad30","creator":"xli","date_updated":"2020-12-22T10:55:56Z","file_id":"8967","content_type":"application/pdf","success":1,"file_name":"THESIS_Xiang_Li.pdf","date_created":"2020-12-22T10:55:56Z"},{"file_id":"8968","content_type":"application/x-zip-compressed","date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip","file_size":4018859,"relation":"source_file","access_level":"closed","date_updated":"2020-12-30T07:18:03Z","creator":"xli","checksum":"0954ecfc5554c05615c14de803341f00"}],"has_accepted_license":"1","page":"125","abstract":[{"text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.","lang":"eng"}],"article_processing_charge":"No","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"date_created":"2020-12-21T09:44:30Z","ec_funded":1,"ddc":["539"],"oa":1,"title":"Rotation of coupled cold molecules in the presence of a many-body environment","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","supervisor":[{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"date_published":"2020-12-21T00:00:00Z","month":"12","alternative_title":["ISTA Thesis"],"department":[{"_id":"MiLe"}],"_id":"8958","day":"21","related_material":{"record":[{"id":"5886","relation":"part_of_dissertation","status":"public"},{"id":"8587","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1120","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","year":"2020","date_updated":"2023-09-20T11:30:58Z","file_date_updated":"2020-12-30T07:18:03Z","author":[{"full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","last_name":"Li"}],"doi":"10.15479/AT:ISTA:8958","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","status":"public","publication_status":"published","citation":{"ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958."}},{"oa":1,"ddc":["003"],"ec_funded":1,"date_created":"2020-09-14T01:04:53Z","supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"has_accepted_license":"1","abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"page":"148","file":[{"file_id":"8388","content_type":"application/x-zip-compressed","file_name":"Thesis_Ran.zip","date_created":"2020-09-14T01:02:59Z","file_size":1245800191,"access_level":"closed","relation":"source_file","date_updated":"2020-09-14T12:18:43Z","creator":"rzhang","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba"},{"checksum":"817e20c33be9247f906925517c56a40d","creator":"rzhang","date_updated":"2020-09-15T12:51:53Z","access_level":"open_access","relation":"main_file","file_size":161385316,"file_name":"PhD_thesis_Ran Zhang_20200915.pdf","date_created":"2020-09-15T12:51:53Z","success":1,"file_id":"8396","content_type":"application/pdf"}],"project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","doi":"10.15479/AT:ISTA:8386","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"}],"file_date_updated":"2020-09-15T12:51:53Z","citation":{"short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria."},"status":"public","type":"dissertation","publication_status":"published","_id":"8386","department":[{"_id":"BeBi"}],"month":"09","date_published":"2020-09-14T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2020","date_updated":"2023-09-22T09:49:31Z","day":"14","related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1002","relation":"part_of_dissertation"}]},"degree_awarded":"PhD"},{"citation":{"ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996."},"publication_status":"published","status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7996","author":[{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip"}],"file_date_updated":"2020-07-14T12:48:07Z","date_updated":"2023-09-26T15:50:22Z","year":"2020","related_material":{"record":[{"status":"public","id":"1328","relation":"part_of_dissertation"},{"status":"public","id":"7541","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"77","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"23"},{"id":"840","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","day":"22","_id":"7996","department":[{"_id":"GeKa"}],"alternative_title":["ISTA Thesis"],"month":"06","date_published":"2020-06-22T00:00:00Z","supervisor":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","oa":1,"ddc":["530"],"date_created":"2020-06-22T09:22:23Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity."}],"file":[{"file_size":392794743,"access_level":"closed","relation":"main_file","date_updated":"2020-07-14T12:48:07Z","creator":"dernst","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","file_id":"7997","content_type":"application/x-zip-compressed","file_name":"JK_thesis_latex_source_files.zip","date_created":"2020-06-22T09:22:04Z"},{"content_type":"application/pdf","file_id":"7998","file_name":"PhD_thesis_JK_pdfa.pdf","date_created":"2020-06-22T09:21:29Z","access_level":"open_access","relation":"main_file","file_size":28453247,"creator":"dernst","checksum":"1de716bf110dbd77d383e479232bf496","date_updated":"2020-07-14T12:48:07Z"}],"has_accepted_license":"1","page":"178"},{"title":"Stochastic games with lexicographic reachability-safety objectives","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","oa_version":"Published Version","quality_controlled":"1","ddc":["000"],"oa":1,"date_created":"2020-08-16T22:00:58Z","ec_funded":1,"external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"scopus_import":"1","has_accepted_license":"1","page":"398-420","abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"file":[{"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","creator":"dernst","date_updated":"2020-08-17T11:32:44Z","relation":"main_file","access_level":"open_access","file_size":625056,"date_created":"2020-08-17T11:32:44Z","file_name":"2020_LNCS_CAV_Chatterjee.pdf","success":1,"content_type":"application/pdf","file_id":"8276"}],"article_processing_charge":"No","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420."},"volume":12225,"type":"conference","status":"public","conference":{"name":"CAV: Computer Aided Verification"},"publication_status":"published","publication":"International Conference on Computer Aided Verification","doi":"10.1007/978-3-030-53291-8_21","intvolume":" 12225","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030532901"],"eissn":["16113349"],"issn":["03029743"]},"file_date_updated":"2020-08-17T11:32:44Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen","full_name":"Katoen, Joost P"},{"full_name":"Weininger, Maximilian","first_name":"Maximilian","last_name":"Weininger"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"year":"2020","date_updated":"2023-10-03T11:36:13Z","day":"14","related_material":{"record":[{"status":"public","relation":"later_version","id":"12738"}]},"department":[{"_id":"KrCh"}],"isi":1,"_id":"8272","date_published":"2020-07-14T00:00:00Z","month":"07","alternative_title":["LNCS"]},{"oa":1,"date_created":"2020-03-08T23:00:47Z","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","quality_controlled":"1","page":"145-161","abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"article_processing_charge":"No","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000611826500008"]},"scopus_import":"1","publication":"Methods in Cell Biology","doi":"10.1016/bs.mcb.2020.01.006","language":[{"iso":"eng"}],"intvolume":" 158","publication_identifier":{"issn":["0091679X"]},"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461"},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"}],"citation":{"chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161."},"volume":158,"type":"book_chapter","editor":[{"full_name":"Tran, Phong ","first_name":"Phong ","last_name":"Tran"}],"status":"public","publication_status":"published","isi":1,"department":[{"_id":"MaLo"}],"_id":"7572","date_published":"2020-02-27T00:00:00Z","month":"02","alternative_title":["Methods in Cell Biology"],"year":"2020","date_updated":"2023-10-04T09:50:24Z","day":"27","related_material":{"record":[{"id":"8358","relation":"part_of_dissertation","status":"public"}]}},{"year":"2020","date_updated":"2023-10-06T12:22:38Z","day":"20","related_material":{"record":[{"id":"14280","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release","description":"News on IST Homepage"}]},"_id":"7387","isi":1,"department":[{"_id":"MaLo"}],"month":"01","date_published":"2020-01-20T00:00:00Z","citation":{"ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5."},"status":"public","type":"journal_article","volume":5,"publication_status":"published","doi":"10.1038/s41564-019-0657-5","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","publication":"Nature Microbiology","publication_identifier":{"issn":["2058-5276"]},"intvolume":" 5","language":[{"iso":"eng"}],"author":[{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124"},{"last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"first_name":"Carlos","last_name":"Alfonso","full_name":"Alfonso, Carlos"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin"},{"last_name":"Rivas","first_name":"Germán","full_name":"Rivas, Germán"},{"full_name":"Vollmer, Waldemar","first_name":"Waldemar","last_name":"Vollmer"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"}],"external_id":{"isi":["000508584700007"],"pmid":["31959972"]},"pmid":1,"scopus_import":"1","abstract":[{"text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.","lang":"eng"}],"page":"407-417","project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","quality_controlled":"1","oa_version":"Submitted Version","oa":1,"article_type":"letter_note","ec_funded":1,"date_created":"2020-01-28T16:14:41Z"},{"publication_status":"published","status":"public","volume":57,"type":"journal_article","citation":{"ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454"},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"file_date_updated":"2020-07-24T07:09:06Z","publication_identifier":{"eissn":["1588-2896"],"issn":["0081-6906"]},"intvolume":" 57","language":[{"iso":"eng"}],"acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","doi":"10.1556/012.2020.57.2.1454","publication":"Studia Scientiarum Mathematicarum Hungarica","day":"24","date_updated":"2023-10-10T13:05:27Z","year":"2020","month":"07","date_published":"2020-07-24T00:00:00Z","_id":"8163","department":[{"_id":"HeEd"}],"isi":1,"quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Akadémiai Kiadó","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","issue":"2","ec_funded":1,"date_created":"2020-07-24T07:09:18Z","oa":1,"ddc":["510"],"article_type":"original","scopus_import":"1","external_id":{"isi":["000570978400005"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"}],"article_processing_charge":"No","has_accepted_license":"1","page":"193-199","file":[{"relation":"main_file","access_level":"open_access","file_size":1476072,"creator":"mwintrae","date_updated":"2020-07-24T07:09:06Z","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_created":"2020-07-24T07:09:06Z","content_type":"application/pdf","file_id":"8164"}],"abstract":[{"lang":"eng","text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces."}]},{"day":"01","date_updated":"2023-10-16T09:25:00Z","year":"2020","month":"10","date_published":"2020-10-01T00:00:00Z","_id":"8671","department":[{"_id":"KrCh"}],"publication_status":"published","status":"public","type":"journal_article","volume":15,"citation":{"apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117"},"author":[{"first_name":"A.","last_name":"Shakiba","full_name":"Shakiba, A."},{"last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Hooshmandasl, M.R.","last_name":"Hooshmandasl","first_name":"M.R."},{"first_name":"M.","last_name":"Alambardar Meybodi","full_name":"Alambardar Meybodi, M."}],"file_date_updated":"2020-10-19T11:14:20Z","publication_identifier":{"issn":["1735-4463"],"eissn":["2008-9473"]},"language":[{"iso":"eng"}],"intvolume":" 15","doi":"10.29252/ijmsi.15.2.117","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","publication":"Iranian Journal of Mathematical Sciences and Informatics","scopus_import":"1","external_id":{"arxiv":["1805.10672"]},"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","has_accepted_license":"1","page":"117-128","file":[{"date_created":"2020-10-19T11:14:20Z","file_name":"2020_ijmsi_Shakiba_accepted.pdf","success":1,"content_type":"application/pdf","file_id":"8676","checksum":"f299661a6d51cda6d255a76be696f48d","creator":"dernst","date_updated":"2020-10-19T11:14:20Z","access_level":"open_access","relation":"main_file","file_size":261688}],"abstract":[{"text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ","lang":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Iranian Academic Center for Education, Culture and Research","title":"A note on belief structures and s-approximation spaces","issue":"2","date_created":"2020-10-18T22:01:36Z","oa":1,"ddc":["000"],"article_type":"original"},{"has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"8549","success":1,"file_name":"2020_EJournProbab_Dareiotis.pdf","date_created":"2020-09-21T13:15:02Z","access_level":"open_access","relation":"main_file","file_size":273042,"creator":"dernst","checksum":"8e7c42e72596f6889d786e8e8b89994f","date_updated":"2020-09-21T13:15:02Z"}],"abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"article_processing_charge":"No","scopus_import":"1","external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"date_created":"2019-04-30T07:40:17Z","oa":1,"article_type":"original","ddc":["510"],"publisher":"Institute of Mathematical Statistics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","quality_controlled":"1","oa_version":"Published Version","month":"07","date_published":"2020-07-16T00:00:00Z","article_number":"82","_id":"6359","isi":1,"department":[{"_id":"JaMa"}],"day":"16","year":"2020","date_updated":"2023-10-16T09:22:50Z","author":[{"last_name":"Dareiotis","first_name":"Konstantinos","full_name":"Dareiotis, Konstantinos"},{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser"}],"file_date_updated":"2020-09-21T13:15:02Z","doi":"10.1214/20-EJP479","publication":"Electronic Journal of Probability","publication_identifier":{"eissn":["1083-6489"]},"language":[{"iso":"eng"}],"intvolume":" 25","status":"public","type":"journal_article","volume":25,"publication_status":"published","citation":{"mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.","chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479.","ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"supervisor":[{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"oa_version":"Published Version","ddc":["000"],"oa":1,"date_created":"2020-09-14T13:42:09Z","page":"197","file":[{"success":1,"content_type":"application/pdf","file_id":"8391","date_created":"2020-09-14T13:39:14Z","file_name":"2020_Thesis_Royer.pdf","creator":"dernst","checksum":"c914d2f88846032f3d8507734861b6ee","date_updated":"2020-09-14T13:39:14Z","relation":"main_file","access_level":"open_access","file_size":30224591},{"file_id":"8392","content_type":"application/x-zip-compressed","date_created":"2020-09-14T13:39:17Z","file_name":"thesis_sources.zip","checksum":"ae98fb35d912cff84a89035ae5794d3c","creator":"dernst","date_updated":"2020-09-14T13:39:17Z","relation":"main_file","access_level":"closed","file_size":74227627}],"has_accepted_license":"1","abstract":[{"text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. ","lang":"eng"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"citation":{"ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390."},"type":"dissertation","status":"public","publication_status":"published","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","doi":"10.15479/AT:ISTA:8390","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"file_date_updated":"2020-09-14T13:39:17Z","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705"}],"year":"2020","date_updated":"2023-10-16T10:04:02Z","day":"14","related_material":{"record":[{"relation":"part_of_dissertation","id":"7936","status":"public"},{"relation":"part_of_dissertation","id":"7937","status":"public"},{"id":"8193","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8092"},{"relation":"part_of_dissertation","id":"911","status":"public"}]},"degree_awarded":"PhD","department":[{"_id":"ChLa"}],"_id":"8390","date_published":"2020-09-14T00:00:00Z","month":"09","alternative_title":["ISTA Thesis"]},{"date_updated":"2023-10-17T07:37:11Z","year":"2020","day":"01","_id":"8186","department":[{"_id":"ChLa"}],"month":"07","date_published":"2020-07-01T00:00:00Z","citation":{"chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507."},"conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2020-06-14","location":"Virtual","end_date":"2020-06-19"},"publication_status":"published","status":"public","type":"conference","publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"language":[{"iso":"eng"}],"doi":"10.1109/CVPR42600.2020.00752","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"full_name":"Tsiminaki, Vagia","last_name":"Tsiminaki","first_name":"Vagia"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"file_date_updated":"2020-07-31T16:57:12Z","external_id":{"arxiv":["2004.04180"]},"scopus_import":"1","article_processing_charge":"No","page":"7498-7507","abstract":[{"lang":"eng","text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes."}],"has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"8187","success":1,"file_name":"paper.pdf","date_created":"2020-07-31T16:57:12Z","relation":"main_file","access_level":"open_access","file_size":10262773,"creator":"phenders","date_updated":"2020-07-31T16:57:12Z"}],"main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"quality_controlled":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","title":"Leveraging 2D data to learn textured 3D mesh generation","oa":1,"ddc":["004"],"date_created":"2020-07-31T16:53:49Z"},{"article_processing_charge":"No","abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"pmid":1,"scopus_import":"1","oa":1,"article_type":"original","date_created":"2020-01-30T10:12:04Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"issue":"1","oa_version":"Submitted Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Taylor & Francis","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","_id":"7416","department":[{"_id":"JiFr"}],"isi":1,"article_number":"1687175","month":"01","date_published":"2020-01-01T00:00:00Z","date_updated":"2023-10-17T09:01:48Z","year":"2020","day":"01","publication_identifier":{"issn":["1559-2324"]},"language":[{"iso":"eng"}],"intvolume":" 15","doi":"10.1080/15592324.2019.1687175","publication":"Plant Signaling & Behavior","author":[{"full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair"},{"first_name":"U.","last_name":"Krämer","full_name":"Krämer, U."}],"citation":{"ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175.","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175"},"publication_status":"published","status":"public","volume":15,"type":"journal_article"},{"department":[{"_id":"JuFi"},{"_id":"GradSch"}],"isi":1,"_id":"9196","date_published":"2020-03-01T00:00:00Z","month":"03","year":"2020","date_updated":"2023-10-17T09:15:53Z","day":"01","publication":"Studia Mathematica","doi":"10.4064/sm180411-11-2","intvolume":" 252","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"keyword":["General Mathematics"],"author":[{"last_name":"Hensel","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"},{"full_name":"Rosati, Tommaso","last_name":"Rosati","first_name":"Tommaso"}],"citation":{"chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2.","mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2.","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2","ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297.","short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297.","apa":"Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020."},"volume":252,"type":"journal_article","status":"public","publication_status":"published","page":"251-297","abstract":[{"text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces.","lang":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000558100500002"],"arxiv":["1709.05202"]},"scopus_import":"1","article_type":"original","date_created":"2021-02-25T08:55:03Z","issue":"3","title":"Modelled distributions of Triebel–Lizorkin type","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Instytut Matematyczny","oa_version":"Preprint","quality_controlled":"1"},{"issue":"1","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","oa_version":"Published Version","ddc":["570"],"article_type":"original","oa":1,"date_created":"2020-02-06T18:47:17Z","pmid":1,"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"scopus_import":"1","has_accepted_license":"1","file":[{"file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","content_type":"application/pdf","file_id":"7484","checksum":"a297f54d1fef0efe4789ca00f37f241e","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","relation":"main_file","access_level":"open_access","file_size":4551246}],"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"article_processing_charge":"No","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277."},"type":"journal_article","volume":16,"status":"public","publication_status":"published","publication":"PLOS Pathogens","doi":"10.1371/journal.ppat.1008277","language":[{"iso":"eng"}],"intvolume":" 16","publication_identifier":{"issn":["1553-7374"]},"file_date_updated":"2020-07-14T12:47:59Z","author":[{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"full_name":"Morado, Dustin R.","last_name":"Morado","first_name":"Dustin R."},{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","last_name":"Kravchuk"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Lyddon, Terri D.","first_name":"Terri D.","last_name":"Lyddon"},{"first_name":"Arianna M.","last_name":"Broad","full_name":"Broad, Arianna M."},{"first_name":"J. Ryan","last_name":"Feathers","full_name":"Feathers, J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"full_name":"Perilla, Juan R.","last_name":"Perilla","first_name":"Juan R."},{"full_name":"Briggs, John A. G.","first_name":"John A. G.","last_name":"Briggs"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"year":"2020","date_updated":"2023-10-17T12:29:34Z","day":"27","related_material":{"record":[{"status":"deleted","id":"9723","relation":"research_data"}]},"isi":1,"department":[{"_id":"FlSc"}],"_id":"7464","date_published":"2020-01-27T00:00:00Z","month":"01","article_number":"e1008277"},{"author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"file_date_updated":"2020-07-14T12:47:53Z","publication_identifier":{"eissn":["15537358"]},"language":[{"iso":"eng"}],"intvolume":" 16","doi":"10.1371/journal.pcbi.1007494","publication":"PLoS computational biology","publication_status":"published","status":"public","volume":16,"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494."},"article_number":"e1007494","month":"01","date_published":"2020-01-17T00:00:00Z","_id":"7212","isi":1,"department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"}]},"day":"17","date_updated":"2023-10-17T12:29:47Z","year":"2020","ec_funded":1,"date_created":"2019-12-23T13:45:11Z","oa":1,"ddc":["000"],"article_type":"original","quality_controlled":"1","oa_version":"Published Version","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Limits on amplifiers of natural selection under death-Birth updating","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"article_processing_charge":"No","file":[{"access_level":"open_access","relation":"main_file","file_size":1817531,"creator":"dernst","checksum":"ce32ee2d2f53aed832f78bbd47e882df","date_updated":"2020-07-14T12:47:53Z","file_id":"7441","content_type":"application/pdf","date_created":"2020-02-03T07:32:42Z","file_name":"2020_PlosCompBio_Tkadlec.pdf"}],"abstract":[{"lang":"eng","text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process."}],"has_accepted_license":"1","scopus_import":"1","external_id":{"isi":["000510916500025"],"arxiv":["1906.02785"]}},{"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"_id":"7196","alternative_title":["ISTA Thesis"],"date_published":"2020-01-12T00:00:00Z","month":"01","date_updated":"2023-10-17T12:29:46Z","year":"2020","degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7210"},{"id":"5751","relation":"dissertation_contains","status":"public"},{"id":"7212","relation":"dissertation_contains","status":"public"}]},"day":"12","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7196","file_date_updated":"2020-07-14T12:47:52Z","author":[{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020."},"publication_status":"published","type":"dissertation","status":"public","article_processing_charge":"No","page":"144","has_accepted_license":"1","file":[{"access_level":"closed","relation":"source_file","file_size":21100497,"creator":"jtkadlec","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","file_name":"thesis.zip","content_type":"application/zip","file_id":"7255"},{"checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","access_level":"open_access","relation":"main_file","file_size":11670983,"content_type":"application/pdf","file_id":"7367","file_name":"2020_Tkadlec_Thesis.pdf","date_created":"2020-01-28T07:32:42Z"}],"abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"ddc":["519"],"oa":1,"date_created":"2019-12-20T12:26:36Z","supervisor":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"oa_version":"Published Version","title":"A role of graphs in evolutionary processes","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"ddc":["000"],"oa":1,"date_created":"2021-02-25T09:36:22Z","oa_version":"Published Version","quality_controlled":"1","title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"page":"8773-8784","has_accepted_license":"1","file":[{"success":1,"file_id":"9217","content_type":"application/pdf","date_created":"2021-03-02T15:38:14Z","file_name":"2020_PMLR_Shevchenko.pdf","date_updated":"2021-03-02T15:38:14Z","creator":"dernst","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","file_size":5336380,"relation":"main_file","access_level":"open_access"}],"external_id":{"arxiv":["1912.10095"]},"language":[{"iso":"eng"}],"intvolume":" 119","publication":"Proceedings of the 37th International Conference on Machine Learning","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","file_date_updated":"2021-03-02T15:38:14Z","author":[{"full_name":"Shevchenko, Alexander","first_name":"Alexander","last_name":"Shevchenko"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"citation":{"short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784."},"publication_status":"published","type":"conference","volume":119,"status":"public","department":[{"_id":"MaMo"}],"_id":"9198","date_published":"2020-07-13T00:00:00Z","month":"07","date_updated":"2023-10-17T12:43:19Z","year":"2020","day":"13"},{"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"article_processing_charge":"No","page":"51-67","file":[{"content_type":"application/pdf","file_id":"9171","success":1,"date_created":"2021-02-19T13:56:24Z","file_name":"2020_CompMathBiophysics_Akopyan2.pdf","file_size":562359,"access_level":"open_access","relation":"main_file","date_updated":"2021-02-19T13:56:24Z","checksum":"cea41de9937d07a3b927d71ee8b4e432","creator":"dernst"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"oa_version":"Published Version","quality_controlled":"1","publisher":"De Gruyter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The weighted mean curvature derivative of a space-filling diagram","issue":"1","ec_funded":1,"date_created":"2021-02-17T15:13:01Z","oa":1,"ddc":["510"],"article_type":"original","day":"20","date_updated":"2023-10-17T12:34:51Z","year":"2020","month":"06","date_published":"2020-06-20T00:00:00Z","_id":"9157","department":[{"_id":"HeEd"}],"publication_status":"published","status":"public","type":"journal_article","volume":8,"citation":{"chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"file_date_updated":"2021-02-19T13:56:24Z","publication_identifier":{"issn":["2544-7297"]},"language":[{"iso":"eng"}],"intvolume":" 8","doi":"10.1515/cmb-2020-0100","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also 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).","publication":"Computational and Mathematical Biophysics"},{"ec_funded":1,"date_created":"2021-02-17T15:12:44Z","oa":1,"ddc":["510"],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"De Gruyter","title":"The weighted Gaussian curvature derivative of a space-filling diagram","oa_version":"Published Version","quality_controlled":"1","issue":"1","has_accepted_license":"1","page":"74-88","file":[{"success":1,"file_id":"9170","content_type":"application/pdf","file_name":"2020_CompMathBiophysics_Akopyan.pdf","date_created":"2021-02-19T13:33:19Z","creator":"dernst","checksum":"ca43a7440834eab6bbea29c59b56ef3a","date_updated":"2021-02-19T13:33:19Z","relation":"main_file","access_level":"open_access","file_size":707452}],"abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.06777"]},"author":[{"last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"file_date_updated":"2021-02-19T13:33:19Z","doi":"10.1515/cmb-2020-0101","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also 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).","publication":"Computational and Mathematical Biophysics","publication_identifier":{"issn":["2544-7297"]},"intvolume":" 8","language":[{"iso":"eng"}],"status":"public","type":"journal_article","volume":8,"publication_status":"published","citation":{"mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"07","date_published":"2020-07-21T00:00:00Z","_id":"9156","department":[{"_id":"HeEd"}],"day":"21","year":"2020","date_updated":"2023-10-17T12:35:10Z"},{"type":"journal_article","volume":25,"status":"public","publication_status":"published","citation":{"ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536."},"file_date_updated":"2020-12-28T08:24:08Z","author":[{"full_name":"Redig, Frank","last_name":"Redig","first_name":"Frank"},{"first_name":"Ellen","last_name":"Saada","full_name":"Saada, Ellen"},{"last_name":"Sau","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"publication":"Electronic Journal of Probability","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","doi":"10.1214/20-EJP536","language":[{"iso":"eng"}],"intvolume":" 25","publication_identifier":{"eissn":["1083-6489"]},"day":"21","year":"2020","date_updated":"2023-10-17T12:51:56Z","date_published":"2020-10-21T00:00:00Z","month":"10","article_number":"138","isi":1,"department":[{"_id":"JaMa"}],"_id":"8973","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","publisher":" Institute of Mathematical Statistics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","date_created":"2020-12-27T23:01:17Z","ec_funded":1,"ddc":["510"],"article_type":"original","oa":1,"scopus_import":"1","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"file":[{"creator":"dernst","checksum":"d75359b9814e78d57c0a481b7cde3751","date_updated":"2020-12-28T08:24:08Z","access_level":"open_access","relation":"main_file","file_size":696653,"success":1,"file_id":"8976","content_type":"application/pdf","file_name":"2020_ElectronJProbab_Redig.pdf","date_created":"2020-12-28T08:24:08Z"}],"article_processing_charge":"No","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}]},{"publication":"Duke Mathematical Journal","doi":"10.1215/00127094-2020-0031","language":[{"iso":"eng"}],"intvolume":" 169","publication_identifier":{"issn":["0012-7094"]},"author":[{"last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"last_name":"Heath Brown","first_name":"Roger","full_name":"Heath Brown, Roger"}],"citation":{"ieee":"T. 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Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031."},"volume":169,"type":"journal_article","status":"public","publication_status":"published","department":[{"_id":"TiBr"}],"isi":1,"_id":"179","date_published":"2020-09-10T00:00:00Z","month":"09","year":"2020","date_updated":"2023-10-17T12:51:10Z","day":"10","article_type":"original","oa":1,"date_created":"2018-12-11T11:45:02Z","issue":"16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","publisher":"Duke University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","page":"3099-3165","abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed."}],"article_processing_charge":"No","external_id":{"arxiv":["1805.10715"],"isi":["000582676300002"]}},{"related_material":{"record":[{"relation":"used_in_publication","id":"198","status":"public"}]},"day":"15","date_updated":"2023-10-18T06:36:00Z","year":"2020","date_published":"2020-10-15T00:00:00Z","month":"10","article_processing_charge":"No","department":[{"_id":"KrCh"}],"_id":"9814","abstract":[{"lang":"eng","text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners"}],"oa_version":"Published Version","type":"research_data_reference","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","publisher":"Royal Society","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","citation":{"chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.","mla":"Ibsen-Jensen, Rasmus, et al. 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Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5973013.v1"}],"author":[{"last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"date_created":"2021-08-06T13:09:57Z","oa":1,"doi":"10.6084/m9.figshare.5973013.v1"},{"intvolume":" 125","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.125.043202","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","author":[{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"last_name":"Martínez-Rincón","first_name":"Julián","full_name":"Martínez-Rincón, Julián"},{"last_name":"Wu","first_name":"Yunfan","full_name":"Wu, Yunfan"},{"orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"full_name":"Kasevich, Mark A.","last_name":"Kasevich","first_name":"Mark A."}],"citation":{"chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020."},"publication_status":"published","type":"journal_article","volume":125,"status":"public","department":[{"_id":"OnHo"}],"isi":1,"_id":"8285","article_number":"043202","date_published":"2020-07-24T00:00:00Z","month":"07","date_updated":"2023-10-18T08:38:35Z","year":"2020","day":"24","article_type":"original","oa":1,"date_created":"2020-08-24T06:24:04Z","issue":"4","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"quality_controlled":"1","oa_version":"Preprint","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"pmid":1,"external_id":{"arxiv":["1912.10218"],"isi":["000552227400008"],"pmid":["32794788"]},"scopus_import":"1"},{"author":[{"full_name":"Lambert, Nicholas J.","first_name":"Nicholas J.","last_name":"Lambert"},{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"date_created":"2021-11-21T23:01:31Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9-781-5575-2820-9"]},"publication":"OSA Quantum 2.0 Conference","doi":"10.1364/QUANTUM.2020.QTu8A.1","conference":{"end_date":"2020-09-17","location":"Washington, DC, United States","start_date":"2020-09-14","name":"OSA: Optical Society of America"},"oa_version":"None","quality_controlled":"1","publication_status":"published","type":"conference","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","publisher":"Optica Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","citation":{"ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1.","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1."},"alternative_title":["OSA Technical Digest"],"article_number":"QTu8A.1","date_published":"2020-01-01T00:00:00Z","month":"01","department":[{"_id":"JoFi"}],"article_processing_charge":"No","_id":"10328","abstract":[{"lang":"eng","text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient."}],"scopus_import":"1","day":"01","date_updated":"2023-10-18T08:32:34Z","year":"2020"},{"abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"page":"16398-16408","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."},{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"article_processing_charge":"No","scopus_import":"1","ec_funded":1,"date_created":"2021-07-04T22:01:27Z","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html"}],"month":"12","date_published":"2020-12-06T00:00:00Z","_id":"9633","department":[{"_id":"TiVo"}],"day":"06","related_material":{"link":[{"relation":"is_continued_by","url":"https://doi.org/10.1101/2020.10.24.353409"}],"record":[{"id":"14422","relation":"dissertation_contains","status":"public"}]},"year":"2020","date_updated":"2023-10-18T09:20:55Z","author":[{"last_name":"Confavreux","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","full_name":"Confavreux, Basile J"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"},{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J."},{"last_name":"Lillicrap","first_name":"Timothy","full_name":"Lillicrap, Timothy"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels"}],"acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","publication":"Advances in Neural Information Processing Systems","publication_identifier":{"issn":["1049-5258"]},"language":[{"iso":"eng"}],"intvolume":" 33","status":"public","type":"conference","volume":33,"publication_status":"published","conference":{"location":"Vancouver, Canada","start_date":"2020-12-06","name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2020-12-12"},"citation":{"ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408."}},{"_id":"8943","department":[{"_id":"JiFr"}],"isi":1,"month":"12","date_published":"2020-12-01T00:00:00Z","article_number":"108463","year":"2020","date_updated":"2023-11-16T13:03:31Z","day":"01","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/plants-on-aspirin/"}]},"doi":"10.1016/j.celrep.2020.108463","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","publication":"Cell Reports","publication_identifier":{"eissn":["22111247"]},"intvolume":" 33","language":[{"iso":"eng"}],"author":[{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Di Donato, Martin","first_name":"Martin","last_name":"Di Donato"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"first_name":"Jie","last_name":"Liu","full_name":"Liu, Jie"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Ferro, Noel","last_name":"Ferro","first_name":"Noel"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"file_date_updated":"2020-12-14T07:33:39Z","citation":{"chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","type":"journal_article","volume":33,"publication_status":"published","file":[{"checksum":"ed18cba0fb48ed2e789381a54cc21904","creator":"dernst","date_updated":"2020-12-14T07:33:39Z","relation":"main_file","access_level":"open_access","file_size":8056434,"date_created":"2020-12-14T07:33:39Z","file_name":"2020_CellReports_Tan.pdf","success":1,"file_id":"8948","content_type":"application/pdf"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}],"article_processing_charge":"Yes","external_id":{"pmid":["33264621"],"isi":["000595658100018"]},"pmid":1,"scopus_import":"1","oa":1,"article_type":"original","ddc":["580"],"ec_funded":1,"date_created":"2020-12-13T23:01:21Z","issue":"9","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","quality_controlled":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}]},{"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"scopus_import":"1","article_processing_charge":"No","project":[{"grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"page":"11233-11239","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"issue":"21","main_file_link":[{"url":"https://arxiv.org/abs/2005.11190","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"National Academy of Sciences","article_type":"original","oa":1,"date_created":"2020-06-07T22:00:51Z","ec_funded":1,"date_updated":"2023-11-30T10:55:13Z","year":"2020","related_material":{"link":[{"url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"12726","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14530"}]},"day":"26","isi":1,"department":[{"_id":"BjHo"}],"_id":"7932","date_published":"2020-05-26T00:00:00Z","month":"05","citation":{"apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239."},"publication_status":"published","type":"journal_article","volume":117,"status":"public","language":[{"iso":"eng"}],"intvolume":" 117","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","doi":"10.1073/pnas.1913716117","author":[{"full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","first_name":"Duo","last_name":"Xu"},{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney"},{"first_name":"Xingyu","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","last_name":"Ma","full_name":"Ma, Xingyu","orcid":"0000-0002-0179-9737"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}]},{"citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","status":"public","type":"journal_article","volume":25,"publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"intvolume":" 25","language":[{"iso":"eng"}],"doi":"10.4171/dm/780","publication":"Documenta Mathematica","author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger"}],"file_date_updated":"2023-12-18T10:42:32Z","keyword":["General Mathematics"],"date_updated":"2023-12-18T10:46:09Z","year":"2020","related_material":{"record":[{"id":"6183","relation":"earlier_version","status":"public"}]},"day":"01","_id":"14694","department":[{"_id":"LaEr"}],"month":"09","date_published":"2020-09-01T00:00:00Z","quality_controlled":"1","oa_version":"Published Version","publisher":"EMS Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","oa":1,"article_type":"original","ddc":["510"],"date_created":"2023-12-18T10:37:43Z","external_id":{"arxiv":["1804.07752"]},"article_processing_charge":"Yes","file":[{"success":1,"file_id":"14695","content_type":"application/pdf","file_name":"2020_DocumentaMathematica_Alt.pdf","date_created":"2023-12-18T10:42:32Z","date_updated":"2023-12-18T10:42:32Z","creator":"dernst","checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","file_size":1374708,"access_level":"open_access","relation":"main_file"}],"page":"1421-1539","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}]},{"abstract":[{"lang":"eng","text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry."}],"page":"119","file":[{"date_updated":"2020-07-27T12:44:51Z","creator":"savvakum","file_size":1061740,"relation":"source_file","access_level":"closed","file_id":"8178","content_type":"application/zip","date_created":"2020-07-27T12:44:51Z","file_name":"source.zip"},{"file_name":"thesis_pdfa.pdf","date_created":"2020-07-27T12:46:53Z","file_id":"8179","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access","file_size":1336501,"creator":"savvakum","date_updated":"2020-07-27T12:46:53Z"}],"has_accepted_license":"1","article_processing_charge":"No","date_created":"2020-07-23T09:51:29Z","oa":1,"ddc":["514"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","title":"Topological methods in geometry and discrete mathematics","oa_version":"Published Version","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"month":"07","date_published":"2020-07-24T00:00:00Z","alternative_title":["ISTA Thesis"],"_id":"8156","department":[{"_id":"UlWa"}],"day":"24","related_material":{"record":[{"id":"8182","relation":"part_of_dissertation","status":"public"},{"id":"8183","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8185","status":"public"},{"id":"8184","relation":"part_of_dissertation","status":"public"},{"id":"6355","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"75","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","year":"2020","date_updated":"2023-12-18T10:51:01Z","author":[{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"}],"file_date_updated":"2020-07-27T12:46:53Z","doi":"10.15479/AT:ISTA:8156","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"status":"public","type":"dissertation","publication_status":"published","citation":{"chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020."}},{"article_processing_charge":"No","abstract":[{"text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space.","lang":"eng"}],"page":"35-73","scopus_import":"1","external_id":{"arxiv":["1903.04046"]},"date_created":"2024-01-28T23:01:44Z","oa":1,"article_type":"original","quality_controlled":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Mathematical Sciences Publishers","title":" The local density approximation in density functional theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1903.04046"}],"issue":"1","month":"01","date_published":"2020-01-01T00:00:00Z","_id":"14891","department":[{"_id":"RoSe"}],"day":"01","date_updated":"2024-01-29T09:01:12Z","year":"2020","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"full_name":"Lieb, Elliott H.","last_name":"Lieb","first_name":"Elliott H."},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"intvolume":" 2","language":[{"iso":"eng"}],"doi":"10.2140/paa.2020.2.35","publication":"Pure and Applied Analysis","publication_status":"published","status":"public","type":"journal_article","volume":2,"citation":{"ama":"Lewin M, Lieb EH, Seiringer R. The local density approximation in density functional theory. Pure and Applied Analysis. 2020;2(1):35-73. doi:10.2140/paa.2020.2.35","ista":"Lewin M, Lieb EH, Seiringer R. 2020. The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/paa.2020.2.35.","mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation in density functional theory,” Pure and Applied Analysis, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020.","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2020). The local density approximation in density functional theory. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2020.2.35","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73."}},{"title":"Differential loss of spinal interneurons in a mouse model of ALS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa_version":"Published Version","article_type":"original","ddc":["570"],"oa":1,"date_created":"2020-12-03T11:47:31Z","pmid":1,"external_id":{"isi":["000595588700008"],"pmid":["32858144"]},"scopus_import":"1","file":[{"file_name":"2020_Neuroscience_Salamatina.pdf","date_created":"2020-12-03T11:45:26Z","file_id":"8915","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":4071247,"creator":"dernst","checksum":"da7413c819e079720669c82451b49294","date_updated":"2020-12-03T11:45:26Z"}],"has_accepted_license":"1","abstract":[{"text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"page":"81-95","article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2020.08.011","short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95.","ieee":"A. Salamatina et al., “Differential loss of spinal interneurons in a mouse model of ALS,” Neuroscience, vol. 450. Elsevier, pp. 81–95, 2020.","chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience. Elsevier, 2020. https://doi.org/10.1016/j.neuroscience.2020.08.011.","mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience, vol. 450, Elsevier, 2020, pp. 81–95, doi:10.1016/j.neuroscience.2020.08.011.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95.","ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 2020;450:81-95. doi:10.1016/j.neuroscience.2020.08.011"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"type":"journal_article","volume":450,"status":"public","publication_status":"published","publication":"Neuroscience","acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","doi":"10.1016/j.neuroscience.2020.08.011","language":[{"iso":"eng"}],"intvolume":" 450","publication_identifier":{"issn":["0306-4522"]},"file_date_updated":"2020-12-03T11:45:26Z","author":[{"first_name":"Alina","last_name":"Salamatina","full_name":"Salamatina, Alina"},{"full_name":"Yang, Jerry H","first_name":"Jerry H","last_name":"Yang"},{"full_name":"Brenner-Morton, Susan","first_name":"Susan","last_name":"Brenner-Morton"},{"last_name":"Bikoff","first_name":"Jay B ","full_name":"Bikoff, Jay B "},{"full_name":"Fang, Linjing","first_name":"Linjing","last_name":"Fang"},{"full_name":"Kintner, Christopher R","first_name":"Christopher R","last_name":"Kintner"},{"last_name":"Jessell","first_name":"Thomas M","full_name":"Jessell, Thomas M"},{"full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney"}],"year":"2020","date_updated":"2024-01-31T10:15:34Z","day":"01","department":[{"_id":"LoSw"}],"isi":1,"_id":"8914","date_published":"2020-12-01T00:00:00Z","month":"12"},{"ddc":["530"],"oa":1,"doi":"10.15479/AT:ISTA:8834","file_date_updated":"2020-12-02T10:46:27Z","author":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"}],"date_created":"2020-12-02T10:49:30Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"citation":{"ieee":"G. 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Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"has_accepted_license":"1","_id":"8097","department":[{"_id":"GaTk"}],"article_processing_charge":"No","month":"07","date_published":"2020-07-15T00:00:00Z","year":"2020","date_updated":"2024-02-21T12:40:51Z","day":"15","doi":"10.15479/AT:ISTA:8097","oa":1,"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"date_created":"2020-07-06T20:40:19Z","author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic"}],"file_date_updated":"2020-07-14T12:48:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"contributor":[{"contributor_type":"research_group","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","first_name":"Tobias","last_name":"Bollenbach"}],"citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","short":"B. Kavcic, (2020).","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Institute of Science and Technology Austria","type":"research_data","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}]},{"department":[{"_id":"NiBa"}],"article_processing_charge":"No","_id":"8254","has_accepted_license":"1","file":[{"file_size":5778420,"relation":"main_file","access_level":"open_access","date_updated":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","creator":"dernst","file_id":"8280","content_type":"application/x-zip-compressed","success":1,"date_created":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip"}],"abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"date_published":"2020-08-18T00:00:00Z","month":"08","date_updated":"2024-02-21T12:41:09Z","year":"2020","related_material":{"record":[{"relation":"later_version","id":"11321","status":"public"},{"id":"9192","relation":"later_version","status":"public"}]},"day":"18","ddc":["576"],"oa":1,"doi":"10.15479/AT:ISTA:8254","file_date_updated":"2020-08-18T08:03:23Z","author":[{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X"}],"date_created":"2020-08-12T12:49:23Z","contributor":[{"contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","contributor_type":"project_member","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Nicholas H"},{"orcid":"0000-0002-4014-8478","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Pickup","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","orcid":"0000-0001-6118-0541"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","short":"L.S. Arathoon, (2020).","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254."},"oa_version":"Published Version","type":"research_data","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Institute of Science and Technology Austria"},{"external_id":{"isi":["000516660900001"]},"scopus_import":"1","has_accepted_license":"1","file":[{"access_level":"open_access","relation":"main_file","file_size":5242880,"checksum":"c622737dc295972065782558337124a2","creator":"dernst","date_updated":"2020-11-20T10:11:35Z","file_id":"8782","content_type":"application/pdf","success":1,"file_name":"2020_AdvancedMaterials_Gao.pdf","date_created":"2020-11-20T10:11:35Z"}],"abstract":[{"lang":"eng","text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon."}],"article_processing_charge":"Yes (via OA deal)","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"},{"grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"issue":"16","title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"quality_controlled":"1","oa_version":"Published Version","ddc":["530"],"article_type":"original","oa":1,"date_created":"2020-02-28T09:47:00Z","ec_funded":1,"year":"2020","date_updated":"2024-02-21T12:42:12Z","day":"23","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7996"},{"status":"public","relation":"research_data","id":"9222"}]},"isi":1,"department":[{"_id":"GeKa"}],"_id":"7541","date_published":"2020-04-23T00:00:00Z","month":"04","article_number":"1906523","citation":{"mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523.","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","volume":32,"status":"public","publication_status":"published","publication":"Advanced Materials","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","doi":"10.1002/adma.201906523","intvolume":" 32","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0935-9648"]},"file_date_updated":"2020-11-20T10:11:35Z","author":[{"full_name":"Gao, Fei","last_name":"Gao","first_name":"Fei"},{"last_name":"Wang","first_name":"Jian-Huan","full_name":"Wang, Jian-Huan"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"},{"full_name":"Hu, Hao","last_name":"Hu","first_name":"Hao"},{"last_name":"Rančić","first_name":"Marko J.","full_name":"Rančić, Marko J."},{"last_name":"Zhang","first_name":"Jie-Yin","full_name":"Zhang, Jie-Yin"},{"last_name":"Wang","first_name":"Ting","full_name":"Wang, Ting"},{"full_name":"Yao, Yuan","first_name":"Yuan","last_name":"Yao"},{"last_name":"Wang","first_name":"Gui-Lei","full_name":"Wang, Gui-Lei"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636"},{"last_name":"Kloeffel","first_name":"Christoph","full_name":"Kloeffel, Christoph"},{"full_name":"Loss, Daniel","last_name":"Loss","first_name":"Daniel"},{"full_name":"Liu, Feng","last_name":"Liu","first_name":"Feng"},{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"first_name":"Jian-Jun","last_name":"Zhang","full_name":"Zhang, Jian-Jun"}]}]