[{"citation":{"ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13."},"page":"215 - 232","date_published":"2018-08-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"78","title":"Online timed pattern matching using automata","ddc":["000"],"status":"public","intvolume":" 11022","oa_version":"Submitted Version","file":[{"checksum":"436b7574934324cfa7d1d3986fddc65b","date_created":"2020-05-14T11:34:34Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7831","content_type":"application/pdf","file_size":374851,"creator":"dernst","access_level":"open_access","file_name":"2018_LNCS_Bakhirkin.pdf"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"external_id":{"isi":["000884993200013"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"conference":{"end_date":"2018-09-06","start_date":"2018-09-04","location":"Bejing, China","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"doi":"10.1007/978-3-030-00151-3_13","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"isbn":["978-3-030-00150-6"]},"year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"full_name":"Bakhirkin, Alexey","first_name":"Alexey","last_name":"Bakhirkin"},{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"last_name":"Asarin","first_name":"Eugene","full_name":"Asarin, Eugene"}],"date_updated":"2023-09-13T09:35:46Z","date_created":"2018-12-11T11:44:31Z","volume":11022,"file_date_updated":"2020-07-14T12:48:03Z","publist_id":"7976"},{"file_date_updated":"2020-07-14T12:46:02Z","publist_id":"7548","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"5690","author":[{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","last_name":"Brauns","first_name":"Matthias","full_name":"Brauns, Matthias"},{"full_name":"Amitonov, Sergey","first_name":"Sergey","last_name":"Amitonov"},{"full_name":"Spruijtenburg, Paul","first_name":"Paul","last_name":"Spruijtenburg"},{"full_name":"Zwanenburg, Floris","last_name":"Zwanenburg","first_name":"Floris"}],"date_updated":"2023-09-13T09:38:00Z","date_created":"2018-12-11T11:45:47Z","volume":8,"year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"GeKa"}],"month":"04","doi":"10.1038/s41598-018-24004-y","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429404300013"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"issue":"1","type":"journal_article","pubrep_id":"1016","oa_version":"Published Version","file":[{"checksum":"20af238ca4ba6491b77270be8d826bf5","date_created":"2018-12-12T10:17:04Z","date_updated":"2020-07-14T12:46:02Z","file_id":"5256","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1850530,"access_level":"open_access","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"317","title":"Palladium gates for reproducible quantum dots in silicon","ddc":["539"],"status":"public","intvolume":" 8","day":"09","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-04-09T00:00:00Z","publication":"Scientific Reports","citation":{"ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y."}},{"project":[{"name":"Individual function and social role of oxytocin-like neuropeptides in ants","_id":"25E3D34E-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1096/fj.201800443","publication_identifier":{"issn":["08926638"]},"month":"11","publisher":"FASEB","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"year":"2018","volume":32,"date_updated":"2023-09-13T09:37:32Z","date_created":"2018-12-11T11:45:08Z","author":[{"first_name":"Zita","last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita"},{"full_name":"Gil Mansilla, Esther","last_name":"Gil Mansilla","first_name":"Esther"},{"last_name":"Eder","first_name":"Thomas","full_name":"Eder, Thomas"},{"full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Giulia Di Giglio, Maria","first_name":"Maria","last_name":"Giulia Di Giglio"},{"first_name":"Edin","last_name":"Muratspahić","full_name":"Muratspahić, Edin"},{"first_name":"Florian","last_name":"Grebien","full_name":"Grebien, Florian"},{"last_name":"Rattei","first_name":"Thomas","full_name":"Rattei, Thomas"},{"full_name":"Muttenthaler, Markus","last_name":"Muttenthaler","first_name":"Markus"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"},{"full_name":"Gruber, Christian","first_name":"Christian","last_name":"Gruber"}],"publist_id":"7721","page":"6808-6821","article_type":"original","citation":{"ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821."},"publication":"The FASEB Journal","date_published":"2018-11-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"29","intvolume":" 32","status":"public","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","_id":"194","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion."}]},{"doi":"10.1038/s41589-018-0090-8","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000438970200010"]},"quality_controlled":"1","isi":1,"month":"07","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41589-021-00744-3"}]},"author":[{"first_name":"Timm","last_name":"Fehrentz","full_name":"Fehrentz, Timm"},{"full_name":"Huber, Florian","first_name":"Florian","last_name":"Huber"},{"first_name":"Nina","last_name":"Hartrampf","full_name":"Hartrampf, Nina"},{"full_name":"Bruegmann, Tobias","last_name":"Bruegmann","first_name":"Tobias"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"full_name":"Fine, Nicholas","first_name":"Nicholas","last_name":"Fine"},{"last_name":"Malan","first_name":"Daniela","full_name":"Malan, Daniela"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"first_name":"Maritn","last_name":"Sumser","full_name":"Sumser, Maritn"},{"full_name":"Sasse, Philipp","first_name":"Philipp","last_name":"Sasse"},{"first_name":"David","last_name":"Hodson","full_name":"Hodson, David"},{"full_name":"Zhorov, Boris","last_name":"Zhorov","first_name":"Boris"},{"full_name":"Klocker, Nikolaj","first_name":"Nikolaj","last_name":"Klocker"},{"first_name":"Dirk","last_name":"Trauner","full_name":"Trauner, Dirk"}],"volume":14,"date_updated":"2023-09-13T09:36:35Z","date_created":"2018-12-11T11:44:56Z","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"JoDa"}],"publication_status":"published","publist_id":"7762","file_date_updated":"2020-07-14T12:45:03Z","date_published":"2018-07-16T00:00:00Z","citation":{"chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8"},"publication":"Nature Chemical Biology","page":"764 - 767","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"16","scopus_import":"1","file":[{"date_created":"2020-05-14T12:14:09Z","date_updated":"2020-07-14T12:45:03Z","checksum":"d42935094ec845f54a0688bf12986d62","file_id":"7832","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6321000,"file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"159","intvolume":" 14","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","status":"public","ddc":["570"],"issue":"8","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"type":"journal_article"},{"article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-08-15T00:00:00Z","citation":{"ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70."},"page":"53-70","abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11024","title":"Parameter-independent strategies for pMDPs via POMDPs","status":"public","month":"08","doi":"10.1007/978-3-319-99154-2_4","conference":{"end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04","name":"QEST: Quantitative Evaluation of Systems"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"quality_controlled":"1","isi":1,"publist_id":"7975","author":[{"full_name":"Arming, Sebastian","first_name":"Sebastian","last_name":"Arming"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"volume":11024,"date_updated":"2023-09-13T09:38:28Z","date_created":"2018-12-11T11:44:31Z","year":"2018","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published"},{"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1804.11130","date_published":"2018-04-30T00:00:00Z","publication":"arXiv","external_id":{"arxiv":["1804.11130"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1804.11130"}],"citation":{"ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. arXiv. https://doi.org/10.48550/arXiv.1804.11130","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” arXiv. .","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130."},"month":"04","day":"30","article_processing_charge":"No","date_created":"2023-09-13T12:20:49Z","date_updated":"2023-09-13T12:23:03Z","oa_version":"Preprint","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Vincent, Damien","last_name":"Vincent","first_name":"Damien"},{"full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin","first_name":"Ilya"},{"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"}],"status":"public","publication_status":"submitted","title":"Competitive training of mixtures of independent deep generative models","department":[{"_id":"FrLo"}],"year":"2018","_id":"14327","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples."}],"article_number":"1804.11130","type":"preprint"},{"file":[{"access_level":"open_access","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","file_size":582680,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4966","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:12:47Z"}],"oa_version":"Published Version","pubrep_id":"1011","ddc":["510"],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","status":"public","intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"400","abstract":[{"lang":"eng","text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case."}],"issue":"5","type":"journal_article","date_published":"2018-05-01T00:00:00Z","page":"1507 - 1527","publication":"Annales Henri Poincare","citation":{"mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7"},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_created":"2018-12-11T11:46:15Z","date_updated":"2023-09-15T12:04:15Z","volume":19,"author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas"},{"full_name":"Geisinge, Alissa","first_name":"Alissa","last_name":"Geisinge"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"full_name":"Loss, Michael","last_name":"Loss","first_name":"Michael"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","year":"2018","file_date_updated":"2020-07-14T12:46:22Z","ec_funded":1,"publist_id":"7429","language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0665-7","quality_controlled":"1","isi":1,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429799900008"]},"oa":1,"month":"05"},{"citation":{"ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049."},"publication":"PLoS One","date_published":"2018-03-07T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"406","intvolume":" 13","title":"Probabilistic models of individual and collective animal behavior","ddc":["530","571"],"status":"public","pubrep_id":"995","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","creator":"system","file_size":6887358,"content_type":"application/pdf","file_id":"5165","relation":"main_file","checksum":"684229493db75b43e98a46cd922da497","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z"}],"type":"journal_article","issue":"3","abstract":[{"text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ","lang":"eng"}],"external_id":{"isi":["000426896800032"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0193049","language":[{"iso":"eng"}],"month":"03","year":"2018","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9831"}]},"author":[{"full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová","first_name":"Katarína"},{"full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","first_name":"Gabriel"},{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"volume":13,"date_updated":"2023-09-15T12:06:19Z","date_created":"2018-12-11T11:46:18Z","publist_id":"7423","file_date_updated":"2020-07-14T12:46:22Z"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"external_id":{"isi":["000426516400027"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41559-017-0424-z","month":"02","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Springer Nature","year":"2018","date_updated":"2023-09-15T12:04:57Z","date_created":"2018-12-11T11:46:35Z","volume":2,"author":[{"full_name":"Pleska, Maros","first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479"},{"full_name":"Lang, Moritz","first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik","last_name":"Refardt","full_name":"Refardt, Dominik"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"202"}]},"ec_funded":1,"publist_id":"7364","page":"359 - 366","publication":"Nature Ecology and Evolution","citation":{"ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z","ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z.","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366."},"date_published":"2018-02-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","intvolume":" 2","_id":"457","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","abstract":[{"text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages","lang":"eng"}],"issue":"2"},{"date_published":"2018-10-08T00:00:00Z","page":"R1139 - R1140","article_type":"original","citation":{"mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063"},"publication":"Current Biology","article_processing_charge":"No","day":"08","scopus_import":"1","oa_version":"Published Version","intvolume":" 28","status":"public","title":"Protection against the lethal side effects of social immunity in ants","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"55","issue":"19","abstract":[{"lang":"eng","text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2018.08.063","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"external_id":{"isi":["000446693400008"]},"month":"10","volume":28,"date_updated":"2023-09-15T12:06:46Z","date_created":"2018-12-11T11:44:23Z","author":[{"first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina"},{"full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"publisher":"Cell Press","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2018","publist_id":"7999"},{"page":"3271 - 3290","publication":"SIAM Journal on Mathematical Analysis","citation":{"ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125","chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125."},"date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Power law decay for systems of randomly coupled differential equations","intvolume":" 50","_id":"181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2."}],"issue":"3","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"name":"Structured Non-Hermitian Random Matrices","call_identifier":"FWF","grant_number":"M02080","_id":"258F40A4-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"oa":1,"external_id":{"isi":["000437018500032"],"arxiv":["1708.01546"]},"language":[{"iso":"eng"}],"doi":"10.1137/17M1143125","month":"01","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"LaEr"}],"year":"2018","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","date_created":"2018-12-11T11:45:03Z","date_updated":"2023-09-15T12:05:52Z","volume":50,"author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H"},{"full_name":"Renfrew, David T","orcid":"0000-0003-3493-121X","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","last_name":"Renfrew","first_name":"David T"}],"publist_id":"7740","ec_funded":1},{"type":"journal_article","abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"322","intvolume":" 506","title":"Quantizations of multiplicative hypertoric varieties at a root of unity","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"15","citation":{"ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128."},"publication":"Journal of Algebra","page":"92 - 128","date_published":"2018-07-15T00:00:00Z","publist_id":"7543","ec_funded":1,"year":"2018","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","department":[{"_id":"TaHa"}],"publisher":"World Scientific Publishing","publication_status":"published","author":[{"full_name":"Ganev, Iordan V","first_name":"Iordan V","last_name":"Ganev","id":"447491B8-F248-11E8-B48F-1D18A9856A87"}],"volume":506,"date_updated":"2023-09-15T12:08:38Z","date_created":"2018-12-11T11:45:49Z","month":"07","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"main_file_link":[{"url":"https://arxiv.org/abs/1412.7211","open_access":"1"}],"oa":1,"project":[{"grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.jalgebra.2018.03.015","language":[{"iso":"eng"}]},{"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"title":"Implementation of the inference method in Matlab","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9831","year":"2018","oa_version":"Published Version","date_created":"2021-08-09T07:01:24Z","date_updated":"2023-09-15T12:06:18Z","related_material":{"record":[{"id":"406","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Katarína","last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína"},{"last_name":"Mitchell","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel"},{"full_name":"Harpaz, Roy","last_name":"Harpaz","first_name":"Roy"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"type":"research_data_reference","abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}],"citation":{"short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","mla":"Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001."},"date_published":"2018-03-07T00:00:00Z","doi":"10.1371/journal.pone.0193049.s001","article_processing_charge":"No","month":"03","day":"07"},{"date_published":"2018-07-18T00:00:00Z","page":"449 - 467","citation":{"ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24."},"article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5591566,"creator":"dernst","access_level":"open_access","file_name":"2018_LNCS_Kong.pdf","checksum":"fd95e8026deacef3dc752a733bb9355f","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-17T15:57:06Z","relation":"main_file","file_id":"5718"}],"intvolume":" 10981","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","ddc":["000"],"status":"public","_id":"142","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_24","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","location":"Oxford, United Kingdom","start_date":"2018-07-14"},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600024"]},"oa":1,"month":"07","volume":10981,"date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-15T12:12:08Z","author":[{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","publist_id":"7781","file_date_updated":"2020-07-14T12:44:53Z"},{"article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2018-02-21T00:00:00Z","citation":{"short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510","ieee":"P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018.","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510."},"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","article_type":"original","issue":"2","abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"type":"journal_article","oa_version":"Preprint","_id":"427","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 97","status":"public","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","month":"02","doi":"10.1103/PhysRevA.97.022510","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1802.07920","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1802.07920"],"isi":["000425601000004"]},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publist_id":"7396","ec_funded":1,"article_number":"022510","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"last_name":"Loureiro","first_name":"Ulisses","full_name":"Loureiro, Ulisses"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"full_name":"Indelicato, Paul","first_name":"Paul","last_name":"Indelicato"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"volume":97,"date_updated":"2023-09-15T12:09:35Z","date_created":"2018-12-11T11:46:25Z","acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","year":"2018","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published"},{"oa_version":"Preprint","_id":"309","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Recognizing weak embeddings of graphs","abstract":[{"text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.","lang":"eng"}],"type":"conference","date_published":"2018-01-01T00:00:00Z","citation":{"chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.","mla":"Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20.","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20"},"page":"274 - 292","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Akitaya, Hugo","first_name":"Hugo","last_name":"Akitaya"},{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"first_name":"Csaba","last_name":"Tóth","full_name":"Tóth, Csaba"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"6982"}]},"date_created":"2018-12-11T11:45:45Z","date_updated":"2023-09-15T12:19:32Z","year":"2018","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"publist_id":"7556","conference":{"end_date":"2018-01-10","start_date":"2018-01-07","location":"New Orleans, LA, USA","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611975031.20","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"external_id":{"arxiv":["1709.09209"],"isi":["000483921200021"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"month":"01"},{"ec_funded":1,"article_number":"255302","author":[{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp","last_name":"Yakaboylu"},{"full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"volume":121,"date_updated":"2023-09-15T12:09:06Z","date_created":"2019-01-06T22:59:12Z","year":"2018","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","publication_identifier":{"issn":["00319007"]},"month":"12","doi":"10.1103/PhysRevLett.121.255302","language":[{"iso":"eng"}],"external_id":{"isi":["000454178600009"],"arxiv":["1809.00222"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.00222","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"issue":"25","abstract":[{"lang":"eng","text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems."}],"type":"journal_article","oa_version":"Preprint","_id":"5794","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 121","status":"public","title":"Quantum groups as hidden symmetries of quantum impurities","article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2018-12-17T00:00:00Z","citation":{"chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018.","ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302"},"publication":"Physical Review Letters","article_type":"original"},{"year":"2018","department":[{"_id":"HeEd"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton"}],"volume":28,"date_created":"2018-12-11T11:44:33Z","date_updated":"2023-09-15T12:10:35Z","publist_id":"7967","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"external_id":{"isi":["000442893500018"],"arxiv":["1705.02870"]},"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"isi":1,"quality_controlled":"1","doi":"10.1214/18-AAP1389","language":[{"iso":"eng"}],"month":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"87","intvolume":" 28","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","status":"public","oa_version":"Preprint","type":"journal_article","issue":"5","abstract":[{"text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics.","lang":"eng"}],"citation":{"ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389."},"publication":"Annals of Applied Probability","page":"3215 - 3238","article_type":"original","date_published":"2018-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"doi":"10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"quality_controlled":"1","isi":1,"month":"06","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"full_name":"Hagihara, Shinya","first_name":"Shinya","last_name":"Hagihara"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"full_name":"Uchida, Naoyuki","first_name":"Naoyuki","last_name":"Uchida"},{"first_name":"Keiko U","last_name":"Torii","full_name":"Torii, Keiko U"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":4,"date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-15T12:11:03Z","pmid":1,"year":"2018","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publisher":"Springer Nature","publication_status":"published","publist_id":"7728","date_published":"2018-06-25T00:00:00Z","citation":{"chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1"},"publication":"Nature Plants","page":"453 - 459","article_type":"original","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"192","intvolume":" 4","status":"public","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","issue":"7","abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","citation":{"mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2018-11-12T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14","intvolume":" 19","status":"public","ddc":["580"],"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_IJMS_Hille.pdf","file_size":2200593,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5719","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","date_updated":"2020-07-14T12:44:50Z","date_created":"2018-12-17T16:04:11Z"}],"publication_identifier":{"eissn":["1422-0067"]},"month":"11","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000451528500282"]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.3390/ijms19113566","language":[{"iso":"eng"}],"publist_id":"8042","ec_funded":1,"file_date_updated":"2020-07-14T12:44:50Z","year":"2018","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"publisher":"MDPI","publication_status":"published","author":[{"last_name":"Hille","first_name":"Sander","full_name":"Hille, Sander"},{"last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":19,"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-18T08:09:32Z"},{"oa_version":"Preprint","status":"public","title":"Replicability of introgression under linked, polygenic selection","intvolume":" 210","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"39","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2018-12-04T00:00:00Z","article_type":"original","page":"1411-1427","publication":"Genetics","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018."},"day":"04","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-18T08:10:29Z","date_created":"2018-12-11T11:44:18Z","volume":210,"author":[{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"year":"2018","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"external_id":{"isi":["000452315900021"]},"month":"12","publication_identifier":{"issn":["00166731"]}},{"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1710.11171","open_access":"1"}],"oa":1,"external_id":{"isi":["000438217300007"]},"quality_controlled":"1","isi":1,"doi":"10.1142/S0217979218400222","language":[{"iso":"eng"}],"publist_id":"7402","year":"2018","department":[{"_id":"MiLe"}],"publisher":"World Scientific Publishing","publication_status":"published","author":[{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"},{"first_name":"Luca","last_name":"Salasnich","full_name":"Salasnich, Luca"}],"volume":32,"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-18T08:09:59Z","scopus_import":"1","article_processing_charge":"No","day":"10","citation":{"chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222"},"publication":"International Journal of Modern Physics B","page":"1840022","date_published":"2018-07-10T00:00:00Z","type":"journal_article","issue":"17","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"420","intvolume":" 32","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","status":"public","oa_version":"Preprint"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","volume":115,"author":[{"last_name":"Tavares","first_name":"Hugo","full_name":"Tavares, Hugo"},{"full_name":"Whitley, Annabel","first_name":"Annabel","last_name":"Whitley"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"last_name":"Elleouet","first_name":"Joane","full_name":"Elleouet, Joane"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"full_name":"Li, Qun","last_name":"Li","first_name":"Qun"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"full_name":"Rebocho, Alexandra B","first_name":"Alexandra B","last_name":"Rebocho"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"year":"2018","acknowledgement":" ERC Grant 201252 (to N.H.B.)","pmid":1,"month":"10","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"11006.full.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1911302,"creator":"dernst","relation":"main_file","file_id":"5683","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1"}],"status":"public","ddc":["570"],"title":"Selection and gene flow shape genomic islands that control floral guides","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","day":"23","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-23T00:00:00Z","page":"11006 - 11011","publication":"PNAS","citation":{"chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"}},{"alternative_title":["Proceedings of SPIE"],"type":"conference","abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"intvolume":" 10672","status":"public","title":"Routing thermal noise through quantum networks","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"155","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"04","citation":{"chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928"},"date_published":"2018-05-04T00:00:00Z","article_number":"106721N","publist_id":"7766","editor":[{"first_name":"D L","last_name":"Andrews","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"full_name":"Bain, A J","last_name":"Bain","first_name":"A J"},{"full_name":"Nunzi, J M","first_name":"J M","last_name":"Nunzi"}],"publisher":"SPIE","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2018","volume":10672,"date_updated":"2023-09-18T08:12:24Z","date_created":"2018-12-11T11:44:55Z","author":[{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"},{"last_name":"Aquilina","first_name":"Matteo","full_name":"Aquilina, Matteo"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh"}],"month":"05","isi":1,"quality_controlled":"1","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1117/12.2309928","conference":{"end_date":"2018-04-26","location":"Strasbourg, France","start_date":"2018-04-22","name":"SPIE: The international society for optical engineering"}},{"citation":{"ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980."},"publication":"Science","page":"1271-1275","article_type":"original","date_published":"2018-12-14T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"14","_id":"5767","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 362","status":"public","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","oa_version":"Published Version","type":"journal_article","issue":"6420","abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"oa":1,"external_id":{"isi":["000452994400048"]},"main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1126/science.aao0980","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"12","year":"2018","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","department":[{"_id":"MaSe"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"first_name":"Kenneth","last_name":"Gotlieb","full_name":"Gotlieb, Kenneth"},{"full_name":"Lin, Chiu-Yun","last_name":"Lin","first_name":"Chiu-Yun"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Zhang","first_name":"Wentao","full_name":"Zhang, Wentao"},{"first_name":"Christopher L.","last_name":"Smallwood","full_name":"Smallwood, Christopher L."},{"full_name":"Jozwiak, Christopher","first_name":"Christopher","last_name":"Jozwiak"},{"last_name":"Eisaki","first_name":"Hiroshi","full_name":"Eisaki, Hiroshi"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"first_name":"Ashvin","last_name":"Vishwanath","full_name":"Vishwanath, Ashvin"},{"first_name":"Alessandra","last_name":"Lanzara","full_name":"Lanzara, Alessandra"}],"volume":362,"date_created":"2018-12-19T14:53:50Z","date_updated":"2023-09-18T08:11:56Z"},{"month":"01","quality_controlled":"1","isi":1,"external_id":{"isi":["000446651100020"]},"language":[{"iso":"eng"}],"doi":"10.1109/TITS.2017.2778077","publist_id":"7389","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2018","date_updated":"2023-09-18T08:12:49Z","date_created":"2018-12-11T11:46:27Z","volume":19,"author":[{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"last_name":"Liu","first_name":"Han","full_name":"Liu, Han"},{"first_name":"Huobing","last_name":"Song","full_name":"Song, Huobing"},{"first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"full_name":"Wang, Rui","last_name":"Wang","first_name":"Rui"},{"full_name":"Guan, Yong","last_name":"Guan","first_name":"Yong"},{"last_name":"Sha","first_name":"Lui","full_name":"Sha, Lui"}],"related_material":{"record":[{"id":"1205","status":"public","relation":"earlier_version"}]},"scopus_import":"1","day":"01","article_processing_charge":"No","page":"3320 - 3333","publication":"IEEE Transactions on Intelligent Transportation Systems","citation":{"ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077."},"date_published":"2018-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"issue":"10","title":"Safety-assured model-driven design of the multifunction vehicle bus controller","status":"public","intvolume":" 19","_id":"434","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None"},{"article_number":"e34465","publist_id":"7759","ec_funded":1,"file_date_updated":"2020-07-14T12:45:07Z","year":"2018","department":[{"_id":"AnKi"}],"publisher":"eLife Sciences Publications","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9838"}]},"author":[{"full_name":"Kaucka, Marketa","first_name":"Marketa","last_name":"Kaucka"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","first_name":"Bara","full_name":"Szarowska, Bara"},{"last_name":"Kastriti","first_name":"Maria","full_name":"Kastriti, Maria"},{"last_name":"Xie","first_name":"Meng","full_name":"Xie, Meng"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","first_name":"Karl","last_name":"Annusver"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"last_name":"Kaiser","first_name":"Jozef","full_name":"Kaiser, Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"first_name":"Kazunori","last_name":"Sunadome","full_name":"Sunadome, Kazunori"},{"last_name":"Matise","first_name":"Michael P","full_name":"Matise, Michael P"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"first_name":"Ulrika","last_name":"Marklund","full_name":"Marklund, Ulrika"},{"full_name":"Abdo, Hind","first_name":"Hind","last_name":"Abdo"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","first_name":"Pascal","last_name":"Maire"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"last_name":"Fried","first_name":"Kaj","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"volume":7,"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-09-18T09:29:07Z","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000436227500001"]},"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.34465","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"_id":"162","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 7","status":"public","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","ddc":["571"],"file":[{"relation":"main_file","file_id":"5727","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-17T16:41:58Z","checksum":"da2378cdcf6b5461dcde194e4d608343","file_name":"2018_eLife_Kaucka.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9816484,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"13","citation":{"short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465."},"publication":"eLife","date_published":"2018-06-13T00:00:00Z"},{"month":"05","language":[{"iso":"eng"}],"conference":{"name":"Eurocrypt: Advances in Cryptology","end_date":"2018-05-03","start_date":"2018-04-29","location":"Tel Aviv, Israel"},"doi":"10.1007/978-3-319-78375-8_15","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000517098700015"]},"main_file_link":[{"url":"https://eprint.iacr.org/2018/183.pdf","open_access":"1"}],"ec_funded":1,"publist_id":"7579","date_updated":"2023-09-18T09:29:33Z","date_created":"2018-12-11T11:45:42Z","volume":10821,"author":[{"last_name":"Cohen","first_name":"Bram","full_name":"Cohen, Bram"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"year":"2018","day":"29","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-29T00:00:00Z","page":"451 - 467","citation":{"ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15","mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15."},"abstract":[{"lang":"eng","text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","status":"public","title":"Simple proofs of sequential work","intvolume":" 10821","_id":"302","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"31","intvolume":" 98","status":"public","title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus."}],"citation":{"mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410"},"publication":"Physical Review E","article_type":"original","date_published":"2018-10-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"17","year":"2018","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","department":[{"_id":"GaTk"}],"publisher":"American Physical Society","publication_status":"published","author":[{"last_name":"Ferrari","first_name":"Ulisse","full_name":"Ferrari, Ulisse"},{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Matthew J","last_name":"Chalk","full_name":"Chalk, Matthew J"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"}],"volume":98,"date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-18T09:18:44Z","article_number":"042410","publist_id":"8024","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"oa":1,"external_id":{"isi":["000447486100004"]},"project":[{"name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.98.042410","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24700045"]},"month":"10"},{"year":"2018","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"full_name":"Prieto, Y","first_name":"Y","last_name":"Prieto"},{"full_name":"Shkolnikov, Mikhail","first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"},{"first_name":"V","last_name":"Kalinina","full_name":"Kalinina, V"},{"first_name":"Ernesto","last_name":"Lupercio","full_name":"Lupercio, Ernesto"}],"date_updated":"2023-09-18T08:41:16Z","date_created":"2018-12-11T11:44:26Z","volume":115,"ec_funded":1,"publist_id":"7990","oa":1,"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1073/pnas.1805847115","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["00278424"]},"_id":"64","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","status":"public","intvolume":" 115","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation.","lang":"eng"}],"issue":"35","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115"},"article_type":"original","page":"E8135 - E8142","date_published":"2018-08-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"department":[{"_id":"AnKi"}],"publisher":"Dryad","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","status":"public","year":"2018","_id":"9838","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-09-18T09:29:07Z","date_created":"2021-08-09T12:54:35Z","related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Kaucka, Marketa","first_name":"Marketa","last_name":"Kaucka"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","last_name":"Tesarova","first_name":"Marketa"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"last_name":"Kastriti","first_name":"Maria Eleni","full_name":"Kastriti, Maria Eleni"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"first_name":"Tomas","last_name":"Zikmund","full_name":"Zikmund, Tomas"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"last_name":"Matise","first_name":"Michael P","full_name":"Matise, Michael P"},{"full_name":"Wang, Hui","first_name":"Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"article_processing_charge":"No","month":"06","day":"14","main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"citation":{"chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2"},"oa":1,"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","date_published":"2018-09-19T00:00:00Z","citation":{"ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311.","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018)."},"publication":"Frontiers in Cellular Neuroscience","article_type":"original","abstract":[{"text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"fncel-12-00311.pdf","access_level":"open_access","file_size":6834251,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5684","date_created":"2018-12-17T08:49:03Z","date_updated":"2020-07-14T12:46:23Z","checksum":"0bcaec8d596162af0b7fe3f31325d480"}],"oa_version":"Published Version","_id":"41","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 12","ddc":["570"],"status":"public","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","publication_identifier":{"issn":["16625102"]},"month":"09","doi":"10.3389/fncel.2018.00311","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000445090100002"]},"project":[{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270"}],"isi":1,"quality_controlled":"1","publist_id":"8013","ec_funded":1,"file_date_updated":"2020-07-14T12:46:23Z","article_number":"311","author":[{"full_name":"Luján, Rafæl","last_name":"Luján","first_name":"Rafæl"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"last_name":"Ciruela","first_name":"Francisco","full_name":"Ciruela, Francisco"},{"first_name":"Xavier","last_name":"Arus","full_name":"Arus, Xavier"},{"full_name":"Martín Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín Belmonte"},{"full_name":"Alfaro Ruiz, Rocío","last_name":"Alfaro Ruiz","first_name":"Rocío"},{"last_name":"Martinez Gomez","first_name":"Jesus","full_name":"Martinez Gomez, Jesus"},{"last_name":"De La Ossa","first_name":"Luis","full_name":"De La Ossa, Luis"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Adelman, John","last_name":"Adelman","first_name":"John"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"volume":12,"date_updated":"2023-09-18T09:31:18Z","date_created":"2018-12-11T11:44:19Z","year":"2018","publisher":"Frontiers Media","department":[{"_id":"RySh"}],"publication_status":"published"},{"project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1021/acs.nanolett.8b03217","publication_identifier":{"issn":["15306984"]},"month":"10","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"publication_status":"published","pmid":1,"year":"2018","volume":18,"date_updated":"2023-09-18T09:30:37Z","date_created":"2018-12-11T11:44:13Z","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"status":"public","relation":"dissertation_contains","id":"69"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","first_name":"Lada"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"full_name":"Milem, Joshua M","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M","last_name":"Milem"},{"last_name":"Schäffler","first_name":"Friedrich","full_name":"Schäffler, Friedrich"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"ec_funded":1,"publist_id":"8032","file_date_updated":"2020-07-14T12:45:37Z","page":"7141 - 7145","citation":{"ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145."},"publication":"Nano Letters","date_published":"2018-10-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"25","intvolume":" 18","ddc":["530"],"title":"Single-shot readout of hole spins in Ge","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"23","oa_version":"Published Version","file":[{"file_id":"5194","relation":"main_file","date_created":"2018-12-12T10:16:08Z","date_updated":"2020-07-14T12:45:37Z","checksum":"3e6034a94c6b5335e939145d88bdb371","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1361441}],"pubrep_id":"1065","type":"journal_article","issue":"11","abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}]},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use.","lang":"eng"}],"status":"public","ddc":["000"],"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","intvolume":" 11014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"85","file":[{"date_created":"2019-02-12T07:40:40Z","date_updated":"2020-07-14T12:48:14Z","checksum":"13a3f250be8878405e791b53c19722ad","relation":"main_file","file_id":"5954","content_type":"application/pdf","file_size":665372,"creator":"dernst","file_name":"2018_Brown.pdf","access_level":"open_access"}],"oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","page":"465 - 479","citation":{"ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33."},"date_published":"2018-08-01T00:00:00Z","file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7969","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Springer","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","year":"2018","date_created":"2018-12-11T11:44:33Z","date_updated":"2023-09-18T09:32:36Z","volume":11014,"author":[{"last_name":"Gilad","first_name":"Eran","full_name":"Gilad, Eran"},{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"first_name":"Mark","last_name":"Oskin","full_name":"Oskin, Mark"},{"first_name":"Yoav","last_name":"Etsion","full_name":"Etsion, Yoav"}],"month":"08","publication_identifier":{"issn":["03029743"]},"quality_controlled":"1","isi":1,"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000851042300031"]},"language":[{"iso":"eng"}],"conference":{"name":"Euro-Par: European Conference on Parallel Processing","location":"Turin, Italy","start_date":"2018-08-27","end_date":"2018-08-31"},"doi":"10.1007/978-3-319-96983-1_33"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.97.104307","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.05026","open_access":"1"}],"oa":1,"external_id":{"isi":["000427798800005"]},"month":"03","volume":97,"date_updated":"2023-09-18T09:31:46Z","date_created":"2018-12-11T11:45:50Z","author":[{"full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Žnidarič, Marko","first_name":"Marko","last_name":"Žnidarič"},{"full_name":"Medvedyeva, Mariya","first_name":"Mariya","last_name":"Medvedyeva"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"full_name":"Prosen, Tomaž","first_name":"Tomaž","last_name":"Prosen"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","year":"2018","publist_id":"7538","article_number":"104307","date_published":"2018-03-19T00:00:00Z","citation":{"ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018.","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018)."},"publication":"Physical Review B","article_processing_charge":"No","day":"19","scopus_import":"1","oa_version":"Preprint","intvolume":" 97","title":"Slow dynamics in translation-invariant quantum lattice models","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"327","issue":"10","abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","issue":"22","abstract":[{"lang":"eng","text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses."}],"intvolume":" 8","title":"Social environment affects the transcriptomic response to bacteria in ant queens","status":"public","ddc":["576","591"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"29","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5682","date_created":"2018-12-17T08:27:04Z","date_updated":"2020-07-14T12:45:52Z","checksum":"0d1355c78627ca7210aadd9a17a01915","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1272096,"creator":"dernst"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"11031-11070","citation":{"short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573.","chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070."},"publication":"Ecology and Evolution","date_published":"2018-11-01T00:00:00Z","publist_id":"8026","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","year":"2018","volume":8,"date_updated":"2023-09-19T09:29:12Z","date_created":"2018-12-11T11:44:15Z","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"first_name":"Jaana","last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana"},{"first_name":"Ida","last_name":"Holmberg","full_name":"Holmberg, Ida"},{"first_name":"Tobias","last_name":"Pamminger","full_name":"Pamminger, Tobias"},{"last_name":"Erler","first_name":"Silvio","full_name":"Erler, Silvio"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publication_identifier":{"issn":["20457758"]},"month":"11","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000451611000032"]},"language":[{"iso":"eng"}],"doi":"10.1002/ece3.4573"},{"publist_id":"6844","year":"2018","publication_status":"published","publisher":"Annual Reviews","department":[{"_id":"SyCr"}],"author":[{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher"},{"full_name":"Fürst, Matthias","first_name":"Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"819"}]},"date_created":"2018-12-11T11:48:36Z","date_updated":"2023-09-19T09:29:45Z","volume":63,"month":"01","publication_identifier":{"issn":["1545-4487"]},"external_id":{"isi":["000424633700008"]},"quality_controlled":"1","isi":1,"doi":"10.1146/annurev-ento-020117-043110","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology.","lang":"eng"}],"_id":"806","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Social immunity: Emergence and evolution of colony-level disease protection","intvolume":" 63","oa_version":"None","scopus_import":"1","day":"07","article_processing_charge":"No","publication":"Annual Review of Entomology","citation":{"chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.","mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","apa":"Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” Annual Review of Entomology, vol. 63. Annual Reviews, pp. 105–123, 2018.","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110"},"page":"105 - 123","date_published":"2018-01-07T00:00:00Z"},{"article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","date_published":"2018-07-18T00:00:00Z","page":"468 - 486","citation":{"ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25."},"abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:17:53Z","date_updated":"2020-07-14T12:44:50Z","checksum":"6dca832f575d6b3f0ea9dff56f579142","file_id":"5310","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":563710,"file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","access_level":"open_access"}],"pubrep_id":"1010","intvolume":" 10981","title":"Space-time interpolants","ddc":["005"],"status":"public","_id":"140","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["03029743"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_25","conference":{"name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17"},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600025"]},"oa":1,"publist_id":"7783","file_date_updated":"2020-07-14T12:44:50Z","volume":10981,"date_updated":"2023-09-19T09:30:43Z","date_created":"2018-12-11T11:44:50Z","related_material":{"record":[{"id":"6894","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","first_name":"Mirco","full_name":"Giacobbe, Mirco"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2018"},{"file":[{"date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-17T16:49:02Z","checksum":"411c4db5700d7297c9cd8ebc5dd29091","file_id":"5729","relation":"main_file","creator":"dernst","file_size":496973,"content_type":"application/pdf","file_name":"2018_MathPhysics_Moser.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"154","status":"public","ddc":["530"],"title":"Stability of the 2+2 fermionic system with point interactions","intvolume":" 21","abstract":[{"text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2018-09-01T00:00:00Z","publication":"Mathematical Physics Analysis and Geometry","citation":{"short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018.","apa":"Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"article_type":"original","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser","full_name":"Moser, Thomas"},{"full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"related_material":{"record":[{"id":"52","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T09:31:15Z","volume":21,"year":"2018","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:45:01Z","publist_id":"7767","ec_funded":1,"article_number":"19","doi":"10.1007/s11040-018-9275-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000439639700001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"month":"09","publication_identifier":{"eissn":["15729656"],"issn":["13850172"]}},{"file_date_updated":"2020-07-14T12:47:11Z","year":"2018","publisher":"Wiley","department":[{"_id":"EdHa"}],"author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."}],"volume":60,"date_updated":"2023-09-19T09:32:49Z","date_created":"2018-12-30T22:59:14Z","publication_identifier":{"issn":["00121592"]},"month":"12","external_id":{"isi":["000453555100002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/dgd.12570","language":[{"iso":"eng"}],"type":"journal_article","issue":"9","abstract":[{"text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"_id":"5787","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 60","title":"Statistical theory of branching morphogenesis","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-06T10:40:46Z","checksum":"a6d30b0785db902c734a84fecb2eadd9","relation":"main_file","file_id":"5933","file_size":1313606,"content_type":"application/pdf","creator":"dernst","file_name":"2018_DevGrowh_Hannezo.pdf","access_level":"open_access"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","citation":{"chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570"},"publication":"Development Growth and Differentiation","page":"512-521","date_published":"2018-12-09T00:00:00Z"},{"month":"04","language":[{"iso":"eng"}],"conference":{"location":"Thessaloniki, Greece","start_date":"2018-04-14","end_date":"2018-04-20","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-319-89960-2_21","isi":1,"quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000546326300021"]},"oa":1,"file_date_updated":"2020-07-14T12:45:57Z","publist_id":"7584","ec_funded":1,"date_updated":"2023-09-19T09:57:08Z","date_created":"2018-12-11T11:45:41Z","volume":10805,"author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"full_name":"Toman, Viktor","last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","year":"2018","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-04-12T00:00:00Z","page":"385 - 407","citation":{"short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21.","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407."},"abstract":[{"lang":"eng","text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs."}],"alternative_title":["LNCS"],"type":"conference","file":[{"checksum":"b13874ffb114932ad9cc2586b7469db4","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-17T16:29:08Z","file_id":"5723","relation":"main_file","creator":"dernst","file_size":1829940,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LNCS_Brazdil.pdf"}],"oa_version":"Published Version","title":"Strategy representation by decision trees in reactive synthesis","status":"public","ddc":["000"],"intvolume":" 10805","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"297"},{"page":"178-197","citation":{"ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13."},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","ddc":["000"],"intvolume":" 10982","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"141","file":[{"date_created":"2018-12-18T08:52:38Z","date_updated":"2020-07-14T12:44:53Z","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":675606,"file_name":"2018_LNCS_Chatterjee.pdf","access_level":"open_access"}],"oa_version":"Published Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples."}],"quality_controlled":"1","isi":1,"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491469700013"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17"},"doi":"10.1007/978-3-319-96142-2_13","month":"07","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"year":"2018","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-19T09:59:55Z","volume":10982,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"full_name":"Oraee, Simin","last_name":"Oraee","first_name":"Simin"},{"orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor","full_name":"Toman, Viktor"}],"related_material":{"record":[{"id":"10199","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"7782","ec_funded":1},{"month":"03","quality_controlled":"1","isi":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05313"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2018-04-29","location":"Tel Aviv, Israel","end_date":"2018-05-03","name":"Eurocrypt 2018: Advances in Cryptology"},"doi":"10.1007/978-3-319-78375-8_4","publist_id":"7583","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2018","date_created":"2018-12-11T11:45:41Z","date_updated":"2023-09-19T09:59:30Z","volume":10821,"author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F"},{"full_name":"Blocki, Jeremiah","first_name":"Jeremiah","last_name":"Blocki"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"scopus_import":"1","day":"31","article_processing_charge":"No","page":"99 - 130","citation":{"ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4","chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4."},"date_published":"2018-03-31T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅","lang":"eng"}],"status":"public","title":"Sustained space complexity","intvolume":" 10821","_id":"298","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint"},{"file":[{"access_level":"open_access","file_name":"2018_JournalExperimBotany_Vu.pdf","creator":"dernst","file_size":3359316,"content_type":"application/pdf","file_id":"5741","relation":"main_file","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","date_updated":"2020-07-14T12:46:13Z","date_created":"2018-12-18T09:47:51Z"}],"oa_version":"Published Version","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","status":"public","ddc":["581"],"intvolume":" 69","_id":"36","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"issue":"19","type":"journal_article","date_published":"2018-08-31T00:00:00Z","page":"4609 - 4624","publication":"Journal of Experimental Botany","citation":{"apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204."},"day":"31","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-09-19T10:00:46Z","date_created":"2018-12-11T11:44:17Z","volume":69,"author":[{"last_name":"Vu","first_name":"Lam","full_name":"Vu, Lam"},{"full_name":"Zhu, Tingting","last_name":"Zhu","first_name":"Tingting"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","first_name":"Brigitte","last_name":"Van De Cotte"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"last_name":"De Smet","first_name":"Ive","full_name":"De Smet, Ive"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","file_date_updated":"2020-07-14T12:46:13Z","publist_id":"8019","language":[{"iso":"eng"}],"doi":"10.1093/jxb/ery204","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443568700010"]},"oa":1,"month":"08"},{"month":"03","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000431496400001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1111/ejn.13901","license":"https://creativecommons.org/licenses/by-nc/4.0/","publist_id":"7539","file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"RySh"}],"publisher":"Wiley","publication_status":"published","year":"2018","volume":47,"date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-19T09:58:40Z","author":[{"first_name":"Kazuaki","last_name":"Sawada","full_name":"Sawada, Kazuaki"},{"first_name":"Ryosuke","last_name":"Kawakami","full_name":"Kawakami, Ryosuke"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Nemoto","first_name":"Tomomi","full_name":"Nemoto, Tomomi"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","page":"1033 - 1042","citation":{"apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901."},"publication":"European Journal of Neuroscience","date_published":"2018-03-07T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites."}],"intvolume":" 47","ddc":["570"],"status":"public","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"326","file":[{"date_created":"2018-12-17T16:16:50Z","date_updated":"2020-07-14T12:46:06Z","checksum":"98e901d8229e44aa8f3b51d248dedd09","file_id":"5721","relation":"main_file","creator":"dernst","file_size":4850261,"content_type":"application/pdf","file_name":"2018_EJN_Sawada.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry."}],"issue":"50","_id":"5770","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Structure and architecture of immature and mature murine leukemia virus capsids","intvolume":" 115","oa_version":"Submitted Version","scopus_import":"1","day":"11","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115."},"page":"E11751-E11760","date_published":"2018-12-11T00:00:00Z","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Proceedings of the National Academy of Sciences","author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"full_name":"Glass, Bärbel","last_name":"Glass","first_name":"Bärbel"},{"last_name":"Doležal","first_name":"Michal","full_name":"Doležal, Michal"},{"first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"last_name":"Rein","first_name":"Alan","full_name":"Rein, Alan"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"full_name":"Ruml, Tomáš","first_name":"Tomáš","last_name":"Ruml"},{"last_name":"Kräusslich","first_name":"Hans-Georg","full_name":"Kräusslich, Hans-Georg"},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."}],"date_updated":"2023-09-19T09:57:45Z","date_created":"2018-12-20T21:09:37Z","volume":115,"month":"12","publication_identifier":{"issn":["00278424"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1811580115","language":[{"iso":"eng"}]},{"_id":"608","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 712","status":"public","title":"Synthesis from component libraries with costs","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game."}],"citation":{"chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001"},"publication":"Theoretical Computer Science","page":"50 - 72","article_type":"original","date_published":"2018-02-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","year":"2018","department":[{"_id":"ToHe"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"volume":712,"date_updated":"2023-09-19T10:00:21Z","date_created":"2018-12-11T11:47:28Z","ec_funded":1,"publist_id":"7197","external_id":{"isi":["000424959200003"]},"main_file_link":[{"open_access":"1","url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.tcs.2017.11.001","language":[{"iso":"eng"}],"month":"02"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y","ieee":"A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y.","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869."},"publication":"Molecular Neurobiology","page":"4857 – 4869","date_published":"2018-06-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins.","lang":"eng"}],"_id":"705","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 55","title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","status":"public","oa_version":"None","month":"06","external_id":{"isi":["000431991500025"]},"quality_controlled":"1","isi":1,"doi":"10.1007/s12035-017-0688-y","language":[{"iso":"eng"}],"publist_id":"6991","year":"2018","department":[{"_id":"RySh"}],"publisher":"Springer","publication_status":"published","author":[{"first_name":"Andras","last_name":"Miklosi","full_name":"Miklosi, Andras"},{"full_name":"Del Favero, Giorgia","first_name":"Giorgia","last_name":"Del Favero"},{"full_name":"Bulat, Tanja","first_name":"Tanja","last_name":"Bulat"},{"full_name":"Höger, Harald","first_name":"Harald","last_name":"Höger"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"full_name":"Lubec, Gert","first_name":"Gert","last_name":"Lubec"}],"volume":55,"date_updated":"2023-09-19T09:58:11Z","date_created":"2018-12-11T11:48:02Z"},{"date_published":"2018-07-12T00:00:00Z","page":"448 - 464.e24","publication":"Cell","citation":{"ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033."},"day":"12","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","intvolume":" 174","_id":"148","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2018.06.033","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"oa":1,"external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"month":"07","date_updated":"2023-09-19T10:02:47Z","date_created":"2018-12-11T11:44:53Z","volume":174,"author":[{"last_name":"Nishiyama","first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"first_name":"Jan","last_name":"De Vries","full_name":"De Vries, Jan"},{"first_name":"Henrik","last_name":"Buschmann","full_name":"Buschmann, Henrik"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"last_name":"Ullrich","first_name":"Kristian","full_name":"Ullrich, Kristian"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"full_name":"Becker, Dirk","last_name":"Becker","first_name":"Dirk"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"full_name":"Wilhelmsson, Per","first_name":"Per","last_name":"Wilhelmsson"},{"last_name":"Janitza","first_name":"Philipp","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"first_name":"Alexander","last_name":"Heyl","full_name":"Heyl, Alexander"},{"last_name":"Rümpler","first_name":"Florian","full_name":"Rümpler, Florian"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"full_name":"Skokan, Roman","first_name":"Roman","last_name":"Skokan"},{"last_name":"Toyoda","first_name":"Atsushi","full_name":"Toyoda, Atsushi"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"first_name":"Hiroshi","last_name":"Kagoshima","full_name":"Kagoshima, Hiroshi"},{"full_name":"Schijlen, Elio","first_name":"Elio","last_name":"Schijlen"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"full_name":"Catarino, Bruno","first_name":"Bruno","last_name":"Catarino"},{"last_name":"Hetherington","first_name":"Alexander","full_name":"Hetherington, Alexander"},{"last_name":"Saltykova","first_name":"Assia","full_name":"Saltykova, Assia"},{"full_name":"Bonnot, Clemence","last_name":"Bonnot","first_name":"Clemence"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"first_name":"Aikaterini","last_name":"Symeonidi","full_name":"Symeonidi, Aikaterini"},{"last_name":"Radhakrishnan","first_name":"Guru","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"last_name":"Deforce","first_name":"Dieter","full_name":"Deforce, Dieter"},{"last_name":"Chang","first_name":"Caren","full_name":"Chang, Caren"},{"full_name":"Karol, Kenneth","first_name":"Kenneth","last_name":"Karol"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"full_name":"Ulvskov, Peter","first_name":"Peter","last_name":"Ulvskov"},{"full_name":"Glöckner, Gernot","first_name":"Gernot","last_name":"Glöckner"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Van De Peer","first_name":"Yves","full_name":"Van De Peer, Yves"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Mary","last_name":"Beilby","full_name":"Beilby, Mary"},{"first_name":"Liam","last_name":"Dolan","full_name":"Dolan, Liam"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"full_name":"Sugano, Sumio","last_name":"Sugano","first_name":"Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"full_name":"Delaux, Pierre Marc","first_name":"Pierre Marc","last_name":"Delaux"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"full_name":"Theissen, Gunter","first_name":"Gunter","last_name":"Theissen"},{"full_name":"Hagemann, Martin","first_name":"Martin","last_name":"Hagemann"},{"full_name":"Harholt, Jesper","last_name":"Harholt","first_name":"Jesper"},{"full_name":"Dunand, Christophe","last_name":"Dunand","first_name":"Christophe"},{"full_name":"Zachgo, Sabine","first_name":"Sabine","last_name":"Zachgo"},{"last_name":"Langdale","first_name":"Jane","full_name":"Langdale, Jane"},{"first_name":"Florian","last_name":"Maumus","full_name":"Maumus, Florian"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"full_name":"Gould, Sven B","last_name":"Gould","first_name":"Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","acknowledgement":"In-Data-Review","year":"2018","pmid":1,"publist_id":"7774","ec_funded":1},{"publist_id":"7426","file_date_updated":"2020-07-14T12:46:22Z","volume":94,"date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-19T10:07:08Z","author":[{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"full_name":"Nibau, Candida","first_name":"Candida","last_name":"Nibau"},{"full_name":"Fuchs, Armin","last_name":"Fuchs","first_name":"Armin"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"full_name":"Barta, Andrea","last_name":"Barta","first_name":"Andrea"},{"first_name":"John","last_name":"Doonan","full_name":"Doonan, John"}],"department":[{"_id":"EvBe"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","year":"2018","month":"06","language":[{"iso":"eng"}],"doi":"10.1111/tpj.13914","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434365500008"]},"oa":1,"issue":"6","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"d9d3ad3215ac0e581731443fca312266","date_created":"2019-02-06T11:40:54Z","date_updated":"2020-07-14T12:46:22Z","file_id":"5934","relation":"main_file","creator":"dernst","file_size":1543354,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_PlantJourn_Cavallari.pdf"}],"intvolume":" 94","ddc":["580"],"status":"public","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","_id":"403","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","page":"1010 - 1022","citation":{"mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914"},"publication":"The Plant Journal"},{"scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9."},"page":"147 - 164","date_published":"2018-07-12T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"156","title":"The compound interest in relaxing punctuality","ddc":["000"],"status":"public","intvolume":" 10951","file":[{"access_level":"open_access","file_name":"2018_LNCS_Ferrere.pdf","creator":"dernst","content_type":"application/pdf","file_size":485576,"file_id":"8637","relation":"main_file","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","date_updated":"2020-10-09T06:22:41Z","date_created":"2020-10-09T06:22:41Z"}],"oa_version":"Submitted Version","month":"07","external_id":{"isi":["000489765800009"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"FM: International Symposium on Formal Methods","start_date":"2018-07-15","location":"Oxford, UK","end_date":"2018-07-17"},"doi":"10.1007/978-3-319-95582-7_9","language":[{"iso":"eng"}],"file_date_updated":"2020-10-09T06:22:41Z","publist_id":"7765","year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas"}],"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T10:05:37Z","volume":10951},{"file_date_updated":"2018-12-18T09:46:00Z","publist_id":"7950","author":[{"first_name":"Denise","last_name":"Seitner","full_name":"Seitner, Denise"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","full_name":"Gallei, Michelle C"},{"full_name":"Djamei, Armin","first_name":"Armin","last_name":"Djamei"}],"date_updated":"2023-09-19T10:06:42Z","date_created":"2018-12-11T11:44:39Z","volume":19,"year":"2018","acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","publication_status":"published","publisher":"Wiley","department":[{"_id":"GradSch"}],"month":"10","doi":"10.1111/mpp.12698","language":[{"iso":"eng"}],"external_id":{"isi":["000445624100006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"issue":"10","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":682335,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_MolecPlantPath_Seitner.pdf","success":1,"date_updated":"2018-12-18T09:46:00Z","date_created":"2018-12-18T09:46:00Z","file_id":"5740","relation":"main_file"}],"_id":"104","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["580"],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","status":"public","intvolume":" 19","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-01T00:00:00Z","publication":"Molecular Plant Pathology","citation":{"ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287."},"page":"2277 - 2287"},{"pmid":1,"year":"2018","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9805"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":27,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-19T10:06:08Z","publist_id":"8014","file_date_updated":"2020-07-14T12:46:22Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/mec.14950","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1365294X"]},"month":"12","_id":"40","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 27","status":"public","ddc":["576"],"title":"The consequences of an introgression event","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","relation":"main_file","file_id":"6652","content_type":"application/pdf","file_size":295452,"creator":"apreinsp","access_level":"open_access","file_name":"2018_MolecularEcology_BartonNick.pdf"}],"type":"journal_article","issue":"24","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"citation":{"short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975."},"publication":"Molecular Ecology","page":"4973-4975","article_type":"letter_note","date_published":"2018-12-31T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"31"},{"author":[{"full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:01:39Z","volume":7,"year":"2018","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:13Z","article_number":"e37888","doi":"10.7554/eLife.37888","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434375000001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"06","publication_identifier":{"issn":["2050084X"]},"file":[{"access_level":"open_access","file_name":"2018_eLife_Alanko.pdf","file_size":358141,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5973","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","date_created":"2019-02-13T10:52:11Z","date_updated":"2020-07-14T12:47:13Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5861","title":"The cell sets the tone","status":"public","ddc":["570"],"intvolume":" 7","abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"type":"journal_article","date_published":"2018-06-06T00:00:00Z","publication":"eLife","citation":{"chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888"},"article_type":"original","day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"oa_version":"Published Version","intvolume":" 30","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","status":"public","_id":"147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"10","abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"type":"journal_article","date_published":"2018-11-12T00:00:00Z","page":"2553 - 2572","article_type":"original","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127"},"publication":"The Plant Cell","article_processing_charge":"No","day":"12","scopus_import":"1","volume":30,"date_updated":"2023-09-19T10:09:12Z","date_created":"2018-12-11T11:44:52Z","author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"full_name":"Hicks, Glenn R","last_name":"Hicks","first_name":"Glenn R"},{"last_name":"Nerinckx","first_name":"Wim","full_name":"Nerinckx, Wim"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"first_name":"Francois","last_name":"Peurois","full_name":"Peurois, Francois"},{"last_name":"Cherfils","first_name":"Jacqueline","full_name":"Cherfils, Jacqueline"},{"full_name":"De, Rycke Riet Maria","last_name":"De","first_name":"Rycke Riet Maria"},{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2018","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","ec_funded":1,"publist_id":"7776","language":[{"iso":"eng"}],"doi":"10.1105/tpc.18.00127","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"publication_identifier":{"issn":["1040-4651"]},"month":"11"},{"month":"07","doi":"10.1038/s41477-018-0212-z","language":[{"iso":"eng"}],"external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"oa":1,"quality_controlled":"1","isi":1,"publist_id":"7777","file_date_updated":"2020-07-14T12:44:56Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"author":[{"full_name":"Shi, Chun Lin","last_name":"Shi","first_name":"Chun Lin"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"full_name":"Herrmann, Ullrich","first_name":"Ullrich","last_name":"Herrmann"},{"full_name":"Wildhagen, Mari","last_name":"Wildhagen","first_name":"Mari"},{"full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","first_name":"Ivan","last_name":"Kulik"},{"full_name":"Kopf, Andreas","first_name":"Andreas","last_name":"Kopf"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"first_name":"Vilde","last_name":"Olsson","full_name":"Olsson, Vilde"},{"full_name":"Anker, Mari Kristine","last_name":"Anker","first_name":"Mari Kristine"},{"full_name":"Albert, Markus","last_name":"Albert","first_name":"Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"last_name":"Felix","first_name":"Georg","full_name":"Felix, Georg"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"first_name":"Manfred","last_name":"Claassen","full_name":"Claassen, Manfred"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Aalen","first_name":"Reidunn B","full_name":"Aalen, Reidunn B"}],"volume":4,"date_updated":"2023-09-19T10:08:45Z","date_created":"2018-12-11T11:44:52Z","pmid":1,"year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","citation":{"mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z"},"publication":"Nature Plants","page":"596 - 604","article_type":"original","issue":"8","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2018_NaturePlants_Shi.pdf","content_type":"application/pdf","file_size":226829,"creator":"dernst","relation":"main_file","file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","date_created":"2019-11-18T16:24:07Z","date_updated":"2020-07-14T12:44:56Z"}],"oa_version":"Submitted Version","_id":"146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 4","ddc":["580"],"status":"public","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling"},{"_id":"293","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2","status":"public","ddc":["000"],"title":"The signal-burying game can explain why we obscure positive traits and good deeds","oa_version":"Submitted Version","file":[{"file_id":"7051","relation":"main_file","checksum":"32efaf06a597495c184df91b3fbb19c0","date_created":"2019-11-19T08:17:23Z","date_updated":"2020-07-14T12:45:54Z","access_level":"open_access","file_name":"2018_NatureHumanBeh_Hoffman.pdf","creator":"dernst","file_size":194734,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness.","lang":"eng"}],"citation":{"ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z."},"publication":"Nature Human Behaviour","page":"397 - 404","article_type":"original","date_published":"2018-05-28T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"28","year":"2018","acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"last_name":"Hoffman","first_name":"Moshe","full_name":"Hoffman, Moshe"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"volume":2,"date_created":"2018-12-11T11:45:39Z","date_updated":"2023-09-19T10:12:03Z","publist_id":"7588","ec_funded":1,"file_date_updated":"2020-07-14T12:45:54Z","external_id":{"isi":["000435551300009"]},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41562-018-0354-z","language":[{"iso":"eng"}],"month":"05"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","citation":{"chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z"},"publication":"Annales Henri Poincare","page":"1167 - 1214","issue":"4","abstract":[{"text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities","lang":"eng"}],"type":"journal_article","alternative_title":["Annales Henri Poincare"],"pubrep_id":"993","oa_version":"Published Version","file":[{"checksum":"883eeccba8384ad7fcaa28761d99a0fa","date_created":"2018-12-12T10:11:57Z","date_updated":"2020-07-14T12:46:31Z","relation":"main_file","file_id":"4914","content_type":"application/pdf","file_size":923252,"creator":"system","access_level":"open_access","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf"}],"_id":"455","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 19","ddc":["510","539"],"status":"public","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","month":"04","doi":"10.1007/s00023-018-0644-z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000427578900006"]},"oa":1,"quality_controlled":"1","isi":1,"publist_id":"7367","file_date_updated":"2020-07-14T12:46:31Z","author":[{"full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P"},{"full_name":"Sok, Jérémy","last_name":"Sok","first_name":"Jérémy"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"volume":19,"date_updated":"2023-09-19T10:07:41Z","date_created":"2018-12-11T11:46:34Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","year":"2018","department":[{"_id":"RoSe"}],"publisher":"Birkhäuser","publication_status":"published"},{"doi":"10.1016/j.cels.2018.04.003","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2018.04.003"}],"external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2405-4712"]},"month":"04","author":[{"first_name":"Guntram","last_name":"Bauer","full_name":"Bauer, Guntram"},{"first_name":"Nikta","last_name":"Fakhri","full_name":"Fakhri, Nikta"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kondev, Jané","last_name":"Kondev","first_name":"Jané"},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"},{"last_name":"Noji","first_name":"Hiroyuki","full_name":"Noji, Hiroyuki"},{"first_name":"Daniel","last_name":"Riveline","full_name":"Riveline, Daniel"},{"last_name":"Saunders","first_name":"Timothy","full_name":"Saunders, Timothy"},{"full_name":"Thatta, Mukund","first_name":"Mukund","last_name":"Thatta"},{"full_name":"Wieschaus, Eric","last_name":"Wieschaus","first_name":"Eric"}],"volume":6,"date_updated":"2023-09-19T10:11:25Z","date_created":"2018-12-11T11:45:46Z","pmid":1,"year":"2018","publisher":"Cell Press","department":[{"_id":"AnKi"}],"publication_status":"published","publist_id":"7551","date_published":"2018-04-25T00:00:00Z","citation":{"ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003."},"publication":"Cell Systems","page":"400 - 402","article_type":"letter_note","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"314","intvolume":" 6","status":"public","title":"The science of living matter for tomorrow","issue":"4","abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"type":"journal_article"},{"volume":208,"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics ","publication_status":"published","pmid":1,"year":"2018","publist_id":"7249","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"oa":1,"external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"month":"01","oa_version":"Published Version","intvolume":" 208","title":"The spread of an inversion with migration and selection","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","issue":"1","abstract":[{"text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ","lang":"eng"}],"type":"journal_article","date_published":"2018-01-01T00:00:00Z","page":"377 - 382","article_type":"original","citation":{"chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426"},"publication":"Genetics","article_processing_charge":"No","day":"01","scopus_import":"1"},{"article_type":"original","page":"577 - 614","publication":"Communications on Pure and Applied Mathematics","citation":{"ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614."},"date_published":"2018-03-01T00:00:00Z","day":"01","article_processing_charge":"No","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","status":"public","intvolume":" 71","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"446","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"issue":"3","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21717","month":"03","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"RoSe"}],"acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","year":"2018","date_created":"2018-12-11T11:46:31Z","date_updated":"2023-09-19T10:09:40Z","volume":71,"author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"first_name":"Nam","last_name":"Phan Thanh","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam"},{"last_name":"Van Den Bosch","first_name":"Hanne","full_name":"Van Den Bosch, Hanne"}],"publist_id":"7377"},{"month":"04","external_id":{"isi":["000429094400005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"publist_id":"7393","file_date_updated":"2020-07-14T12:46:26Z","year":"2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"last_name":"Novembre","first_name":"John","full_name":"Novembre, John"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":208,"date_updated":"2023-09-19T10:17:30Z","date_created":"2018-12-11T11:46:26Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786."},"publication":"Genetics","page":"1351 - 1355","date_published":"2018-04-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"430","intvolume":" 208","status":"public","title":"Tread lightly interpreting polygenic tests of selection","ddc":["576"],"pubrep_id":"1012","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":500129,"file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-12T10:12:40Z","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958","relation":"main_file"}]},{"publist_id":"7714","file_date_updated":"2020-07-14T12:45:22Z","article_number":"294","volume":9,"date_updated":"2023-09-19T10:15:31Z","date_created":"2018-12-11T11:45:09Z","author":[{"full_name":"Ma, Wen","first_name":"Wen","last_name":"Ma"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"last_name":"Rodrigues","first_name":"Nicolas","full_name":"Rodrigues, Nicolas"},{"full_name":"Sermier, Roberto","last_name":"Sermier","first_name":"Roberto"},{"last_name":"Jeffries","first_name":"Daniel","full_name":"Jeffries, Daniel"},{"full_name":"Perrin, Nicolas","first_name":"Nicolas","last_name":"Perrin"}],"department":[{"_id":"BeVi"}],"publisher":"MDPI AG","publication_status":"published","year":"2018","month":"06","language":[{"iso":"eng"}],"doi":"10.3390/genes9060294","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000436494200026"]},"oa":1,"issue":"6","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3985796,"creator":"dernst","access_level":"open_access","file_name":"2018_Genes_Ma.pdf","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","date_created":"2019-02-01T07:52:28Z","date_updated":"2020-07-14T12:45:22Z","relation":"main_file","file_id":"5905"}],"intvolume":" 9","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"199","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-06-12T00:00:00Z","citation":{"ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018)."},"publication":"Genes"},{"month":"01","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"external_id":{"isi":["000419128700049"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1711114115","publist_id":"7273","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2018","volume":115,"date_updated":"2023-09-19T10:16:35Z","date_created":"2018-12-11T11:47:04Z","author":[{"full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"scopus_import":"1","article_processing_charge":"No","day":"02","page":"186 - 191","citation":{"short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191."},"publication":"PNAS","date_published":"2018-01-02T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}],"intvolume":" 115","status":"public","title":"Toward a unified theory of efficient, predictive, and sparse coding","_id":"543","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version"},{"citation":{"apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022."},"publication":"Biophysical Journal","page":"968 - 977","date_published":"2018-02-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"421","intvolume":" 114","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients."}],"main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"oa":1,"external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.bpj.2017.12.022","language":[{"iso":"eng"}],"month":"02","year":"2018","publisher":"Biophysical Society","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"first_name":"Kinjal","last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal"},{"full_name":"Hannezo, Claude-Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Claude-Edouard B"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"}],"volume":114,"date_updated":"2023-09-19T10:13:55Z","date_created":"2018-12-11T11:46:23Z","publist_id":"7403"},{"month":"10","doi":"10.3390/genes9100480","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000448656700018"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"file_date_updated":"2020-07-14T12:47:27Z","publist_id":"7991","ec_funded":1,"article_number":"480","author":[{"full_name":"Gammerdinger, William J","last_name":"Gammerdinger","first_name":"William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Kocher","full_name":"Kocher, Thomas"}],"date_created":"2018-12-11T11:44:26Z","date_updated":"2023-09-19T10:37:03Z","volume":9,"acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","year":"2018","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-04T00:00:00Z","publication":"Genes","citation":{"short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480.","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480."},"abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5743","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-18T09:54:46Z","checksum":"bec527692e2c9b56919c0429634ff337","file_name":"2018_Genes_Gammerdinger.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1415791,"creator":"dernst"}],"_id":"63","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Unusual diversity of sex chromosomes in African cichlid fishes","intvolume":" 9"},{"publist_id":"7585","department":[{"_id":"MaSe"}],"publisher":"Nature Publishing Group","publication_status":"published","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","year":"2018","volume":14,"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-19T10:37:55Z","author":[{"first_name":"Christopher","last_name":"Turner","full_name":"Turner, Christopher"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"month":"05","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000438253600028"]},"main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/130860/"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41567-018-0137-5","type":"journal_article","abstract":[{"text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable.","lang":"eng"}],"intvolume":" 14","title":"Weak ergodicity breaking from quantum many-body scars","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"296","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"14","page":"745 - 749","article_type":"original","citation":{"mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5.","ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5"},"publication":"Nature Physics","date_published":"2018-05-14T00:00:00Z"},{"publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","year":"2018","volume":"376-377","date_updated":"2023-09-19T10:38:34Z","date_created":"2018-12-11T11:47:28Z","author":[{"orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bodova","first_name":"Katarina","full_name":"Bodova, Katarina"},{"first_name":"Jan","last_name":"Haskovec","full_name":"Haskovec, Jan"},{"full_name":"Markowich, Peter","first_name":"Peter","last_name":"Markowich"}],"publist_id":"7198","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.physd.2017.10.015","month":"08","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"607","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.","lang":"eng"}],"page":"108-120","citation":{"ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015."},"publication":"Physica D: Nonlinear Phenomena","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"oa_version":"Submitted Version","intvolume":" 97","status":"public","title":"Two-photon processes based on quantum commutators","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"294","issue":"4","abstract":[{"lang":"eng","text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed."}],"type":"journal_article","date_published":"2018-04-18T00:00:00Z","citation":{"ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842."},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","article_processing_charge":"No","day":"18","scopus_import":"1","volume":97,"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-19T10:17:56Z","author":[{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh","full_name":"Safari, Laleh"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","publist_id":"7587","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043842","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1801.06892","open_access":"1"}],"external_id":{"arxiv":["1801.06892"],"isi":["000430296800008"]},"month":"04"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","page":"1267-1319","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","citation":{"ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004."},"abstract":[{"lang":"eng","text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data."}],"issue":"5","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Well-posedness for mean-field evolutions arising in superconductivity","intvolume":" 35","_id":"606","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","language":[{"iso":"eng"}],"doi":"10.1016/j.anihpc.2017.11.004","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"publist_id":"7199","date_created":"2018-12-11T11:47:27Z","date_updated":"2023-09-19T10:39:09Z","volume":35,"author":[{"first_name":"Mitia","last_name":"Duerinckx","full_name":"Duerinckx, Mitia"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"}],"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Elsevier","year":"2018","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n"},{"publication_identifier":{"isbn":["9781538655603"]},"month":"09","oa":1,"external_id":{"isi":["000492828500005"]},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1109/emsoft.2018.8537203","conference":{"location":"Turin, Italy","start_date":"2018-09-30","end_date":"2018-10-05","name":"EMSOFT: International Conference on Embedded Software"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:13Z","year":"2018","department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Deian","last_name":"Nickovicl","full_name":"Nickovicl, Deian"}],"date_created":"2019-02-13T09:19:28Z","date_updated":"2023-09-19T10:41:29Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","citation":{"ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203."},"publication":"2018 International Conference on Embedded Software","page":"1-10","date_published":"2018-09-30T00:00:00Z","type":"conference","abstract":[{"text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5959","title":"Keynote: The first-order logic of signals","ddc":["000"],"status":"public","oa_version":"Published Version","file":[{"checksum":"234a33ad9055b3458fcdda6af251b33a","date_created":"2020-05-14T16:01:29Z","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_id":"7839","content_type":"application/pdf","file_size":338006,"creator":"dernst","access_level":"open_access","file_name":"2018_EMSOFT_Bakhirkin.pdf"}]},{"date_published":"2018-07-23T00:00:00Z","page":"169-178","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178.","ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763"},"day":"23","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"The convergence of stochastic gradient descent in asynchronous shared memory","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5962","abstract":[{"lang":"eng","text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently."}],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","location":"Egham, United Kingdom","start_date":"2018-07-23"},"doi":"10.1145/3212734.3212763","isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1803.08841"],"isi":["000458186900022"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08841"}],"month":"07","publication_identifier":{"isbn":["9781450357951"]},"date_updated":"2023-09-19T10:42:53Z","date_created":"2019-02-13T09:58:58Z","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Christopher","last_name":"De Sa","full_name":"De Sa, Christopher"},{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov"}],"publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"year":"2018"},{"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.01605"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0395","publication_identifier":{"issn":["17425689"]},"month":"12","publisher":"Royal Society Publishing","department":[{"_id":"EdHa"}],"publication_status":"published","year":"2018","volume":15,"date_updated":"2023-09-19T10:40:38Z","date_created":"2019-01-20T22:59:19Z","author":[{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"first_name":"Luís F.","last_name":"Seoane","full_name":"Seoane, Luís F."},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"article_number":"20180395","citation":{"mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395"},"publication":"Journal of the Royal Society Interface","date_published":"2018-12-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"12","intvolume":" 15","title":"Zipf's Law, unbounded complexity and open-ended evolution","status":"public","_id":"5860","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","issue":"149","abstract":[{"lang":"eng","text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems."}]},{"language":[{"iso":"eng"}],"conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom"},"date_published":"2018-07-27T00:00:00Z","doi":"10.1145/3212734.3212798","isi":1,"quality_controlled":"1","page":"487-488","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"ista":"Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 487–488.","apa":"Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798","ieee":"D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 487–488.","ama":"Alistarh D-A. A brief tutorial on distributed and concurrent machine learning. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798","chicago":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798.","mla":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798.","short":"D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–488."},"external_id":{"isi":["000458186900063"]},"month":"07","day":"27","publication_identifier":{"isbn":["9781450357951"]},"article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-19T10:42:28Z","date_created":"2019-02-13T09:48:55Z","oa_version":"None","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"status":"public","publication_status":"published","title":"A brief tutorial on distributed and concurrent machine learning","publisher":"ACM Press","department":[{"_id":"DaAl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5961","year":"2018","abstract":[{"text":"The area of machine learning has made considerable progress over the past decade, enabled by the widespread availability of large datasets, as well as by improved algorithms and models. Given the large computational demands of machine learning workloads, parallelism, implemented either through single-node concurrency or through multi-node distribution, has been a third key ingredient to advances in machine learning.\r\nThe goal of this tutorial is to provide the audience with an overview of standard distribution techniques in machine learning, with an eye towards the intriguing trade-offs between synchronization and communication costs of distributed machine learning algorithms, on the one hand, and their convergence, on the other.The tutorial will focus on parallelization strategies for the fundamental stochastic gradient descent (SGD) algorithm, which is a key tool when training machine learning models, from classical instances such as linear regression, to state-of-the-art neural network architectures.\r\nThe tutorial will describe the guarantees provided by this algorithm in the sequential case, and then move on to cover both shared-memory and message-passing parallelization strategies, together with the guarantees they provide, and corresponding trade-offs. The presentation will conclude with a broad overview of ongoing research in distributed and concurrent machine learning. The tutorial will assume no prior knowledge beyond familiarity with basic concepts in algebra and analysis.\r\n","lang":"eng"}],"type":"conference"},{"publication_status":"published","publisher":"SAGE Publications","department":[{"_id":"UlWa"}],"year":"2018","date_updated":"2023-09-19T10:41:59Z","date_created":"2019-02-13T09:36:20Z","volume":37,"author":[{"last_name":"Rohou","first_name":"Simon","full_name":"Rohou, Simon"},{"full_name":"Franek, Peter","last_name":"Franek","first_name":"Peter","orcid":"0000-0001-8878-8397","id":"473294AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aubry, Clément","first_name":"Clément","last_name":"Aubry"},{"last_name":"Jaulin","first_name":"Luc","full_name":"Jaulin, Luc"}],"month":"10","publication_identifier":{"eissn":["1741-3176"],"issn":["0278-3649"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000456881100004"],"arxiv":["1712.01341"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.01341"}],"language":[{"iso":"eng"}],"doi":"10.1177/0278364918808367","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion."}],"issue":"12","status":"public","title":"Proving the existence of loops in robot trajectories","intvolume":" 37","_id":"5960","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","day":"24","article_processing_charge":"No","page":"1500-1516","publication":"The International Journal of Robotics Research","citation":{"chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367.","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367"},"date_published":"2018-10-24T00:00:00Z"},{"author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"date_updated":"2023-09-19T10:43:21Z","date_created":"2019-02-13T10:03:25Z","year":"2018","publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"conference":{"end_date":"2018-07-27","location":"Egham, United Kingdom","start_date":"2018-07-23","name":"PODC: Principles of Distributed Computing"},"doi":"10.1145/3212734.3212756","language":[{"iso":"eng"}],"external_id":{"arxiv":["1808.04155"],"isi":["000458186900048"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04155"}],"oa":1,"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"isbn":["9781450357951"]},"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5963","title":"Relaxed schedulers can efficiently parallelize iterative algorithms","status":"public","abstract":[{"text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion.","lang":"eng"}],"type":"conference","date_published":"2018-07-23T00:00:00Z","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756."},"page":"377-386","day":"23","article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"16","page":"133-142","citation":{"short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, J.Z. Li, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–142.","mla":"Alistarh, Dan-Adrian, et al. “Distributionally Linearizable Data Structures.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–42, doi:10.1145/3210377.3210411.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, Jerry Z. Li, and Giorgi Nadiradze. “Distributionally Linearizable Data Structures.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 133–42. ACM Press, 2018. https://doi.org/10.1145/3210377.3210411.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. Distributionally linearizable data structures. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:133-142. doi:10.1145/3210377.3210411","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, J. Z. Li, and G. Nadiradze, “Distributionally linearizable data structures,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 133–142.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., Li, J. Z., & Nadiradze, G. (2018). Distributionally linearizable data structures. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 133–142). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210411","ista":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. 2018. Distributionally linearizable data structures. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 133–142."},"publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","date_published":"2018-07-16T00:00:00Z","type":"conference","abstract":[{"text":"Relaxed concurrent data structures have become increasingly popular, due to their scalability in graph processing and machine learning applications (\\citeNguyen13, gonzalez2012powergraph ). Despite considerable interest, there exist families of natural, high performing randomized relaxed concurrent data structures, such as the popular MultiQueue~\\citeMQ pattern for implementing relaxed priority queue data structures, for which no guarantees are known in the concurrent setting~\\citeAKLN17. Our main contribution is in showing for the first time that, under a set of analytic assumptions, a family of relaxed concurrent data structures, including variants of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter, provides strong probabilistic guarantees on the degree of relaxation with respect to the sequential specification, in arbitrary concurrent executions. We formalize these guarantees via a new correctness condition called distributional linearizability, tailored to concurrent implementations with randomized relaxations. Our result is based on a new analysis of an asynchronous variant of the classic power-of-two-choices load balancing algorithm, in which placement choices can be based on inconsistent, outdated information (this result may be of independent interest). We validate our results empirically, showing that the MultiCounter algorithm can implement scalable relaxed timestamps.","lang":"eng"}],"status":"public","title":"Distributionally linearizable data structures","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5965","oa_version":"Preprint","publication_identifier":{"isbn":["9781450357999"]},"month":"07","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.01018"}],"external_id":{"isi":["000545269600016"],"arxiv":["1804.01018"]},"language":[{"iso":"eng"}],"doi":"10.1145/3210377.3210411","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2018-07-16","location":"Vienna, Austria","end_date":"2018-07-18"},"department":[{"_id":"DaAl"}],"publisher":"ACM Press","publication_status":"published","year":"2018","date_updated":"2023-09-19T10:44:13Z","date_created":"2019-02-13T10:17:19Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"last_name":"Li","first_name":"Jerry Z.","full_name":"Li, Jerry Z."},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"}]},{"abstract":[{"lang":"eng","text":"The Big Match is a multi-stage two-player game. In each stage Player 1 hides one or two pebbles in his hand, and his opponent has to guess that number; Player 1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon as Player 1 hides one pebble, the players cannot change their choices in any future stage.\r\nBlackwell and Ferguson (1968) give an ε-optimal strategy for Player 1 that hides, in each stage, one pebble with a probability that depends on the entire past history. Any strategy that depends just on the clock or on a finite memory is worthless. The long-standing natural open problem has been whether every strategy that depends just on the clock and a finite memory is worthless. We prove that there is such a strategy that is ε-optimal. In fact, we show that just two states of memory are sufficient.\r\n"}],"type":"conference","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":302539,"access_level":"open_access","file_name":"2018_EC18_Hansen.pdf","checksum":"bb52683e349cfd864f4769a8f38f2798","date_created":"2019-11-19T08:24:24Z","date_updated":"2020-07-14T12:47:14Z","file_id":"7054","relation":"main_file"}],"title":"The Big Match with a clock and a bit of memory","ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5967","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-18T00:00:00Z","page":"149-150","publication":"Proceedings of the 2018 ACM Conference on Economics and Computation - EC '18","citation":{"chicago":"Hansen, Kristoffer Arnsfelt, Rasmus Ibsen-Jensen, and Abraham Neyman. “The Big Match with a Clock and a Bit of Memory.” In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, 149–50. ACM Press, 2018. https://doi.org/10.1145/3219166.3219198.","mla":"Hansen, Kristoffer Arnsfelt, et al. “The Big Match with a Clock and a Bit of Memory.” Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–50, doi:10.1145/3219166.3219198.","short":"K.A. Hansen, R. Ibsen-Jensen, A. Neyman, in:, Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–150.","ista":"Hansen KA, Ibsen-Jensen R, Neyman A. 2018. The Big Match with a clock and a bit of memory. Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. EC: Conference on Economics and Computation, 149–150.","ieee":"K. A. Hansen, R. Ibsen-Jensen, and A. Neyman, “The Big Match with a clock and a bit of memory,” in Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, Ithaca, NY, United States, 2018, pp. 149–150.","apa":"Hansen, K. A., Ibsen-Jensen, R., & Neyman, A. (2018). The Big Match with a clock and a bit of memory. In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18 (pp. 149–150). Ithaca, NY, United States: ACM Press. https://doi.org/10.1145/3219166.3219198","ama":"Hansen KA, Ibsen-Jensen R, Neyman A. The Big Match with a clock and a bit of memory. In: Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. ACM Press; 2018:149-150. doi:10.1145/3219166.3219198"},"file_date_updated":"2020-07-14T12:47:14Z","date_created":"2019-02-13T10:31:41Z","date_updated":"2023-09-19T10:45:15Z","author":[{"first_name":"Kristoffer Arnsfelt","last_name":"Hansen","full_name":"Hansen, Kristoffer Arnsfelt"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"first_name":"Abraham","last_name":"Neyman","full_name":"Neyman, Abraham"}],"publication_status":"published","publisher":"ACM Press","department":[{"_id":"KrCh"}],"year":"2018","month":"06","publication_identifier":{"isbn":["9781450358293"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-22","location":"Ithaca, NY, United States","start_date":"2018-06-18","name":"EC: Conference on Economics and Computation"},"doi":"10.1145/3219166.3219198","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000492755100020"]}},{"language":[{"iso":"eng"}],"conference":{"location":"Vienna, Austria","start_date":"2018-07-16","end_date":"2018-07-18","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"doi":"10.1145/3210377.3210406","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.00947","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1804.00947"],"isi":["000545269600046"]},"month":"07","publication_identifier":{"isbn":["9781450357999"]},"date_updated":"2023-09-19T10:44:49Z","date_created":"2019-02-13T10:26:07Z","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Haider, Syed Kamran","last_name":"Haider","first_name":"Syed Kamran"},{"first_name":"Raphael","last_name":"Kübler","full_name":"Kübler, Raphael"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM Press","year":"2018","date_published":"2018-07-16T00:00:00Z","page":"383-392","publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","citation":{"ista":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. 2018. The transactional conflict problem. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 383–392.","ieee":"D.-A. Alistarh, S. K. Haider, R. Kübler, and G. Nadiradze, “The transactional conflict problem,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 383–392.","apa":"Alistarh, D.-A., Haider, S. K., Kübler, R., & Nadiradze, G. (2018). The transactional conflict problem. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 383–392). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210406","ama":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. The transactional conflict problem. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:383-392. doi:10.1145/3210377.3210406","chicago":"Alistarh, Dan-Adrian, Syed Kamran Haider, Raphael Kübler, and Giorgi Nadiradze. “The Transactional Conflict Problem.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 383–92. ACM Press, 2018. https://doi.org/10.1145/3210377.3210406.","mla":"Alistarh, Dan-Adrian, et al. “The Transactional Conflict Problem.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–92, doi:10.1145/3210377.3210406.","short":"D.-A. Alistarh, S.K. Haider, R. Kübler, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–392."},"day":"16","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"The transactional conflict problem","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5966","abstract":[{"text":"The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely \"requestor wins'' and \"requestor aborts'' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constant-competitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to non-trivial performance improvements for classic concurrent data structures.","lang":"eng"}],"type":"conference"},{"issue":"6","abstract":[{"text":"We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N. Har-vey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F. Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms, arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG. Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the method picks aflaw present in the current state and goes to a new state according to some prespecified probabilitydistribution (which depends on the current state and the selected flaw). However, the recent formu-lation is less flexible than the Moser–Tardos method since it requires a specific flaw selection rule,whereas the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially beimplemented more efficiently). We formulate a new “commutativity” condition and prove that it issufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additionalassumption. We then show that existing resampling oracles for perfect matchings and permutationsdo satisfy this condition.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5975","intvolume":" 47","title":"Commutativity in the algorithmic Lovász local lemma","status":"public","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2018-11-08T00:00:00Z","citation":{"mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing, vol. 47, no. 6, Society for Industrial & Applied Mathematics (SIAM), 2018, pp. 2029–56, doi:10.1137/16m1093306.","short":"V. Kolmogorov, SIAM Journal on Computing 47 (2018) 2029–2056.","chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM), 2018. https://doi.org/10.1137/16m1093306.","ama":"Kolmogorov V. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 2018;47(6):2029-2056. doi:10.1137/16m1093306","ista":"Kolmogorov V. 2018. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 47(6), 2029–2056.","apa":"Kolmogorov, V. (2018). Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/16m1093306","ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovász local lemma,” SIAM Journal on Computing, vol. 47, no. 6. Society for Industrial & Applied Mathematics (SIAM), pp. 2029–2056, 2018."},"publication":"SIAM Journal on Computing","page":"2029-2056","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1193"}]},"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"volume":47,"date_updated":"2023-09-19T14:24:58Z","date_created":"2019-02-13T12:59:33Z","year":"2018","publisher":"Society for Industrial & Applied Mathematics (SIAM)","department":[{"_id":"VlKo"}],"publication_status":"published","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"11","doi":"10.1137/16m1093306","language":[{"iso":"eng"}],"external_id":{"arxiv":["1506.08547"],"isi":["000453785100001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.08547"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"date_created":"2019-02-13T10:08:19Z","date_updated":"2023-09-19T10:43:45Z","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuznetsov","first_name":"Petr","full_name":"Kuznetsov, Petr"}],"publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"year":"2018","language":[{"iso":"eng"}],"conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom"},"doi":"10.1145/3212734.3212785","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://hal-univ-lyon3.archives-ouvertes.fr/INRIA/hal-01887733v1","open_access":"1"}],"external_id":{"isi":["000458186900052"]},"oa":1,"month":"07","publication_identifier":{"isbn":["9781450357951"]},"oa_version":"Submitted Version","title":"Brief Announcement: Performance prediction for coarse-grained locking","status":"public","_id":"5964","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"A standard design pattern found in many concurrent data structures, such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarse-grained lock-based algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc."}],"type":"conference","date_published":"2018-07-23T00:00:00Z","page":"411-413","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"ama":"Aksenov V, Alistarh D-A, Kuznetsov P. Brief Announcement: Performance prediction for coarse-grained locking. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:411-413. doi:10.1145/3212734.3212785","ista":"Aksenov V, Alistarh D-A, Kuznetsov P. 2018. Brief Announcement: Performance prediction for coarse-grained locking. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 411–413.","apa":"Aksenov, V., Alistarh, D.-A., & Kuznetsov, P. (2018). Brief Announcement: Performance prediction for coarse-grained locking. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 411–413). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212785","ieee":"V. Aksenov, D.-A. Alistarh, and P. Kuznetsov, “Brief Announcement: Performance prediction for coarse-grained locking,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 411–413.","mla":"Aksenov, Vitaly, et al. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–13, doi:10.1145/3212734.3212785.","short":"V. Aksenov, D.-A. Alistarh, P. Kuznetsov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–413.","chicago":"Aksenov, Vitaly, Dan-Adrian Alistarh, and Petr Kuznetsov. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 411–13. ACM Press, 2018. https://doi.org/10.1145/3212734.3212785."},"day":"23","article_processing_charge":"No","scopus_import":"1"},{"publication":"Random matrices: Theory and applications","citation":{"ieee":"L. Erdös and P. Mühlbacher, “Bounds on the norm of Wigner-type random matrices,” Random matrices: Theory and applications. World Scientific Publishing, 2018.","apa":"Erdös, L., & Mühlbacher, P. (2018). Bounds on the norm of Wigner-type random matrices. Random Matrices: Theory and Applications. World Scientific Publishing. https://doi.org/10.1142/s2010326319500096","ista":"Erdös L, Mühlbacher P. 2018. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications., 1950009.","ama":"Erdös L, Mühlbacher P. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications. 2018. doi:10.1142/s2010326319500096","chicago":"Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications. World Scientific Publishing, 2018. https://doi.org/10.1142/s2010326319500096.","short":"L. Erdös, P. Mühlbacher, Random Matrices: Theory and Applications (2018).","mla":"Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications, 1950009, World Scientific Publishing, 2018, doi:10.1142/s2010326319500096."},"date_published":"2018-09-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5971","title":"Bounds on the norm of Wigner-type random matrices","status":"public","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider a Wigner-type ensemble, i.e. large hermitian N×N random matrices H=H∗ with centered independent entries and with a general matrix of variances Sxy=𝔼∣∣Hxy∣∣2. The norm of H is asymptotically given by the maximum of the support of the self-consistent density of states. We establish a bound on this maximum in terms of norms of powers of S that substantially improves the earlier bound 2∥S∥1/2∞ given in [O. Ajanki, L. Erdős and T. Krüger, Universality for general Wigner-type matrices, Prob. Theor. Rel. Fields169 (2017) 667–727]. The key element of the proof is an effective Markov chain approximation for the contributions of the weighted Dyck paths appearing in the iterative solution of the corresponding Dyson equation.","lang":"eng"}],"external_id":{"isi":["000477677200002"],"arxiv":["1802.05175"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.05175","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"doi":"10.1142/s2010326319500096","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2010-3263"],"eissn":["2010-3271"]},"year":"2018","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"World Scientific Publishing","author":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"full_name":"Mühlbacher, Peter","first_name":"Peter","last_name":"Mühlbacher"}],"date_created":"2019-02-13T10:40:54Z","date_updated":"2023-09-19T14:24:05Z","article_number":"1950009","ec_funded":1},{"doi":"10.1038/s41467-018-04342-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000432280000006"]},"oa":1,"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"month":"12","author":[{"last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","full_name":"Morri, Maurizio"},{"full_name":"Sanchez-Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez-Romero","first_name":"Inmaculada"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine","last_name":"Tichy"},{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie"},{"first_name":"Elliot J.","last_name":"Gerrard","full_name":"Gerrard, Elliot J."},{"full_name":"Hirschfeld, Priscila","last_name":"Hirschfeld","first_name":"Priscila","id":"435ACB3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"volume":9,"date_updated":"2023-09-19T14:29:32Z","date_created":"2019-02-14T10:50:24Z","year":"2018","department":[{"_id":"HaJa"},{"_id":"CaGu"},{"_id":"MiSi"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:14Z","article_number":"1950","date_published":"2018-12-01T00:00:00Z","citation":{"ama":"Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04342-1","ieee":"M. Morri et al., “Optical functionalization of human class A orphan G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","apa":"Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04342-1","ista":"Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P, Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 9(1), 1950.","short":"M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).","mla":"Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications, vol. 9, no. 1, 1950, Springer Nature, 2018, doi:10.1038/s41467-018-04342-1.","chicago":"Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1."},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2018_Springer_Morri.pdf","creator":"kschuh","content_type":"application/pdf","file_size":1349914,"file_id":"5985","relation":"main_file","checksum":"8325fcc194264af4749e662a73bf66b5","date_updated":"2020-07-14T12:47:14Z","date_created":"2019-02-14T10:58:29Z"}],"oa_version":"Published Version","_id":"5984","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 9","ddc":["570"],"title":"Optical functionalization of human class A orphan G-protein-coupled receptors","status":"public","issue":"1","abstract":[{"lang":"eng","text":"G-protein-coupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the light-sensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs."}],"type":"journal_article"},{"publication_identifier":{"issn":["0730-0301"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1145/3272127.3275076","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"},{"_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000455953100064"]},"oa":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:14Z","article_number":"241","volume":37,"date_updated":"2023-09-19T14:25:30Z","date_created":"2019-02-13T13:12:53Z","author":[{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez"},{"id":"33F19F16-F248-11E8-B48F-1D18A9856A87","last_name":"Iarussi","first_name":"Emmanuel","full_name":"Iarussi, Emmanuel"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"last_name":"Miguel","first_name":"Eder","full_name":"Miguel, Eder"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"publisher":"Association for Computing Machinery (ACM)","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2018","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","article_type":"original","citation":{"mla":"Malomo, Luigi, et al. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics, vol. 37, no. 6, 241, Association for Computing Machinery (ACM), 2018, doi:10.1145/3272127.3275076.","short":"L. Malomo, J. Perez Rodriguez, E. Iarussi, N. Pietroni, E. Miguel, P. Cignoni, B. Bickel, ACM Transactions on Graphics 37 (2018).","chicago":"Malomo, Luigi, Jesus Perez Rodriguez, Emmanuel Iarussi, Nico Pietroni, Eder Miguel, Paolo Cignoni, and Bernd Bickel. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3272127.3275076.","ama":"Malomo L, Perez Rodriguez J, Iarussi E, et al. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 2018;37(6). doi:10.1145/3272127.3275076","ista":"Malomo L, Perez Rodriguez J, Iarussi E, Pietroni N, Miguel E, Cignoni P, Bickel B. 2018. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 37(6), 241.","apa":"Malomo, L., Perez Rodriguez, J., Iarussi, E., Pietroni, N., Miguel, E., Cignoni, P., & Bickel, B. (2018). FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. Association for Computing Machinery (ACM). https://doi.org/10.1145/3272127.3275076","ieee":"L. Malomo et al., “FlexMaps: Computational design of flat flexible shells for shaping 3D objects,” ACM Transactions on Graphics, vol. 37, no. 6. Association for Computing Machinery (ACM), 2018."},"publication":"ACM Transactions on Graphics","issue":"6","abstract":[{"text":"We propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2019-09-23T12:48:52Z","date_updated":"2020-07-14T12:47:14Z","checksum":"d0529a41c78b37ab8840685579fb33b4","file_id":"6901","relation":"main_file","creator":"bbickel","file_size":100109811,"content_type":"application/pdf","file_name":"flexmaps_author_version.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"1068","intvolume":" 37","status":"public","title":"FlexMaps: Computational design of flat flexible shells for shaping 3D objects","ddc":["000"],"_id":"5976","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5983","intvolume":" 98","title":"Theory of the rotating polaron: Spectrum and self-localization","status":"public","issue":"22","abstract":[{"text":"We study a quantum impurity possessing both translational and internal rotational degrees of freedom interacting with a bosonic bath. Such a system corresponds to a “rotating polaron,” which can be used to model, e.g., a rotating molecule immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian of the rotating polaron and study its spectrum in the weak- and strong-coupling regimes using a combination of variational, diagrammatic, and mean-field approaches. We reveal how the coupling between linear and angular momenta affects stable quasiparticle states, and demonstrate that internal rotation leads to an enhanced self-localization in the translational degrees of freedom.","lang":"eng"}],"type":"journal_article","date_published":"2018-12-12T00:00:00Z","citation":{"ista":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. 2018. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 98(22), 224506.","apa":"Yakaboylu, E., Midya, B., Deuchert, A., Leopold, N. K., & Lemeshko, M. (2018). Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.98.224506","ieee":"E. Yakaboylu, B. Midya, A. Deuchert, N. K. Leopold, and M. Lemeshko, “Theory of the rotating polaron: Spectrum and self-localization,” Physical Review B, vol. 98, no. 22. American Physical Society, 2018.","ama":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 2018;98(22). doi:10.1103/physrevb.98.224506","chicago":"Yakaboylu, Enderalp, Bikashkali Midya, Andreas Deuchert, Nikolai K Leopold, and Mikhail Lemeshko. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.98.224506.","mla":"Yakaboylu, Enderalp, et al. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B, vol. 98, no. 22, 224506, American Physical Society, 2018, doi:10.1103/physrevb.98.224506.","short":"E. Yakaboylu, B. Midya, A. Deuchert, N.K. Leopold, M. Lemeshko, Physical Review B 98 (2018)."},"publication":"Physical Review B","article_processing_charge":"No","day":"12","scopus_import":"1","author":[{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"},{"id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","first_name":"Bikashkali","full_name":"Midya, Bikashkali"},{"last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas"},{"last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"volume":98,"date_created":"2019-02-14T10:37:09Z","date_updated":"2023-09-19T14:29:03Z","year":"2018","publisher":"American Physical Society","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"article_number":"224506","doi":"10.1103/physrevb.98.224506","language":[{"iso":"eng"}],"external_id":{"arxiv":["1809.01204"],"isi":["000452992700008"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01204"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"12"},{"language":[{"iso":"eng"}],"doi":"10.1002/anie.201809847","quality_controlled":"1","isi":1,"external_id":{"isi":["000454575500020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://upcommons.upc.edu/bitstream/2117/130444/1/Zhang%20preprint.pdf"}],"publication_identifier":{"issn":["1433-7851"]},"month":"12","volume":57,"date_updated":"2023-09-19T14:28:31Z","date_created":"2019-02-14T10:23:27Z","author":[{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"last_name":"Zhang","first_name":"Ting","full_name":"Zhang, Ting"},{"full_name":"Tang, Pengyi","first_name":"Pengyi","last_name":"Tang"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"first_name":"Ka Ming","last_name":"Ng","full_name":"Ng, Ka Ming"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Guardia, Pablo","first_name":"Pablo","last_name":"Guardia"},{"full_name":"Prato, Mirko","last_name":"Prato","first_name":"Mirko"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"publisher":"Wiley","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2018","date_published":"2018-12-21T00:00:00Z","page":"17063-17068","article_type":"original","citation":{"apa":"Zhang, Y., Liu, Y., Lim, K. H., Xing, C., Li, M., Zhang, T., … Cabot, A. (2018). Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201809847","ieee":"Y. Zhang et al., “Tin diselenide molecular precursor for solution-processable thermoelectric materials,” Angewandte Chemie International Edition, vol. 57, no. 52. Wiley, pp. 17063–17068, 2018.","ista":"Zhang Y, Liu Y, Lim KH, Xing C, Li M, Zhang T, Tang P, Arbiol J, Llorca J, Ng KM, Ibáñez M, Guardia P, Prato M, Cadavid D, Cabot A. 2018. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 57(52), 17063–17068.","ama":"Zhang Y, Liu Y, Lim KH, et al. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 2018;57(52):17063-17068. doi:10.1002/anie.201809847","chicago":"Zhang, Yu, Yu Liu, Khak Ho Lim, Congcong Xing, Mengyao Li, Ting Zhang, Pengyi Tang, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201809847.","short":"Y. Zhang, Y. Liu, K.H. Lim, C. Xing, M. Li, T. Zhang, P. Tang, J. Arbiol, J. Llorca, K.M. Ng, M. Ibáñez, P. Guardia, M. Prato, D. Cadavid, A. Cabot, Angewandte Chemie International Edition 57 (2018) 17063–17068.","mla":"Zhang, Yu, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition, vol. 57, no. 52, Wiley, 2018, pp. 17063–68, doi:10.1002/anie.201809847."},"publication":"Angewandte Chemie International Edition","article_processing_charge":"No","day":"21","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 57","status":"public","title":"Tin diselenide molecular precursor for solution-processable thermoelectric materials","_id":"5982","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"52","abstract":[{"lang":"eng","text":"In the present work, we detail a fast and simple solution-based method to synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown through a screw dislocation-driven mechanism. This mechanism typically results in pyramidal structures, but we demonstrate here that the growth from multiple dislocations results in flower-like structures. Crystallographically textured SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures display highly anisotropic charge and heat transport properties and thermoelectric (TE) figures of merit limited by relatively low electrical conductivities. To improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles. The electrical conductivities of the blends are significantly improved with respect to bare SnSe2 NPLs, what translates into a three-fold increase of the TE Figure of merit, reaching unprecedented ZT values up to 0.65."}],"type":"journal_article"},{"title":"Exact MAP-inference by confining combinatorial search with LP relaxation","publication_status":"published","status":"public","department":[{"_id":"VlKo"}],"publisher":"AAAI Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5978","year":"2018","date_updated":"2023-09-19T14:26:52Z","date_created":"2019-02-13T13:32:48Z","oa_version":"Preprint","author":[{"full_name":"Haller, Stefan","first_name":"Stefan","last_name":"Haller"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"type":"conference","abstract":[{"lang":"eng","text":"We consider the MAP-inference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous Sherali-Adams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose the original probleminto two non-overlapping parts: an easy LP-tight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applica-tions the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before."}],"quality_controlled":"1","isi":1,"page":"6581-6588","publication":"Proceedings of the 32st AAAI Conference on Artificial Intelligence","citation":{"chicago":"Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the 32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018.","mla":"Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–88.","short":"S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588.","ista":"Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.","ieee":"S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588.","apa":"Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference by confining combinatorial search with LP relaxation. In Proceedings of the 32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans, LU, United States: AAAI Press.","ama":"Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI Press; 2018:6581-6588."},"external_id":{"arxiv":["2004.06370"],"isi":["000485488906082"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.06370"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2018-02-07","location":"New Orleans, LU, United States","start_date":"2018-02-02","name":"AAAI: Conference on Artificial Intelligence"},"date_published":"2018-02-01T00:00:00Z","scopus_import":"1","day":"01","month":"02","article_processing_charge":"No"},{"article_number":"1802257","year":"2018","publisher":"Wiley","department":[{"_id":"GeKa"}],"publication_status":"published","author":[{"full_name":"Ridderbos, Joost","last_name":"Ridderbos","first_name":"Joost"},{"full_name":"Brauns, Matthias","first_name":"Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shen, Jie","first_name":"Jie","last_name":"Shen"},{"last_name":"de Vries","first_name":"Folkert K.","full_name":"de Vries, Folkert K."},{"full_name":"Li, Ang","first_name":"Ang","last_name":"Li"},{"last_name":"Bakkers","first_name":"Erik P. A. M.","full_name":"Bakkers, Erik P. A. M."},{"first_name":"Alexander","last_name":"Brinkman","full_name":"Brinkman, Alexander"},{"first_name":"Floris A.","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris A."}],"volume":30,"date_updated":"2023-09-19T14:29:58Z","date_created":"2019-02-14T12:14:26Z","publication_identifier":{"issn":["0935-9648"]},"month":"11","oa":1,"external_id":{"isi":["000450232800015"],"arxiv":["1809.08487"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.08487","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1002/adma.201802257","language":[{"iso":"eng"}],"type":"journal_article","issue":"44","abstract":[{"lang":"eng","text":"A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5990","intvolume":" 30","status":"public","title":"Josephson effect in a few-hole quantum dot","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"02","citation":{"apa":"Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257","ieee":"J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018.","ista":"Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257.","ama":"Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257","chicago":"Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257.","short":"J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018).","mla":"Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257."},"publication":"Advanced Materials","date_published":"2018-11-02T00:00:00Z"},{"department":[{"_id":"KrPi"}],"intvolume":" 12","publisher":"AIMS","publication_status":"published","status":"public","title":"Private set-intersection with common set-up","year":"2018","_id":"5980","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":12,"oa_version":"None","date_created":"2019-02-13T13:49:41Z","date_updated":"2023-09-19T14:27:59Z","author":[{"last_name":"Chatterjee","first_name":"Sanjit","full_name":"Chatterjee, Sanjit"},{"first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Kumar, Vikas","last_name":"Kumar","first_name":"Vikas"}],"type":"journal_article","issue":"1","abstract":[{"text":"The problem of private set-intersection (PSI) has been traditionally treated as an instance of the more general problem of multi-party computation (MPC). Consequently, in order to argue security, or compose these protocols one has to rely on the general theory that was developed for the purpose of MPC. The pursuit of efficient protocols, however, has resulted in designs that exploit properties pertaining to PSI. In almost all practical applications where a PSI protocol is deployed, it is expected to be executed multiple times, possibly on related inputs. In this work we initiate a dedicated study of PSI in the multi-interaction (MI) setting. In this model a server sets up the common system parameters and executes set-intersection multiple times with potentially different clients. We discuss a few attacks that arise when protocols are naïvely composed in this manner and, accordingly, craft security definitions for the MI setting and study their inter-relation. Finally, we suggest a set of protocols that are MI-secure, at the same time almost as efficient as their parent, stand-alone, protocols.","lang":"eng"}],"page":"17-47","isi":1,"quality_controlled":"1","citation":{"chicago":"Chatterjee, Sanjit, Chethan Kamath Hosdurg, and Vikas Kumar. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences. AIMS, 2018. https://doi.org/10.3934/amc.2018002.","mla":"Chatterjee, Sanjit, et al. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences, vol. 12, no. 1, AIMS, 2018, pp. 17–47, doi:10.3934/amc.2018002.","short":"S. Chatterjee, C. Kamath Hosdurg, V. Kumar, American Institute of Mathematical Sciences 12 (2018) 17–47.","ista":"Chatterjee S, Kamath Hosdurg C, Kumar V. 2018. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 12(1), 17–47.","apa":"Chatterjee, S., Kamath Hosdurg, C., & Kumar, V. (2018). Private set-intersection with common set-up. American Institute of Mathematical Sciences. AIMS. https://doi.org/10.3934/amc.2018002","ieee":"S. Chatterjee, C. Kamath Hosdurg, and V. Kumar, “Private set-intersection with common set-up,” American Institute of Mathematical Sciences, vol. 12, no. 1. AIMS, pp. 17–47, 2018.","ama":"Chatterjee S, Kamath Hosdurg C, Kumar V. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 2018;12(1):17-47. doi:10.3934/amc.2018002"},"external_id":{"isi":["000430950400002"]},"publication":"American Institute of Mathematical Sciences","language":[{"iso":"eng"}],"date_published":"2018-02-01T00:00:00Z","doi":"10.3934/amc.2018002","scopus_import":"1","article_processing_charge":"No","day":"01","month":"02"},{"month":"10","publication_identifier":{"issn":["1553-7404"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000449328500025"]},"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pgen.1007698","language":[{"iso":"eng"}],"article_number":"e1007698","file_date_updated":"2020-07-14T12:47:15Z","year":"2018","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Public Library of Science","author":[{"first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"last_name":"Meinhardt","first_name":"Gudrun","full_name":"Meinhardt, Gudrun"},{"full_name":"Plessl, Kerstin","last_name":"Plessl","first_name":"Kerstin"},{"full_name":"Vondra, Sigrid","first_name":"Sigrid","last_name":"Vondra"},{"last_name":"Weiss","first_name":"Tamara","full_name":"Weiss, Tamara"},{"full_name":"Haslinger, Peter","last_name":"Haslinger","first_name":"Peter"},{"full_name":"Lendl, Thomas","last_name":"Lendl","first_name":"Thomas"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"last_name":"Mairhofer","first_name":"Mario","full_name":"Mairhofer, Mario"},{"last_name":"Zhu","first_name":"Xiaowei","full_name":"Zhu, Xiaowei"},{"first_name":"Birgit","last_name":"Schütz","full_name":"Schütz, Birgit"},{"last_name":"Hannibal","first_name":"Roberta L.","full_name":"Hannibal, Roberta L."},{"full_name":"Lindau, Robert","last_name":"Lindau","first_name":"Robert"},{"first_name":"Beatrix","last_name":"Weil","full_name":"Weil, Beatrix"},{"last_name":"Ernerudh","first_name":"Jan","full_name":"Ernerudh, Jan"},{"full_name":"Neesen, Jürgen","last_name":"Neesen","first_name":"Jürgen"},{"full_name":"Egger, Gerda","last_name":"Egger","first_name":"Gerda"},{"last_name":"Mikula","first_name":"Mario","full_name":"Mikula, Mario"},{"last_name":"Röhrl","first_name":"Clemens","full_name":"Röhrl, Clemens"},{"first_name":"Alexander E.","last_name":"Urban","full_name":"Urban, Alexander E."},{"first_name":"Julie","last_name":"Baker","full_name":"Baker, Julie"},{"full_name":"Knöfler, Martin","last_name":"Knöfler","first_name":"Martin"},{"full_name":"Pollheimer, Jürgen","first_name":"Jürgen","last_name":"Pollheimer"}],"date_updated":"2023-09-19T14:31:43Z","date_created":"2019-02-14T13:07:45Z","volume":14,"scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","publication":"PLOS Genetics","citation":{"chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.","short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698.","ieee":"P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698.","ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698"},"date_published":"2018-10-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM."}],"issue":"10","_id":"5998","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"Genome amplification and cellular senescence are hallmarks of human placenta development","intvolume":" 14","file":[{"file_name":"2018_PLOS_Velicky.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":4592947,"file_id":"6000","relation":"main_file","date_created":"2019-02-14T13:14:35Z","date_updated":"2020-07-14T12:47:15Z","checksum":"34aa9a5972f61889c19f18be8ee787a0"}],"oa_version":"Published Version"},{"pmid":1,"year":"2018","department":[{"_id":"FyKo"}],"publisher":"Oxford University Press ","publication_status":"published","author":[{"last_name":"Usmanova","first_name":"Dinara R","full_name":"Usmanova, Dinara R"},{"full_name":"Bogatyreva, Natalya S","first_name":"Natalya S","last_name":"Bogatyreva"},{"first_name":"Joan","last_name":"Ariño Bernad","full_name":"Ariño Bernad, Joan"},{"first_name":"Aleksandra A","last_name":"Eremina","full_name":"Eremina, Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","first_name":"Anastasiya A","last_name":"Gorshkova"},{"last_name":"Kanevskiy","first_name":"German M","full_name":"Kanevskiy, German M"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"full_name":"Meister, Alexander V","last_name":"Meister","first_name":"Alexander V"},{"full_name":"Yakupova, Alisa G","first_name":"Alisa G","last_name":"Yakupova"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"}],"volume":34,"date_updated":"2023-09-19T14:31:13Z","date_created":"2019-02-14T12:48:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:15Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["29722803"],"isi":["000450038900008"]},"oa":1,"project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution"}],"quality_controlled":"1","isi":1,"doi":"10.1093/bioinformatics/bty340","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1367-4803","1460-2059"]},"month":"11","_id":"5995","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 34","ddc":["570"],"status":"public","title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","file":[{"access_level":"open_access","file_name":"2018_Oxford_Usmanova.pdf","creator":"kschuh","file_size":291969,"content_type":"application/pdf","file_id":"5997","relation":"main_file","checksum":"7e0495153f44211479674601d7f6ee03","date_created":"2019-02-14T13:00:55Z","date_updated":"2020-07-14T12:47:15Z"}],"oa_version":"Published Version","type":"journal_article","issue":"21","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"citation":{"ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340."},"publication":"Bioinformatics","page":"3653-3658","date_published":"2018-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"date_published":"2018-11-01T00:00:00Z","page":"2674-2686","citation":{"short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082.","chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082","apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082","ieee":"S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686."},"publication":"Molecular Biology of the Cell","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5994","checksum":"e98465b4416b3e804c47f40086932af2","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T12:34:29Z","access_level":"open_access","file_name":"2018_ASCB_Dolati.pdf","content_type":"application/pdf","file_size":6668971,"creator":"kschuh"}],"intvolume":" 29","status":"public","title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","ddc":["570"],"_id":"5992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"22","abstract":[{"lang":"eng","text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1091/mbc.e18-02-0082","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"pmid":["30156465"],"isi":["000455641000011"]},"oa":1,"publication_identifier":{"eissn":["1939-4586"]},"month":"11","volume":29,"date_updated":"2023-09-19T14:30:23Z","date_created":"2019-02-14T12:25:47Z","author":[{"last_name":"Dolati","first_name":"Setareh","full_name":"Dolati, Setareh"},{"full_name":"Kage, Frieda","last_name":"Kage","first_name":"Frieda"},{"last_name":"Mueller","first_name":"Jan","full_name":"Mueller, Jan"},{"full_name":"Müsken, Mathias","last_name":"Müsken","first_name":"Mathias"},{"first_name":"Marieluise","last_name":"Kirchner","full_name":"Kirchner, Marieluise"},{"last_name":"Dittmar","first_name":"Gunnar","full_name":"Dittmar, Gunnar"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"}],"department":[{"_id":"MiSi"}],"publisher":"American Society for Cell Biology ","publication_status":"published","pmid":1,"year":"2018","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:15Z"},{"oa_version":"Submitted Version","intvolume":" 115","title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","status":"public","_id":"6010","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"32","abstract":[{"text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity.","lang":"eng"}],"type":"journal_article","date_published":"2018-08-07T00:00:00Z","page":"E7615-E7623","citation":{"ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115","ieee":"F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"07","scopus_import":"1","volume":115,"date_created":"2019-02-14T14:33:34Z","date_updated":"2023-09-19T14:35:36Z","author":[{"first_name":"Florencia","last_name":"Garrido-Charad","full_name":"Garrido-Charad, Florencia"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A"},{"full_name":"Gutiérrez-Ibáñez, Cristián","last_name":"Gutiérrez-Ibáñez","first_name":"Cristián"},{"first_name":"Pedro","last_name":"Fernandez","full_name":"Fernandez, Pedro"},{"full_name":"López-Jury, Luciana","first_name":"Luciana","last_name":"López-Jury"},{"last_name":"González-Cabrera","first_name":"Cristian","full_name":"González-Cabrera, Cristian"},{"full_name":"Karten, Harvey J.","last_name":"Karten","first_name":"Harvey J."},{"full_name":"Luksch, Harald","last_name":"Luksch","first_name":"Harald"},{"last_name":"Marín","first_name":"Gonzalo J.","full_name":"Marín, Gonzalo J."}],"department":[{"_id":"MaJö"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2018","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1804517115","isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["30026198"],"isi":["000440982000020"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198","open_access":"1"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"08"},{"volume":37,"date_created":"2019-02-14T13:52:25Z","date_updated":"2023-09-19T14:33:40Z","author":[{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"}],"publisher":"Wiley","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2018","ec_funded":1,"file_date_updated":"2020-07-14T12:47:15Z","language":[{"iso":"eng"}],"doi":"10.1111/cgf.13327","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000437272800019"]},"publication_identifier":{"issn":["0167-7055"]},"month":"09","file":[{"checksum":"d2bbe5c658d8159fbe9016a4f5e82b19","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T14:09:28Z","relation":"main_file","file_id":"6004","content_type":"application/pdf","file_size":6209349,"creator":"kschuh","access_level":"open_access","file_name":"StylizedFabricationSTAR-Personal.pdf"}],"oa_version":"Submitted Version","pubrep_id":"1051","intvolume":" 37","ddc":["004"],"status":"public","title":"State of the art on stylized fabrication","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6003","issue":"6","abstract":[{"text":"Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research.","lang":"eng"}],"type":"journal_article","date_published":"2018-09-01T00:00:00Z","page":"325-342","citation":{"ista":"Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342.","apa":"Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327","ieee":"B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342, 2018.","ama":"Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327","chicago":"Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13327.","mla":"Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327.","short":"B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342."},"publication":"Computer Graphics Forum","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-09-01T00:00:00Z","page":"1037-1090","publication":"Archive for Rational Mechanics and Analysis","citation":{"ieee":"M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” Archive for Rational Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6","ista":"Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090.","ama":"Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6.","short":"M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6."},"abstract":[{"lang":"eng","text":"The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram."}],"issue":"3","type":"journal_article","oa_version":"Preprint","status":"public","title":"The Bogoliubov free energy functional I: Existence of minimizers and phase diagram","intvolume":" 229","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6002","month":"09","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00205-018-1232-6","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1511.05935"],"isi":["000435367300003"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05935"}],"oa":1,"date_created":"2019-02-14T13:40:53Z","date_updated":"2023-09-19T14:33:12Z","volume":229,"author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","last_name":"Reuvers","full_name":"Reuvers, Robin"},{"full_name":"Solovej, Jan Philip","first_name":"Jan Philip","last_name":"Solovej"}],"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","year":"2018"},{"year":"2018","acknowledgement":" We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","author":[{"first_name":"Mukund","last_name":"Vasudevan","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","full_name":"Vasudevan, Mukund"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"date_updated":"2023-09-19T14:37:49Z","date_created":"2019-02-14T12:50:50Z","volume":839,"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.06372"}],"external_id":{"isi":["000437858300003"],"arxiv":["1709.06372"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"}],"doi":"10.1017/jfm.2017.923","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5996","status":"public","title":"The critical point of the transition to turbulence in pipe flow","intvolume":" 839","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion.","lang":"eng"}],"publication":"Journal of Fluid Mechanics","citation":{"ama":"Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923","apa":"Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923","ieee":"M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018.","ista":"Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94.","short":"M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94.","mla":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923.","chicago":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923."},"article_type":"original","page":"76-94","date_published":"2018-03-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"No"},{"abstract":[{"text":"In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Submitted Version","_id":"5993","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","intvolume":" 40","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","publication":"ACM Transactions on Programming Languages and Systems","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.","mla":"Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018).","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800"},"ec_funded":1,"article_number":"7","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"full_name":"Hasheminezhad, Rouzbeh","last_name":"Hasheminezhad","first_name":"Rouzbeh"}],"related_material":{"record":[{"id":"1438","status":"public","relation":"earlier_version"}]},"date_created":"2019-02-14T12:29:10Z","date_updated":"2023-09-19T14:38:42Z","volume":40,"year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery (ACM)","month":"06","publication_identifier":{"issn":["0164-0925"]},"doi":"10.1145/3174800","language":[{"iso":"eng"}],"external_id":{"arxiv":["1510.08517"],"isi":["000434634500003"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1510.08517","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}]},{"oa_version":"Preprint","intvolume":" 116","title":"The cohomological Hall algebra of a preprojective algebra","status":"public","_id":"5999","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","abstract":[{"text":"We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. ","lang":"eng"}],"type":"journal_article","date_published":"2018-05-01T00:00:00Z","page":"1029-1074","citation":{"ista":"Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074.","ieee":"Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018.","apa":"Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms.12111","ama":"Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 2018;116(5):1029-1074. doi:10.1112/plms.12111","chicago":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society. Oxford University Press, 2018. https://doi.org/10.1112/plms.12111.","mla":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111.","short":"Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074."},"publication":"Proceedings of the London Mathematical Society","article_processing_charge":"No","day":"01","scopus_import":"1","volume":116,"date_created":"2019-02-14T13:14:22Z","date_updated":"2023-09-19T14:37:19Z","author":[{"last_name":"Yang","first_name":"Yaping","full_name":"Yang, Yaping"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao","first_name":"Gufang","full_name":"Zhao, Gufang"}],"department":[{"_id":"TaHa"}],"publisher":"Oxford University Press","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"doi":"10.1112/plms.12111","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.7994"}],"oa":1,"external_id":{"isi":["000431506400001"],"arxiv":["1407.7994"]},"publication_identifier":{"issn":["0024-6115"]},"month":"05"},{"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evy037","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000429483700013"]},"oa":1,"publication_identifier":{"issn":["1759-6653"]},"month":"03","volume":10,"date_updated":"2023-09-19T14:39:08Z","date_created":"2019-02-14T12:13:52Z","author":[{"full_name":"Kincaid-Smith, Julien","last_name":"Kincaid-Smith","first_name":"Julien"},{"full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard"},{"first_name":"Céline","last_name":"Cosseau","full_name":"Cosseau, Céline"},{"full_name":"Boissier, Jérôme","first_name":"Jérôme","last_name":"Boissier"},{"full_name":"Severac, Dany","first_name":"Dany","last_name":"Severac"},{"first_name":"Christoph","last_name":"Grunau","full_name":"Grunau, Christoph"},{"first_name":"Eve","last_name":"Toulza","full_name":"Toulza, Eve"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication_status":"published","year":"2018","file_date_updated":"2020-07-14T12:47:15Z","date_published":"2018-03-01T00:00:00Z","page":"840-856","citation":{"short":"J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C. Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856.","mla":"Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037.","chicago":"Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037.","ama":"Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 2018;10(3):840-856. doi:10.1093/gbe/evy037","ieee":"J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018.","apa":"Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D., Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy037","ista":"Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 10(3), 840–856."},"publication":"Genome Biology and Evolution","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T12:20:01Z","checksum":"736a459cb77de5824354466bb0331caf","relation":"main_file","file_id":"5991","content_type":"application/pdf","file_size":529755,"creator":"dernst","file_name":"2018_GBE_Kincaid_Smith.pdf","access_level":"open_access"}],"intvolume":" 10","title":"Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites","ddc":["570"],"status":"public","_id":"5989","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"3","abstract":[{"lang":"eng","text":"Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal”displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression couldoccur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds."}],"type":"journal_article"},{"article_number":"8598402","type":"conference","abstract":[{"lang":"eng","text":"We introduce Clover, a new library for efficient computation using low-precision data, providing mathematical routines required by fundamental methods in optimization and sparse recovery. Our library faithfully implements variants of stochastic quantization that guarantee convergence at low precision, and supports data formats from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular, we show that 4-bit can be implemented efficiently using Intel AVX despite the lack of native support for this data format. Experimental results with dot product, matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard thresholding (IHT) demonstrate that the attainable speedups are in many cases close to linear with respect to the reduction of precision due to reduced data movement. Finally, for GD and IHT, we show examples of absolute speedup achieved by 4-bit versus 32-bit, by iterating until a given target error is achieved."}],"_id":"6031","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","title":"Fast quantized arithmetic on x86: Trading compute for data movement","status":"public","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"IEEE","author":[{"full_name":"Stojanov, Alen","first_name":"Alen","last_name":"Stojanov"},{"first_name":"Tyler Michael","last_name":"Smith","full_name":"Smith, Tyler Michael"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puschel, Markus","last_name":"Puschel","first_name":"Markus"}],"date_created":"2019-02-17T22:59:25Z","date_updated":"2023-09-19T14:41:51Z","volume":"2018-October","oa_version":"None","scopus_import":"1","month":"12","day":"31","article_processing_charge":"No","publication":"2018 IEEE International Workshop on Signal Processing Systems","citation":{"ama":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on x86: Trading compute for data movement. In: 2018 IEEE International Workshop on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402","ista":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic on x86: Trading compute for data movement. 2018 IEEE International Workshop on Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October, 8598402.","ieee":"A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol. 2018–October.","apa":"Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE International Workshop on Signal Processing Systems (Vol. 2018–October). Cape Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402","mla":"Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems, vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.","short":"A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International Workshop on Signal Processing Systems, IEEE, 2018.","chicago":"Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018 IEEE International Workshop on Signal Processing Systems, Vol. 2018–October. IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402."},"external_id":{"isi":["000465106800060"]},"quality_controlled":"1","isi":1,"conference":{"name":"SiPS: Workshop on Signal Processing Systems","end_date":"2018-10-24","start_date":"2018-10-21","location":"Cape Town, South Africa"},"doi":"10.1109/SiPS.2018.8598402","date_published":"2018-12-31T00:00:00Z","language":[{"iso":"eng"}]}]