[{"citation":{"chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group, 2018. https://doi.org/10.1136/jmedgenet-2017-104627.","ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54. doi:10.1136/jmedgenet-2017-104627","apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627","short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","ieee":"I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000418199800007"],"pmid":["28626029"]},"publist_id":"7016","author":[{"last_name":"Marin Valencia","full_name":"Marin Valencia, Isaac","first_name":"Isaac"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"last_name":"Rosti","full_name":"Rosti, Başak","first_name":"Başak"},{"full_name":"Issa, Mahmoud","last_name":"Issa","first_name":"Mahmoud"},{"first_name":"Damir","full_name":"Musaev, Damir","last_name":"Musaev"},{"first_name":"Gifty","last_name":"Bhat","full_name":"Bhat, Gifty"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"full_name":"Silhavy, Jennifer","last_name":"Silhavy","first_name":"Jennifer"},{"first_name":"Valentina","full_name":"Stanley, Valentina","last_name":"Stanley"},{"first_name":"Rasim","last_name":"Rosti","full_name":"Rosti, Rasim"},{"first_name":"Jeremy","last_name":"Gleeson","full_name":"Gleeson, Jeremy"},{"last_name":"Imam","full_name":"Imam, Farhad","first_name":"Farhad"},{"first_name":"Maha","full_name":"Zaki, Maha","last_name":"Zaki"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"}],"title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"}],"year":"2018","isi":1,"publication":"Journal of Medical Genetics","day":"01","page":"48 - 54","date_created":"2018-12-11T11:47:57Z","doi":"10.1136/jmedgenet-2017-104627","date_published":"2018-01-01T00:00:00Z","oa":1,"publisher":"BMJ Publishing Group","quality_controlled":"1","date_updated":"2023-10-16T09:55:43Z","department":[{"_id":"GaNo"}],"_id":"691","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0022-2593"]},"language":[{"iso":"eng"}],"volume":55,"issue":"1","abstract":[{"text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"scopus_import":"1","intvolume":" 55","month":"01"},{"date_updated":"2023-10-16T10:29:22Z","department":[{"_id":"LaEr"}],"_id":"284","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"publication_status":"published","issue":"1-2","volume":84,"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere.","lang":"eng"}],"month":"06","intvolume":" 84","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.03305","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. Springer Nature. https://doi.org/10.14232/actasm-018-753-y","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80. doi:10.14232/actasm-018-753-y","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018."},"title":"Maps on probability measures preserving certain distances - a survey and some new results","author":[{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511"}],"publist_id":"7615","external_id":{"arxiv":["1802.03305"]},"article_processing_charge":"No","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"04","publication":"Acta Scientiarum Mathematicarum","year":"2018","date_published":"2018-06-04T00:00:00Z","doi":"10.14232/actasm-018-753-y","date_created":"2018-12-11T11:45:36Z","page":"65 - 80","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"publisher":"Ecole Polytechnique","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","date_published":"2018-07-01T00:00:00Z","doi":"10.5802/jep.64","date_created":"2018-12-11T11:45:03Z","page":"79 - 116","day":"01","publication":"Journal de l'Ecole Polytechnique - Mathematiques","has_accepted_license":"1","year":"2018","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Statistical mechanics of the uniform electron gas","publist_id":"7741","author":[{"full_name":"Lewi, Mathieu","last_name":"Lewi","first_name":"Mathieu"},{"last_name":"Lieb","full_name":"Lieb, Élliott","first_name":"Élliott"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"external_id":{"arxiv":["1705.10676"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64","apa":"Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.64","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:10.5802/jep.64.","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64."},"month":"07","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density.","lang":"eng"}],"volume":5,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","file":[{"date_updated":"2020-07-14T12:45:16Z","file_size":843938,"creator":"dernst","date_created":"2018-12-17T16:38:18Z","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5726","checksum":"1ba7cccdf3900f42c4f715ae75d6813c"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"_id":"180","file_date_updated":"2020-07-14T12:45:16Z","department":[{"_id":"RoSe"}],"ddc":["510"],"date_updated":"2023-10-17T08:05:28Z"},{"volume":66,"issue":"12","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1554"]},"intvolume":" 66","month":"12","main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"date_updated":"2023-10-17T08:42:24Z","status":"public","type":"journal_article","article_type":"original","_id":"163","date_created":"2018-12-11T11:44:57Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1369/0022155418786698","page":"903-921","publication":"Journal of Histochemistry and Cytochemistry","day":"01","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"SAGE Publications","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","article_processing_charge":"No","external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"author":[{"last_name":"Reipert","full_name":"Reipert, Siegfried","first_name":"Siegfried"},{"first_name":"Helmuth","last_name":"Goldammer","full_name":"Goldammer, Helmuth"},{"last_name":"Richardson","full_name":"Richardson, Christine","first_name":"Christine"},{"first_name":"Martin","full_name":"Goldberg, Martin","last_name":"Goldberg"},{"first_name":"Timothy","last_name":"Hawkins","full_name":"Hawkins, Timothy"},{"first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","full_name":"Hollergschwandtner, Elena","last_name":"Hollergschwandtner"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Antreich","full_name":"Antreich, Sebastian","first_name":"Sebastian"},{"first_name":"York","full_name":"Stierhof, York","last_name":"Stierhof"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE Publications. https://doi.org/10.1369/0022155418786698","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","ieee":"S. Reipert et al., “Agitation modules: Flexible means to accelerate automated freeze substitution,” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018."}},{"publication":"Proceedings of the 35th International Conference on Machine Learning","day":"01","year":"2018","isi":1,"date_created":"2019-02-14T15:21:07Z","date_published":"2018-02-01T00:00:00Z","page":"4442-4450","oa":1,"quality_controlled":"1","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450.","chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018."},"title":"Learning equations for extrapolation and control","external_id":{"isi":["000683379204058"],"arxiv":["1806.07259"]},"article_processing_charge":"No","author":[{"first_name":"Subham","full_name":"Sahoo, Subham","last_name":"Sahoo"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":80,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task."}],"intvolume":" 80","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.07259"}],"scopus_import":"1","date_updated":"2023-10-17T09:50:53Z","department":[{"_id":"ChLa"}],"_id":"6012","status":"public","conference":{"end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"type":"conference"},{"page":"2815-2824","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-14T14:51:57Z","isi":1,"year":"2018","day":"01","publication":"Proceedings of the 35 th International Conference on Machine Learning","publisher":"ML Research Press","quality_controlled":"1","oa":1,"author":[{"first_name":"Ilja","last_name":"Kuzborskij","full_name":"Kuzborskij, Ilja"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"article_processing_charge":"No","external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"title":"Data-dependent stability of stochastic gradient descent","citation":{"mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824.","chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":80,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.01678","open_access":"1"}],"month":"02","intvolume":" 80","abstract":[{"lang":"eng","text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. "}],"oa_version":"Preprint","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T09:51:13Z","type":"conference","conference":{"start_date":"2018-07-10","end_date":"2018-07-15","location":"Stockholm, Sweden","name":"ICML: International Conference on Machine Learning"},"status":"public","_id":"6011"},{"has_accepted_license":"1","publication_status":"published","year":"2018","file":[{"file_id":"5872","checksum":"6cb95f8772491d155ce77c6160655fff","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-22T09:06:51Z","file_name":"2018_WorkingPaper_Danowski.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:10Z","file_size":202798}],"day":"09","language":[{"iso":"eng"}],"page":"5","date_published":"2018-05-09T00:00:00Z","doi":"10.5281/zenodo.1244154","related_material":{"record":[{"id":"6657","status":"public","relation":"later_version"}]},"date_created":"2018-12-17T10:28:26Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","scopus_import":1,"oa":1,"month":"05","date_updated":"2023-10-17T11:33:57Z","citation":{"apa":"Danowski, P. (2018). An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. https://doi.org/10.5281/zenodo.1244154","ama":"Danowski P. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.; 2018. doi:10.5281/zenodo.1244154","ieee":"P. Danowski, An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018.","short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","mla":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors. 2018, doi:10.5281/zenodo.1244154.","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p.","chicago":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018. https://doi.org/10.5281/zenodo.1244154."},"ddc":["020"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:10Z","title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","department":[{"_id":"E-Lib"}],"_id":"5686","type":"working_paper","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"oa":1,"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","year":"2018","isi":1,"publication":"Advances in Neural Information Processing Systems 31","day":"01","page":"5973-5983","date_created":"2019-06-27T09:32:55Z","date_published":"2018-12-01T00:00:00Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” Advances in Neural Information Processing Systems 31, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in Advances in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: Advances in Neural Information Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., & Renggli, C. (2018). The convergence of sparsified gradient methods. In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"article_processing_charge":"No","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"full_name":"Johansson, Mikael","last_name":"Johansson","first_name":"Mikael"},{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Khirirat","full_name":"Khirirat, Sarit","first_name":"Sarit"},{"last_name":"Renggli","full_name":"Renggli, Cedric","first_name":"Cedric"}],"title":"The convergence of sparsified gradient methods","abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.10505","open_access":"1"}],"scopus_import":"1","month":"12","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":"Volume 2018","_id":"6589","conference":{"end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-02","name":"NeurIPS: Conference on Neural Information Processing Systems"},"type":"conference","status":"public","date_updated":"2023-10-17T11:47:20Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}]},{"intvolume":" 362","month":"11","main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.","lang":"eng"}],"ec_funded":1,"volume":362,"issue":"6417","related_material":{"record":[{"id":"13055","status":"public","relation":"research_data"}],"link":[{"url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","relation":"press_release","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1095-9203"]},"status":"public","type":"journal_article","article_type":"original","_id":"7","department":[{"_id":"SyCr"}],"date_updated":"2023-10-17T11:50:05Z","oa":1,"quality_controlled":"1","publisher":"AAAS","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","date_created":"2018-12-11T11:44:07Z","date_published":"2018-11-23T00:00:00Z","doi":"10.1126/science.aat4793","page":"941 - 945","publication":"Science","day":"23","year":"2018","isi":1,"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","article_processing_charge":"No","external_id":{"isi":["000451124500041"]},"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Alessandro","full_name":"Crespi, Alessandro","last_name":"Crespi"},{"last_name":"Mersch","full_name":"Mersch, Danielle","first_name":"Danielle"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Keller, Laurent","last_name":"Keller","first_name":"Laurent"}],"publist_id":"8049","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:10.1126/science.aat4793.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Science. AAAS. https://doi.org/10.1126/science.aat4793","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. Science. 2018;362(6417):941-945. doi:10.1126/science.aat4793","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163"},"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","publist_id":"8036","author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"external_id":{"isi":["000452567200006"],"pmid":["30169679"]},"article_processing_charge":"No","day":"28","publication":"Molecular Biology and Evolution","isi":1,"year":"2018","doi":"10.1093/molbev/msy163","date_published":"2018-08-28T00:00:00Z","date_created":"2018-12-11T11:44:11Z","page":"2669 - 2684","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"date_updated":"2023-10-17T11:51:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"19","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"]},"publication_status":"published","issue":"11","volume":35,"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"month":"08","intvolume":" 35","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}]},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13055","department":[{"_id":"SyCr"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","article_processing_charge":"No","author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Crespi","full_name":"Crespi, Alessandro","first_name":"Alessandro"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"first_name":"Laurent","full_name":"Keller, Laurent","last_name":"Keller"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:50:04Z","citation":{"ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669."},"month":"10","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"oa":1,"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n","lang":"eng"}],"date_created":"2023-05-23T13:24:51Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7"}]},"date_published":"2018-10-23T00:00:00Z","doi":"10.5281/ZENODO.1322669","day":"23","year":"2018"},{"citation":{"chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210.","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abdalmalak, Kerlos","last_name":"Abdalmalak","first_name":"Kerlos"},{"first_name":"Elliott","full_name":"Brown, Elliott","last_name":"Brown"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"last_name":"Preu","full_name":"Preu, Sascha","first_name":"Sascha"},{"full_name":"Segovia Vargas, Daniel","last_name":"Segovia Vargas","first_name":"Daniel"},{"last_name":"Strekalov","full_name":"Strekalov, Dmitry","first_name":"Dmitry"},{"first_name":"Luis","last_name":"Munoz","full_name":"Munoz, Luis"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"publist_id":"8033","external_id":{"isi":["000447853100007"]},"article_processing_charge":"No","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","isi":1,"year":"2018","day":"20","publication":"Optica","page":"1210 - 1219","doi":"10.1364/OPTICA.5.001210","date_published":"2018-10-20T00:00:00Z","date_created":"2018-12-11T11:44:12Z","quality_controlled":"1","oa":1,"date_updated":"2023-10-17T12:12:40Z","department":[{"_id":"JoFi"}],"_id":"22","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["23342536"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":5,"issue":"10","abstract":[{"lang":"eng","text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"www.doi.org/10.1364/OPTICA.5.001210 "}],"month":"10","intvolume":" 5"},{"_id":"5677","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-10-17T11:53:09Z","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","abstract":[{"text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.","lang":"eng"}],"month":"05","intvolume":" 12","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1551-3939"]},"publication_status":"published","volume":12,"issue":"2-3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053.","ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053."},"title":"Contracts for system design","author":[{"last_name":"Benveniste","full_name":"Benveniste, Albert","first_name":"Albert"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Caillaud, Benoît","last_name":"Caillaud","first_name":"Benoît"},{"full_name":"Passerone, Roberto","last_name":"Passerone","first_name":"Roberto"},{"full_name":"Raclet, Jean Baptiste","last_name":"Raclet","first_name":"Jean Baptiste"},{"first_name":"Philipp","full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier"},{"full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli","first_name":"Alberto"},{"last_name":"Damm","full_name":"Damm, Werner","first_name":"Werner"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Kim G.","full_name":"Larsen, Kim G.","last_name":"Larsen"}],"article_processing_charge":"No","publisher":"Now Publishers","quality_controlled":"1","oa":1,"day":"01","publication":"Foundations and Trends in Electronic Design Automation","year":"2018","doi":"10.1561/1000000053","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-16T22:59:19Z","page":"124-400"},{"issue":"3","volume":43,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 43","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.01986"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum."}],"department":[{"_id":"MiLe"}],"date_updated":"2023-10-17T12:15:06Z","status":"public","type":"journal_article","_id":"435","doi":"10.1364/OL.43.000607","date_published":"2018-02-01T00:00:00Z","date_created":"2018-12-11T11:46:27Z","page":"607 - 610","day":"01","publication":"Optics Letters","isi":1,"year":"2018","publisher":"Optica Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","title":"Coherent-perfect-absorber and laser for bound states in a continuum","author":[{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali","last_name":"Midya"},{"first_name":"Vladimir","full_name":"Konotop, Vladimir","last_name":"Konotop"}],"publist_id":"7388","article_processing_charge":"No","external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"oa":1,"publisher":"PeerJ","quality_controlled":"1","date_created":"2018-12-11T11:44:50Z","doi":"10.7717/peerj.5198","date_published":"2018-07-30T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"PeerJ","day":"30","article_number":"30083438","article_processing_charge":"No","external_id":{"isi":["000440484800002"]},"publist_id":"7784","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"first_name":"Pierre","full_name":"Gagnaire, Pierre","last_name":"Gagnaire"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","citation":{"ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 2018","month":"07","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"oa_version":"Published Version","issue":"7","volume":2018,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":1480792,"date_updated":"2020-07-14T12:44:48Z","creator":"dernst","file_name":"2018_PeerJ_Fraisse.pdf","date_created":"2018-12-18T09:42:11Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"139","file_date_updated":"2020-07-14T12:44:48Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2023-10-17T12:25:28Z","ddc":["576"]},{"date_published":"2018-10-01T00:00:00Z","doi":"10.7717/peerj.5325","date_created":"2018-12-11T11:44:16Z","day":"01","publication":"PeerJ","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"PeerJ","oa":1,"acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","author":[{"first_name":"Johanna","full_name":"Bertl, Johanna","last_name":"Bertl"},{"orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michaël","last_name":"Blum","full_name":"Blum, Michaël"}],"publist_id":"8022","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325."},"article_number":"e5325","volume":2018,"issue":"10","file":[{"date_created":"2018-12-17T10:46:06Z","file_name":"2018_PeerJ_Bertl.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:06Z","file_size":1328344,"file_id":"5692","checksum":"3334886c4b39678db4c4b74299ca14ba","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 2018","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-10-17T12:24:43Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"33"},{"isi":1,"year":"2018","day":"03","publication":"Nature Plants","page":"1082-1088","doi":"10.1038/s41477-018-0318-3","date_published":"2018-12-03T00:00:00Z","date_created":"2018-12-16T22:59:18Z","quality_controlled":"1","publisher":"Nature Research","oa":1,"citation":{"short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"external_id":{"pmid":["30518833"],"isi":["000454576600017"]},"article_processing_charge":"No","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":4,"issue":"12","ec_funded":1,"abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"month":"12","intvolume":" 4","date_updated":"2023-10-17T12:19:28Z","department":[{"_id":"JiFr"}],"_id":"5673","type":"journal_article","status":"public"},{"ec_funded":1,"volume":15,"issue":"140","related_material":{"record":[{"relation":"research_data","id":"9814","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}]},"publication_status":"published","publication_identifier":{"eissn":["1742-5662"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5955","checksum":"444e1a9d98eb0e780671be82b13025f3","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_size":219837,"date_created":"2019-02-12T07:54:37Z","file_name":"2018_RS_IbsenJensen.pdf"}],"scopus_import":"1","intvolume":" 15","month":"03","abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:22Z","date_updated":"2023-10-18T06:36:00Z","ddc":["000"],"type":"journal_article","article_type":"original","status":"public","_id":"198","date_created":"2018-12-11T11:45:09Z","doi":"10.1098/rsif.2018.0073","date_published":"2018-03-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of the Royal Society Interface","day":"01","oa":1,"publisher":"The Royal Society","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"author":[{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"publist_id":"7715","title":"Language acquisition with communication between learners","citation":{"chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"article_number":"20180073"},{"date_published":"2018-12-12T00:00:00Z","doi":"10.1098/rsos.181286","date_created":"2019-01-20T22:59:18Z","isi":1,"has_accepted_license":"1","year":"2018","day":"12","publication":"Royal Society Open Science","quality_controlled":"1","publisher":"The Royal Society","oa":1,"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","author":[{"orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"first_name":"Martí Sànchez","full_name":"Fibla, Martí Sànchez","last_name":"Fibla"},{"first_name":"Sergi","full_name":"Valverde, Sergi","last_name":"Valverde"},{"first_name":"Ricard","full_name":"Solé, Ricard","last_name":"Solé"}],"external_id":{"pmid":["30662738"],"isi":["000456566500027"]},"article_processing_charge":"No","title":"Chromatic transitions in the emergence of syntax networks","citation":{"mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"181286","issue":"12","volume":5,"publication_identifier":{"issn":["2054-5703"]},"publication_status":"published","file":[{"checksum":"9664d4417f6b792242e31eea77ce9501","file_id":"5924","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_RoyalSocOS_Corominas.pdf","date_created":"2019-02-05T14:38:09Z","file_size":646732,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 5","abstract":[{"lang":"eng","text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations."}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"date_updated":"2023-10-18T06:41:12Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"5859"},{"_id":"14284","article_type":"original","type":"journal_article","status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_updated":"2023-11-07T11:46:12Z","extern":"1","abstract":[{"text":"Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-04139-2","open_access":"1"}],"month":"05","intvolume":" 9","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":9,"article_number":"1806","citation":{"ama":"Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nature Communications. 2018;9. doi:10.1038/s41467-018-04139-2","apa":"Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler, A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2","short":"B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler, K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).","ieee":"B. Bräuning et al., “Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature, 2018.","mla":"Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer Nature, 2018, doi:10.1038/s41467-018-04139-2.","ista":"Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.","chicago":"Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling, Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bräuning, Bastian","last_name":"Bräuning","first_name":"Bastian"},{"full_name":"Bertosin, Eva","last_name":"Bertosin","first_name":"Eva"},{"full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Christian","last_name":"Ihling","full_name":"Ihling, Christian"},{"first_name":"Alexandra","full_name":"Schatt, Alexandra","last_name":"Schatt"},{"first_name":"Agnes","full_name":"Adler, Agnes","last_name":"Adler"},{"first_name":"Klaus","full_name":"Richter, Klaus","last_name":"Richter"},{"first_name":"Andrea","full_name":"Sinz, Andrea","last_name":"Sinz"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"},{"last_name":"Groll","full_name":"Groll, Michael","first_name":"Michael"}],"article_processing_charge":"No","external_id":{"pmid":["29728606"]},"title":"Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB","publisher":"Springer Nature","quality_controlled":"1","oa":1,"year":"2018","day":"04","publication":"Nature Communications","date_published":"2018-05-04T00:00:00Z","doi":"10.1038/s41467-018-04139-2","date_created":"2023-09-06T12:07:33Z"}]