[{"quality_controlled":"1","publisher":"AMS","oa":1,"page":"4597-4604","date_published":"2019-11-01T00:00:00Z","doi":"10.1090/proc/14586","date_created":"2019-11-04T16:10:50Z","isi":1,"year":"2019","day":"01","publication":"Proceedings of the American Mathematical Society","project":[{"grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Penghui","id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Penghui"}],"article_processing_charge":"No","external_id":{"arxiv":["1810.07039"],"isi":["000488621700004"]},"title":"A colimit of traces of reflection groups","citation":{"mla":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586.","short":"P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.","ieee":"P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.","apa":"Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586","ama":"Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586","chicago":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586.","ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1810.07039","open_access":"1"}],"month":"11","intvolume":" 147","abstract":[{"text":"Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. ","lang":"eng"}],"oa_version":"Preprint","issue":"11","volume":147,"ec_funded":1,"publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"6986","department":[{"_id":"TaHa"}],"date_updated":"2023-09-05T12:22:21Z"},{"file_date_updated":"2020-07-14T12:47:30Z","department":[{"_id":"SiHi"}],"ddc":["570"],"date_updated":"2023-09-05T13:02:21Z","status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"_id":"6454","volume":102,"issue":"1","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"date_created":"2019-05-15T09:28:41Z","file_name":"2019_Neuron_Ortiz.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:30Z","file_size":7288572,"checksum":"1fb6e195c583eb0c5cabf26f69ff6675","file_id":"6457","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"publication_status":"published","month":"04","intvolume":" 102","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.","lang":"eng"}],"title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","author":[{"last_name":"Ortiz-Álvarez","full_name":"Ortiz-Álvarez, G","first_name":"G"},{"first_name":"M","full_name":"Daclin, M","last_name":"Daclin"},{"full_name":"Shihavuddin, A","last_name":"Shihavuddin","first_name":"A"},{"full_name":"Lansade, P","last_name":"Lansade","first_name":"P"},{"first_name":"A","last_name":"Fortoul","full_name":"Fortoul, A"},{"first_name":"M","full_name":"Faucourt, M","last_name":"Faucourt"},{"last_name":"Clavreul","full_name":"Clavreul, S","first_name":"S"},{"last_name":"Lalioti","full_name":"Lalioti, ME","first_name":"ME"},{"first_name":"S","last_name":"Taraviras","full_name":"Taraviras, S"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J","last_name":"Livet","full_name":"Livet, J"},{"full_name":"Meunier, A","last_name":"Meunier","first_name":"A"},{"first_name":"A","full_name":"Genovesio, A","last_name":"Genovesio"},{"last_name":"Spassky","full_name":"Spassky, N","first_name":"N"}],"article_processing_charge":"No","external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7.","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.","ieee":"G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051."},"project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2019-04-03T00:00:00Z","doi":"10.1016/j.neuron.2019.01.051","date_created":"2019-05-14T13:06:30Z","page":"159-172.e7","day":"03","publication":"Neuron","has_accepted_license":"1","isi":1,"year":"2019","publisher":"Elsevier","quality_controlled":"1","oa":1},{"author":[{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"article_processing_charge":"No","external_id":{"isi":["000491286200016"],"pmid":["31639357"]},"title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","citation":{"ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093.","chicago":"Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press, 2019. https://doi.org/10.1016/j.cub.2019.08.068.","ama":"Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068","apa":"Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068","short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","ieee":"A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019.","mla":"Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Cell Press","page":"R1091-R1093","date_published":"2019-10-21T00:00:00Z","doi":"10.1016/j.cub.2019.08.068","date_created":"2019-11-04T15:18:29Z","isi":1,"year":"2019","day":"21","publication":"Current Biology","type":"journal_article","article_type":"original","status":"public","_id":"6979","department":[{"_id":"MiSi"}],"date_updated":"2023-09-05T12:43:43Z","scopus_import":"1","month":"10","intvolume":" 29","pmid":1,"oa_version":"None","volume":29,"issue":"20","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"CaHe"}],"ddc":["570"],"date_updated":"2023-09-05T13:04:13Z","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)"},"article_type":"review","type":"journal_article","_id":"6980","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"issue":"20","volume":38,"language":[{"iso":"eng"}],"file":[{"file_id":"6981","checksum":"76f7f4e79ab6d850c30017a69726fd85","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_Embo_Petridou.pdf","date_created":"2019-11-04T15:30:08Z","creator":"dernst","file_size":847356,"date_updated":"2020-07-14T12:47:46Z"}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"intvolume":" 38","month":"10","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development."}],"title":"Tissue rheology in embryonic organization","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["31512749"],"isi":["000485561900001"]},"author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","chicago":"Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497.","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497","apa":"Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019.","mla":"Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019, doi:10.15252/embj.2019102497."},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"2693FD8C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"V00736","name":"Tissue material properties in embryonic development"}],"article_number":"e102497","date_created":"2019-11-04T15:24:29Z","date_published":"2019-10-15T00:00:00Z","doi":"10.15252/embj.2019102497","publication":"The EMBO Journal","day":"15","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"EMBO"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it."}],"intvolume":" 41","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1707.00600","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1939-3539"],"issn":["0162-8828"]},"volume":41,"issue":"9","_id":"6554","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-05T13:18:09Z","department":[{"_id":"ChLa"}],"oa":1,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","quality_controlled":"1","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","day":"01","year":"2019","isi":1,"date_created":"2019-06-11T14:05:59Z","doi":"10.1109/tpami.2018.2857768","date_published":"2019-09-01T00:00:00Z","page":"2251 - 2265","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768","ama":"Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768","ieee":"Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical and Electronics Engineers (IEEE), pp. 2251–2265, 2019.","short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265.","mla":"Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers (IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768.","ista":"Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265.","chicago":"Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768."},"title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","article_processing_charge":"No","external_id":{"isi":["000480343900015"],"arxiv":["1707.00600"]},"author":[{"last_name":"Xian","full_name":"Xian, Yongqin","first_name":"Yongqin"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0002-4561-241X","last_name":"Lampert"},{"first_name":"Bernt","full_name":"Schiele, Bernt","last_name":"Schiele"},{"full_name":"Akata, Zeynep","last_name":"Akata","first_name":"Zeynep"}]},{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"citation":{"mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43, doi:10.1038/s41586-019-1069-7.","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1069-7","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.","ieee":"M. Cao et al., “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243, 2019.","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.","ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"article_processing_charge":"No","author":[{"last_name":"Cao","full_name":"Cao, Min","first_name":"Min"},{"full_name":"Chen, Rong","last_name":"Chen","first_name":"Rong"},{"last_name":"Li","full_name":"Li, Pan","first_name":"Pan"},{"first_name":"Yongqiang","last_name":"Yu","full_name":"Yu, Yongqiang"},{"last_name":"Zheng","full_name":"Zheng, Rui","first_name":"Rui"},{"first_name":"Danfeng","last_name":"Ge","full_name":"Ge, Danfeng"},{"first_name":"Wei","full_name":"Zheng, Wei","last_name":"Zheng"},{"last_name":"Wang","full_name":"Wang, Xuhui","first_name":"Xuhui"},{"last_name":"Gu","full_name":"Gu, Yangtao","first_name":"Yangtao"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Heng","full_name":"Zhang, Heng","last_name":"Zhang"},{"full_name":"Liu, Renyi","last_name":"Liu","first_name":"Renyi"},{"first_name":"Jun","last_name":"He","full_name":"He, Jun"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"}],"title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2019","has_accepted_license":"1","isi":1,"publication":"Nature","day":"11","page":"240-243","date_created":"2019-04-09T08:37:05Z","doi":"10.1038/s41586-019-1069-7","date_published":"2019-04-11T00:00:00Z","_id":"6259","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T14:58:41Z","ddc":["580"],"file_date_updated":"2020-11-13T07:37:41Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 568","month":"04","publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4321328,"date_updated":"2020-11-13T07:37:41Z","file_name":"2019_Nature _Cao_accepted.pdf","date_created":"2020-11-13T07:37:41Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","file_id":"8751"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/","relation":"press_release","description":"News on IST Homepage"}]},"volume":568},{"status":"public","type":"book_chapter","_id":"6987","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:47:46Z","ddc":["570"],"date_updated":"2023-09-05T15:01:12Z","month":"10","intvolume":" 68","scopus_import":"1","alternative_title":["RESULTS"],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.","lang":"eng"}],"volume":68,"file":[{"checksum":"7f43e1e3706d15061475c5c57efc2786","file_id":"7829","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-14T10:09:30Z","file_name":"2019_RESULTS_McDougall.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:46Z","file_size":19317348}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0080-1844"],"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"]},"publication_status":"published","editor":[{"full_name":"Tworzydlo, Waclaw","last_name":"Tworzydlo","first_name":"Waclaw"},{"full_name":"Bilinski, Szczepan M.","last_name":"Bilinski","first_name":"Szczepan M."}],"title":"Emergence of embryo shape during cleavage divisions","author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"first_name":"Janet","full_name":"Chenevert, Janet","last_name":"Chenevert"},{"last_name":"Godard","full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"first_name":"Remi","full_name":"Dumollard, Remi","last_name":"Dumollard"}],"external_id":{"pmid":["31598855"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.","apa":"McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6","ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6."},"publisher":"Springer Nature","quality_controlled":"1","oa":1,"doi":"10.1007/978-3-030-23459-1_6","date_published":"2019-10-10T00:00:00Z","date_created":"2019-11-04T16:20:19Z","page":"127-154","day":"10","publication":"Evo-Devo: Non-model species in cell and developmental biology","has_accepted_license":"1","year":"2019"},{"day":"16","publication":"Multiscale Modeling and Simulation","isi":1,"year":"2019","date_published":"2019-07-16T00:00:00Z","doi":"10.1137/18M1207272","date_created":"2019-08-04T21:59:21Z","page":"926-947","quality_controlled":"1","publisher":"SIAM","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272."},"title":"New optimal control problems in density functional theory motivated by photovoltaics","author":[{"full_name":"Friesecke, Gero","last_name":"Friesecke","first_name":"Gero"},{"first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333"}],"external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"publication_status":"published","issue":"3","volume":17,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size."}],"month":"07","intvolume":" 17","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.04200","open_access":"1"}],"date_updated":"2023-09-05T15:05:45Z","department":[{"_id":"JuFi"}],"_id":"6762","status":"public","type":"journal_article"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","doi":"10.1007/s40993-018-0146-6","date_published":"2019-01-02T00:00:00Z","date_created":"2022-03-18T12:09:48Z","year":"2019","day":"02","publication":"Research in Number Theory","article_number":"9","author":[{"last_name":"Ionica","full_name":"Ionica, Sorina","first_name":"Sorina"},{"last_name":"Kılıçer","full_name":"Kılıçer, Pınar","first_name":"Pınar"},{"first_name":"Kristin","last_name":"Lauter","full_name":"Lauter, Kristin"},{"last_name":"Lorenzo García","full_name":"Lorenzo García, Elisa","first_name":"Elisa"},{"first_name":"Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c","full_name":"Manzateanu, Maria-Adelina","last_name":"Manzateanu"},{"first_name":"Maike","last_name":"Massierer","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","last_name":"Vincent","first_name":"Christelle"}],"external_id":{"arxiv":["1807.08986"]},"article_processing_charge":"No","title":"Modular invariants for genus 3 hyperelliptic curves","citation":{"mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6","chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.08986"}],"month":"01","intvolume":" 5","abstract":[{"text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM.","lang":"eng"}],"oa_version":"Preprint","volume":5,"publication_identifier":{"issn":["2522-0160"],"eissn":["2363-9555"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Algebra and Number Theory"],"_id":"10874","department":[{"_id":"TiBr"}],"date_updated":"2023-09-05T15:39:31Z"},{"date_updated":"2023-09-06T10:47:43Z","ddc":["510"],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:47:49Z","_id":"7100","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)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":884469,"date_updated":"2020-07-14T12:47:49Z","file_name":"2019_CommMathPhys_Jeblick.pdf","date_created":"2019-11-25T08:11:11Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"cd283b475dd739e04655315abd46f528","file_id":"7101"}],"ec_funded":1,"issue":"1","volume":372,"abstract":[{"text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 372","month":"11","citation":{"apa":"Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000495193700002"]},"author":[{"full_name":"Jeblick, Maximilian","last_name":"Jeblick","first_name":"Maximilian"},{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","last_name":"Leopold","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"year":"2019","isi":1,"has_accepted_license":"1","publication":"Communications in Mathematical Physics","day":"08","page":"1-69","date_created":"2019-11-25T08:08:02Z","date_published":"2019-11-08T00:00:00Z","doi":"10.1007/s00220-019-03599-x","acknowledgement":"OA fund by IST Austria","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119."},"title":"PIN-driven auxin transport emerged early in streptophyte evolution","author":[{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"full_name":"Medvecká, Eva","last_name":"Medvecká","first_name":"Eva"},{"last_name":"Viaene","full_name":"Viaene, Tom","first_name":"Tom"},{"first_name":"Stanislav","full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"first_name":"Karel","last_name":"Müller","full_name":"Müller, Karel"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"last_name":"Janacek","full_name":"Janacek, Dorina P.","first_name":"Dorina P."},{"full_name":"Hammes, Ulrich Z.","last_name":"Hammes","first_name":"Ulrich Z."},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Plants","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1038/s41477-019-0542-5","date_published":"2019-11-01T00:00:00Z","date_created":"2019-11-25T09:08:04Z","page":"1114-1119","_id":"7106","status":"public","type":"journal_article","article_type":"original","ddc":["580"],"date_updated":"2023-09-06T11:09:49Z","file_date_updated":"2020-10-14T08:54:49Z","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes."}],"month":"11","intvolume":" 5","scopus_import":"1","file":[{"date_updated":"2020-10-14T08:54:49Z","file_size":1980851,"creator":"dernst","date_created":"2020-10-14T08:54:49Z","file_name":"2019_NaturePlants_Skokan_accepted.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"94e0426856aad9a9bd0135d5436efbf1","file_id":"8660","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","issue":"11","volume":5,"ec_funded":1},{"author":[{"first_name":"Lawrence","last_name":"Yolland","full_name":"Yolland, Lawrence"},{"first_name":"Mubarik","full_name":"Burki, Mubarik","last_name":"Burki"},{"last_name":"Marcotti","full_name":"Marcotti, Stefania","first_name":"Stefania"},{"first_name":"Andrei","full_name":"Luchici, Andrei","last_name":"Luchici"},{"last_name":"Kenny","full_name":"Kenny, Fiona N.","first_name":"Fiona N."},{"first_name":"John Robert","last_name":"Davis","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"full_name":"Müller, Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Davidson, Andrew","last_name":"Davidson","first_name":"Andrew"},{"full_name":"Wood, Will","last_name":"Wood","first_name":"Will"},{"last_name":"Schumacher","full_name":"Schumacher, Linus J.","first_name":"Linus J."},{"full_name":"Endres, Robert G.","last_name":"Endres","first_name":"Robert G."},{"first_name":"Mark","last_name":"Miodownik","full_name":"Miodownik, Mark"},{"last_name":"Stramer","full_name":"Stramer, Brian M.","first_name":"Brian M."}],"external_id":{"pmid":["31685997"],"isi":["000495888300009"]},"article_processing_charge":"No","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","citation":{"ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1370-1381","date_published":"2019-11-01T00:00:00Z","doi":"10.1038/s41556-019-0411-5","date_created":"2019-11-25T08:55:00Z","isi":1,"year":"2019","day":"01","publication":"Nature Cell Biology","quality_controlled":"1","publisher":"Springer Nature","oa":1,"department":[{"_id":"MiSi"}],"date_updated":"2023-09-06T11:08:52Z","article_type":"original","type":"journal_article","status":"public","_id":"7105","volume":21,"issue":"11","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891","open_access":"1"}],"month":"11","intvolume":" 21","abstract":[{"text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-5411"]},"volume":66,"issue":"3","oa_version":"None","abstract":[{"text":"We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended.","lang":"eng"}],"intvolume":" 66","month":"05","scopus_import":"1","date_updated":"2023-09-06T11:11:56Z","department":[{"_id":"ToHe"}],"_id":"7109","status":"public","article_type":"original","type":"journal_article","publication":"Journal of the ACM","day":"01","year":"2019","isi":1,"date_created":"2019-11-26T10:22:32Z","doi":"10.1145/3286976","date_published":"2019-05-01T00:00:00Z","publisher":"ACM","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.","short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. Journal of the ACM. 2019;66(3). doi:10.1145/3286976","apa":"Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976."},"title":"From real-time logic to timed automata","article_processing_charge":"No","external_id":{"isi":["000495406300005"]},"author":[{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"first_name":"Dejan","full_name":"Ničković, Dejan","last_name":"Ničković"},{"full_name":"Pnueli, Amir","last_name":"Pnueli","first_name":"Amir"}],"article_number":"19","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"article_number":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024."},"title":"Shellability is NP-complete","external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"article_processing_charge":"No","author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"full_name":"Patak, Pavel","last_name":"Patak","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"first_name":"Martin","last_name":"Tancer","full_name":"Tancer, Martin"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"oa":1,"quality_controlled":"1","publisher":"ACM","publication":"Journal of the ACM","day":"01","year":"2019","isi":1,"date_created":"2019-11-26T10:13:59Z","doi":"10.1145/3314024","date_published":"2019-06-01T00:00:00Z","_id":"7108","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-06T11:10:58Z","department":[{"_id":"UlWa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"intvolume":" 66","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1711.08436.pdf"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0004-5411"]},"volume":66,"related_material":{"record":[{"id":"184","status":"public","relation":"earlier_version"}]},"issue":"3"},{"date_created":"2019-12-04T16:07:50Z","doi":"10.1007/978-3-030-31304-3_9","date_published":"2019-09-17T00:00:00Z","page":"155-187","publication":"17th International Conference on Computational Methods in Systems Biology","day":"17","year":"2019","isi":1,"publisher":"Springer Nature","quality_controlled":"1","title":"Transient memory in gene regulation","external_id":{"isi":["000557875100009"]},"article_processing_charge":"No","author":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"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":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9."},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture","grant_number":"24573"}],"volume":11773,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030313036","9783030313043"],"eissn":["1611-3349"]},"intvolume":" 11773","month":"09","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","abstract":[{"text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"date_updated":"2023-09-06T11:18:08Z","status":"public","conference":{"name":"CMSB: Computational Methods in Systems Biology","location":"Trieste, Italy","end_date":"2019-09-20","start_date":"2019-09-18"},"type":"conference","_id":"7147"},{"article_number":"8849240","title":"Strong chain rules for min-entropy under few bits spoiled","author":[{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240.","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240."},"publisher":"IEEE","quality_controlled":"1","oa":1,"doi":"10.1109/isit.2019.8849240","date_published":"2019-07-01T00:00:00Z","date_created":"2019-11-28T10:19:21Z","day":"01","publication":"2019 IEEE International Symposium on Information Theory","isi":1,"year":"2019","status":"public","type":"conference","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2019-07-07","end_date":"2019-07-12","location":"Paris, France"},"_id":"7136","department":[{"_id":"KrPi"}],"date_updated":"2023-09-06T11:15:41Z","month":"07","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625.","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in 2018 IEEE Conference on Decision and Control, Miami Beach, FL, United States, 2019.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019.","apa":"Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In 2018 IEEE Conference on Decision and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625","ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: 2018 IEEE Conference on Decision and Control. IEEE; 2019. doi:10.1109/cdc.2018.8619625","mla":"Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE, 2019, doi:10.1109/cdc.2018.8619625."},"date_updated":"2023-09-06T11:14:55Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Sarit","last_name":"Khirirat","full_name":"Khirirat, Sarit"},{"first_name":"Mikael","last_name":"Johansson","full_name":"Johansson, Mikael"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"article_processing_charge":"No","external_id":{"isi":["000458114800023"]},"title":"Gradient compression for communication-limited convex optimization","department":[{"_id":"DaAl"}],"_id":"7122","article_number":"8619625","type":"conference","conference":{"name":"CDC: Conference on Decision and Control","start_date":"2018-12-17","end_date":"2018-12-19","location":"Miami Beach, FL, United States"},"status":"public","isi":1,"publication_identifier":{"isbn":["9781538613955"],"issn":["0743-1546"]},"year":"2019","publication_status":"published","day":"21","publication":"2018 IEEE Conference on Decision and Control","language":[{"iso":"eng"}],"date_published":"2019-01-21T00:00:00Z","doi":"10.1109/cdc.2018.8619625","date_created":"2019-11-26T15:07:49Z","abstract":[{"lang":"eng","text":"Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible."}],"oa_version":"None","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","month":"01"},{"title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","article_processing_charge":"No","external_id":{"isi":["000500728800009"]},"author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641.","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8.","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8","short":"B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8."},"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2019-12-04T16:05:25Z","doi":"10.1038/s41559-019-1050-8","date_published":"2019-11-25T00:00:00Z","page":"1632-1641","publication":"Nature Ecology & Evolution","day":"25","year":"2019","isi":1,"quality_controlled":"1","publisher":"Springer Nature","department":[{"_id":"BeVi"}],"date_updated":"2023-09-06T11:18:59Z","status":"public","article_type":"original","type":"journal_article","_id":"7146","ec_funded":1,"volume":3,"issue":"12","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2397-334X"]},"intvolume":" 3","month":"11","scopus_import":"1","oa_version":"None","abstract":[{"text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.","lang":"eng"}]},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"965-966","doi":"10.1038/s41422-019-0254-4","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-02T12:30:48Z","isi":1,"year":"2019","day":"01","publication":"Cell Research","author":[{"last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"title":"Defying gravity: a plant's quest for moisture","citation":{"apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41422-019-0254-4","open_access":"1"}],"month":"12","intvolume":" 29","abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":29,"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"7143","department":[{"_id":"JiFr"}],"date_updated":"2023-09-06T11:20:58Z"},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"doi":"10.1038/s41534-019-0220-5","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-09T08:18:56Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"npj Quantum Information","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"108","author":[{"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"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","citation":{"short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"12","intvolume":" 5","abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"oa_version":"Published Version","volume":5,"ec_funded":1,"publication_identifier":{"issn":["2056-6387"]},"publication_status":"published","file":[{"checksum":"13e0ea1d4f9b5f5710780d9473364f58","file_id":"7157","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-12-09T08:25:06Z","file_name":"2019_NPJ_Rueda.pdf","date_updated":"2020-07-14T12:47:50Z","file_size":1580132,"creator":"dernst"}],"language":[{"iso":"eng"}],"article_type":"original","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)"},"status":"public","_id":"7156","department":[{"_id":"JoFi"}],"file_date_updated":"2020-07-14T12:47:50Z","date_updated":"2023-09-06T11:22:39Z","ddc":["530"]}]