[{"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.","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.","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","ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604.","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","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."},"publication":"Proceedings of the American Mathematical Society","page":"4597-4604","article_type":"original","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"6986","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 147","status":"public","title":"A colimit of traces of reflection groups","oa_version":"Preprint","type":"journal_article","issue":"11","abstract":[{"lang":"eng","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. "}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.07039","open_access":"1"}],"external_id":{"isi":["000488621700004"],"arxiv":["1810.07039"]},"project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"isi":1,"quality_controlled":"1","doi":"10.1090/proc/14586","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"month":"11","year":"2019","publisher":"AMS","department":[{"_id":"TaHa"}],"publication_status":"published","author":[{"id":"42A24CCC-F248-11E8-B48F-1D18A9856A87","first_name":"Penghui","last_name":"Li","full_name":"Li, Penghui"}],"volume":147,"date_updated":"2023-09-05T12:22:21Z","date_created":"2019-11-04T16:10:50Z","ec_funded":1},{"issue":"1","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"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":7288572,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_Neuron_Ortiz.pdf","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-15T09:28:41Z","relation":"main_file","file_id":"6457"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6454","intvolume":" 102","ddc":["570"],"title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"03","scopus_import":"1","date_published":"2019-04-03T00:00:00Z","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.","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.","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","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.","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.","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."},"publication":"Neuron","page":"159-172.e7","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Ortiz-Álvarez, G","first_name":"G","last_name":"Ortiz-Álvarez"},{"full_name":"Daclin, M","first_name":"M","last_name":"Daclin"},{"full_name":"Shihavuddin, A","first_name":"A","last_name":"Shihavuddin"},{"full_name":"Lansade, P","first_name":"P","last_name":"Lansade"},{"last_name":"Fortoul","first_name":"A","full_name":"Fortoul, A"},{"last_name":"Faucourt","first_name":"M","full_name":"Faucourt, M"},{"full_name":"Clavreul, S","first_name":"S","last_name":"Clavreul"},{"last_name":"Lalioti","first_name":"ME","full_name":"Lalioti, ME"},{"first_name":"S","last_name":"Taraviras","full_name":"Taraviras, S"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"first_name":"J","last_name":"Livet","full_name":"Livet, J"},{"first_name":"A","last_name":"Meunier","full_name":"Meunier, A"},{"full_name":"Genovesio, A","first_name":"A","last_name":"Genovesio"},{"full_name":"Spassky, N","last_name":"Spassky","first_name":"N"}],"volume":102,"date_updated":"2023-09-05T13:02:21Z","date_created":"2019-05-14T13:06:30Z","pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"month":"04","doi":"10.1016/j.neuron.2019.01.051","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"quality_controlled":"1","isi":1},{"external_id":{"isi":["000491286200016"],"pmid":["31639357"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2019.08.068","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"month":"10","pmid":1,"year":"2019","publisher":"Cell Press","department":[{"_id":"MiSi"}],"publication_status":"published","author":[{"first_name":"Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"volume":29,"date_created":"2019-11-04T15:18:29Z","date_updated":"2023-09-05T12:43:43Z","citation":{"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.","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.","short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), 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.","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","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"},"publication":"Current Biology","page":"R1091-R1093","article_type":"original","date_published":"2019-10-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","_id":"6979","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 29","title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","status":"public","oa_version":"None","type":"journal_article","issue":"20"},{"issue":"20","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_Embo_Petridou.pdf","access_level":"open_access","file_size":847356,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6981","date_created":"2019-11-04T15:30:08Z","date_updated":"2020-07-14T12:47:46Z","checksum":"76f7f4e79ab6d850c30017a69726fd85"}],"intvolume":" 38","status":"public","ddc":["570"],"title":"Tissue rheology in embryonic organization","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6980","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"15","scopus_import":"1","date_published":"2019-10-15T00:00:00Z","article_type":"review","citation":{"ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019.","apa":"Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497","ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497","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.","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (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."},"publication":"The EMBO Journal","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","article_number":"e102497","volume":38,"date_created":"2019-11-04T15:24:29Z","date_updated":"2023-09-05T13:04:13Z","author":[{"orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Petridou","first_name":"Nicoletta","full_name":"Petridou, Nicoletta"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"}],"publisher":"EMBO","publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.15252/embj.2019102497","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"2693FD8C-B435-11E9-9278-68D0E5697425","grant_number":"V00736","name":"Tissue material properties in embryonic development","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31512749"],"isi":["000485561900001"]}},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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.","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","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.","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.","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."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"2251 - 2265","article_type":"original","date_published":"2019-09-01T00:00:00Z","type":"journal_article","issue":"9","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6554","intvolume":" 41","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","status":"public","oa_version":"Preprint","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"month":"09","oa":1,"external_id":{"arxiv":["1707.00600"],"isi":["000480343900015"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1707.00600"}],"quality_controlled":"1","isi":1,"doi":"10.1109/tpami.2018.2857768","language":[{"iso":"eng"}],"year":"2019","department":[{"_id":"ChLa"}],"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","publication_status":"published","author":[{"first_name":"Yongqin","last_name":"Xian","full_name":"Xian, Yongqin"},{"full_name":"Lampert, Christoph","orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"},{"full_name":"Schiele, Bernt","first_name":"Bernt","last_name":"Schiele"},{"last_name":"Akata","first_name":"Zeynep","full_name":"Akata, Zeynep"}],"volume":41,"date_updated":"2023-09-05T13:18:09Z","date_created":"2019-06-11T14:05:59Z"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"oa":1,"external_id":{"pmid":["30944466"],"isi":["000464412700050"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1069-7","month":"04","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2019","pmid":1,"date_created":"2019-04-09T08:37:05Z","date_updated":"2023-09-05T14:58:41Z","volume":568,"author":[{"first_name":"Min","last_name":"Cao","full_name":"Cao, Min"},{"last_name":"Chen","first_name":"Rong","full_name":"Chen, Rong"},{"last_name":"Li","first_name":"Pan","full_name":"Li, Pan"},{"full_name":"Yu, Yongqiang","last_name":"Yu","first_name":"Yongqiang"},{"first_name":"Rui","last_name":"Zheng","full_name":"Zheng, Rui"},{"full_name":"Ge, Danfeng","last_name":"Ge","first_name":"Danfeng"},{"first_name":"Wei","last_name":"Zheng","full_name":"Zheng, Wei"},{"first_name":"Xuhui","last_name":"Wang","full_name":"Wang, Xuhui"},{"full_name":"Gu, Yangtao","last_name":"Gu","first_name":"Yangtao"},{"full_name":"Gelová, Zuzana","last_name":"Gelová","first_name":"Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Heng","last_name":"Zhang","full_name":"Zhang, Heng"},{"full_name":"Liu, Renyi","last_name":"Liu","first_name":"Renyi"},{"full_name":"He, Jun","first_name":"Jun","last_name":"He"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/"}]},"file_date_updated":"2020-11-13T07:37:41Z","ec_funded":1,"article_type":"original","page":"240-243","publication":"Nature","citation":{"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","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.","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.","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","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.","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.","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."},"date_published":"2019-04-11T00:00:00Z","scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"No","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","ddc":["580"],"status":"public","intvolume":" 568","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6259","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4321328,"file_name":"2019_Nature _Cao_accepted.pdf","access_level":"open_access","date_created":"2020-11-13T07:37:41Z","date_updated":"2020-11-13T07:37:41Z","success":1,"checksum":"6b84ab602a34382cf0340a37a1378c75","file_id":"8751","relation":"main_file"}],"oa_version":"Submitted Version","type":"journal_article","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."}]},{"author":[{"last_name":"McDougall","first_name":"Alex","full_name":"McDougall, Alex"},{"full_name":"Chenevert, Janet","first_name":"Janet","last_name":"Chenevert"},{"full_name":"Godard, Benoit G","first_name":"Benoit G","last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Remi","last_name":"Dumollard","full_name":"Dumollard, Remi"}],"volume":68,"date_created":"2019-11-04T16:20:19Z","date_updated":"2023-09-05T15:01:12Z","pmid":1,"year":"2019","editor":[{"last_name":"Tworzydlo","first_name":"Waclaw","full_name":"Tworzydlo, Waclaw"},{"first_name":"Szczepan M.","last_name":"Bilinski","full_name":"Bilinski, Szczepan M."}],"department":[{"_id":"CaHe"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:47:46Z","doi":"10.1007/978-3-030-23459-1_6","language":[{"iso":"eng"}],"external_id":{"pmid":["31598855"]},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"],"issn":["0080-1844"]},"month":"10","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":19317348,"content_type":"application/pdf","file_name":"2019_RESULTS_McDougall.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","date_created":"2020-05-14T10:09:30Z","checksum":"7f43e1e3706d15061475c5c57efc2786","file_id":"7829","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6987","intvolume":" 68","status":"public","ddc":["570"],"title":"Emergence of embryo shape during cleavage divisions","abstract":[{"lang":"eng","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."}],"type":"book_chapter","alternative_title":["RESULTS"],"date_published":"2019-10-10T00:00:00Z","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.","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","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.","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","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.","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.","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."},"publication":"Evo-Devo: Non-model species in cell and developmental biology","page":"127-154","has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1"},{"article_processing_charge":"No","day":"16","scopus_import":"1","date_published":"2019-07-16T00:00:00Z","citation":{"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.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 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.","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","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.","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","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."},"publication":"Multiscale Modeling and Simulation","page":"926-947","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6762","intvolume":" 17","title":"New optimal control problems in density functional theory motivated by photovoltaics","status":"public","publication_identifier":{"eissn":["15403467"],"issn":["15403459"]},"month":"07","doi":"10.1137/18M1207272","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1808.04200","open_access":"1"}],"external_id":{"arxiv":["1808.04200"],"isi":["000487931800002"]},"oa":1,"isi":1,"quality_controlled":"1","author":[{"full_name":"Friesecke, Gero","first_name":"Gero","last_name":"Friesecke"},{"full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely"}],"volume":17,"date_created":"2019-08-04T21:59:21Z","date_updated":"2023-09-05T15:05:45Z","year":"2019","department":[{"_id":"JuFi"}],"publisher":"SIAM","publication_status":"published"},{"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"}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10874","title":"Modular invariants for genus 3 hyperelliptic curves","status":"public","intvolume":" 5","day":"02","article_processing_charge":"No","scopus_import":"1","keyword":["Algebra and Number Theory"],"date_published":"2019-01-02T00:00:00Z","publication":"Research in Number Theory","citation":{"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.","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 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.","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.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019)."},"article_type":"original","article_number":"9","author":[{"last_name":"Ionica","first_name":"Sorina","full_name":"Ionica, Sorina"},{"last_name":"Kılıçer","first_name":"Pınar","full_name":"Kılıçer, Pınar"},{"first_name":"Kristin","last_name":"Lauter","full_name":"Lauter, Kristin"},{"full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García","first_name":"Elisa"},{"full_name":"Manzateanu, Maria-Adelina","last_name":"Manzateanu","first_name":"Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c"},{"full_name":"Massierer, Maike","last_name":"Massierer","first_name":"Maike"},{"full_name":"Vincent, Christelle","first_name":"Christelle","last_name":"Vincent"}],"date_created":"2022-03-18T12:09:48Z","date_updated":"2023-09-05T15:39:31Z","volume":5,"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. ","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TiBr"}],"month":"01","publication_identifier":{"issn":["2522-0160"],"eissn":["2363-9555"]},"doi":"10.1007/s40993-018-0146-6","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.08986"}],"oa":1,"external_id":{"arxiv":["1807.08986"]},"quality_controlled":"1"},{"citation":{"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.","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.","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","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.","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.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69."},"publication":"Communications in Mathematical Physics","page":"1-69","article_type":"original","date_published":"2019-11-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"08","_id":"7100","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 372","status":"public","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","ddc":["510"],"oa_version":"Published Version","file":[{"date_created":"2019-11-25T08:11:11Z","date_updated":"2020-07-14T12:47:49Z","checksum":"cd283b475dd739e04655315abd46f528","relation":"main_file","file_id":"7101","content_type":"application/pdf","file_size":884469,"creator":"dernst","file_name":"2019_CommMathPhys_Jeblick.pdf","access_level":"open_access"}],"type":"journal_article","issue":"1","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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000495193700002"]},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00220-019-03599-x","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"11","acknowledgement":"OA fund by IST Austria","year":"2019","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"full_name":"Jeblick, Maximilian","last_name":"Jeblick","first_name":"Maximilian"},{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"}],"volume":372,"date_updated":"2023-09-06T10:47:43Z","date_created":"2019-11-25T08:08:02Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z"},{"month":"11","publication_identifier":{"issn":["2055-0278"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41477-019-0542-5","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"file_date_updated":"2020-10-14T08:54:49Z","ec_funded":1,"date_updated":"2023-09-06T11:09:49Z","date_created":"2019-11-25T09:08:04Z","volume":5,"author":[{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"last_name":"Medvecká","first_name":"Eva","full_name":"Medvecká, Eva"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"last_name":"Vosolsobě","first_name":"Stanislav","full_name":"Vosolsobě, Stanislav"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"last_name":"Müller","first_name":"Karel","full_name":"Müller, Karel"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"last_name":"Karady","first_name":"Michal","full_name":"Karady, Michal"},{"full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"last_name":"Hammes","first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z."},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2019","pmid":1,"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"1114-1119","publication":"Nature Plants","citation":{"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.","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.","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","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","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.","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.","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."},"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."}],"issue":"11","type":"journal_article","file":[{"success":1,"checksum":"94e0426856aad9a9bd0135d5436efbf1","date_updated":"2020-10-14T08:54:49Z","date_created":"2020-10-14T08:54:49Z","file_id":"8660","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1980851,"access_level":"open_access","file_name":"2019_NaturePlants_Skokan_accepted.pdf"}],"oa_version":"Submitted Version","ddc":["580"],"status":"public","title":"PIN-driven auxin transport emerged early in streptophyte evolution","intvolume":" 5","_id":"7106","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"month":"11","external_id":{"pmid":["31685997"],"isi":["000495888300009"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41556-019-0411-5","language":[{"iso":"eng"}],"pmid":1,"year":"2019","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Yolland","first_name":"Lawrence","full_name":"Yolland, Lawrence"},{"full_name":"Burki, Mubarik","first_name":"Mubarik","last_name":"Burki"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"full_name":"Luchici, Andrei","last_name":"Luchici","first_name":"Andrei"},{"full_name":"Kenny, Fiona N.","first_name":"Fiona N.","last_name":"Kenny"},{"full_name":"Davis, John Robert","last_name":"Davis","first_name":"John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"first_name":"Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Davidson, Andrew","last_name":"Davidson","first_name":"Andrew"},{"full_name":"Wood, Will","last_name":"Wood","first_name":"Will"},{"last_name":"Schumacher","first_name":"Linus J.","full_name":"Schumacher, Linus J."},{"first_name":"Robert G.","last_name":"Endres","full_name":"Endres, Robert G."},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"full_name":"Stramer, Brian M.","last_name":"Stramer","first_name":"Brian M."}],"volume":21,"date_created":"2019-11-25T08:55:00Z","date_updated":"2023-09-06T11:08:52Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"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","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.","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.","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","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.","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.","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."},"publication":"Nature Cell Biology","page":"1370-1381","article_type":"original","date_published":"2019-11-01T00:00:00Z","type":"journal_article","issue":"11","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"}],"_id":"7105","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 21","status":"public","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","oa_version":"Submitted Version"},{"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000495406300005"]},"language":[{"iso":"eng"}],"doi":"10.1145/3286976","publication_identifier":{"issn":["0004-5411"]},"month":"05","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","year":"2019","volume":66,"date_created":"2019-11-26T10:22:32Z","date_updated":"2023-09-06T11:11:56Z","author":[{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"first_name":"Dejan","last_name":"Ničković","full_name":"Ničković, Dejan"},{"first_name":"Amir","last_name":"Pnueli","full_name":"Pnueli, Amir"}],"article_number":"19","article_type":"original","citation":{"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.","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.","short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","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.","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","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"},"publication":"Journal of the ACM","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 66","title":"From real-time logic to timed automata","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7109","oa_version":"None","type":"journal_article","issue":"3","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"}]},{"date_published":"2019-06-01T00:00:00Z","article_type":"original","citation":{"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.","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","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.","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","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21."},"publication":"Journal of the ACM","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 66","title":"Shellability is NP-complete","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7108","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/3314024","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/pdf/1711.08436.pdf","open_access":"1"}],"external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"publication_identifier":{"issn":["0004-5411"]},"month":"06","volume":66,"date_updated":"2023-09-06T11:10:58Z","date_created":"2019-11-26T10:13:59Z","related_material":{"record":[{"id":"184","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"last_name":"Patak","first_name":"Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","full_name":"Patak, Pavel"},{"full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova"},{"full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"department":[{"_id":"UlWa"}],"publisher":"ACM","publication_status":"published","year":"2019","article_number":"21"},{"external_id":{"isi":["000557875100009"]},"isi":1,"quality_controlled":"1","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Design principles underlying genetic switch architecture","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2019-09-18","location":"Trieste, Italy","end_date":"2019-09-20","name":"CMSB: Computational Methods in Systems Biology"},"doi":"10.1007/978-3-030-31304-3_9","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"isbn":["9783030313036","9783030313043"],"eissn":["1611-3349"],"issn":["0302-9743"]},"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"author":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali"}],"date_created":"2019-12-04T16:07:50Z","date_updated":"2023-09-06T11:18:08Z","volume":11773,"publication":"17th International Conference on Computational Methods in Systems Biology","citation":{"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","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","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.","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.","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.","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."},"page":"155-187","date_published":"2019-09-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","_id":"7147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Transient memory in gene regulation","intvolume":" 11773","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","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."}]},{"date_updated":"2023-09-06T11:15:41Z","date_created":"2019-11-28T10:19:21Z","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej"}],"department":[{"_id":"KrPi"}],"publisher":"IEEE","publication_status":"published","year":"2019","article_number":"8849240","language":[{"iso":"eng"}],"doi":"10.1109/isit.2019.8849240","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2019-07-12","start_date":"2019-07-07","location":"Paris, France"},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"oa":1,"external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"publication_identifier":{"isbn":["9781538692912"]},"month":"07","oa_version":"Preprint","title":"Strong chain rules for min-entropy under few bits spoiled","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7136","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|X2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/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.","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.","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","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.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","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."},"publication":"2019 IEEE International Symposium on Information Theory","article_processing_charge":"No","day":"01","scopus_import":"1"},{"type":"conference","article_number":"8619625","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"DaAl"}],"publisher":"IEEE","status":"public","publication_status":"published","title":"Gradient compression for communication-limited convex optimization","_id":"7122","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","oa_version":"None","date_updated":"2023-09-06T11:14:55Z","date_created":"2019-11-26T15:07:49Z","author":[{"full_name":"Khirirat, Sarit","last_name":"Khirirat","first_name":"Sarit"},{"first_name":"Mikael","last_name":"Johansson","full_name":"Johansson, Mikael"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"scopus_import":"1","publication_identifier":{"issn":["0743-1546"],"isbn":["9781538613955"]},"article_processing_charge":"No","day":"21","month":"01","isi":1,"quality_controlled":"1","citation":{"ista":"Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625.","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","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.","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","chicago":"Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/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.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019."},"external_id":{"isi":["000458114800023"]},"publication":"2018 IEEE Conference on Decision and Control","language":[{"iso":"eng"}],"doi":"10.1109/cdc.2018.8619625","date_published":"2019-01-21T00:00:00Z","conference":{"end_date":"2018-12-19","start_date":"2018-12-17","location":"Miami Beach, FL, United States","name":"CDC: Conference on Decision and Control"}},{"month":"11","publication_identifier":{"issn":["2397-334X"]},"doi":"10.1038/s41559-019-1050-8","language":[{"iso":"eng"}],"external_id":{"isi":["000500728800009"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"ec_funded":1,"author":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"date_updated":"2023-09-06T11:18:59Z","date_created":"2019-12-04T16:05:25Z","volume":3,"year":"2019","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Springer Nature","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-25T00:00:00Z","publication":"Nature Ecology & Evolution","citation":{"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","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.","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","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641.","short":"B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.","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.","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."},"article_type":"original","page":"1632-1641","abstract":[{"lang":"eng","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."}],"issue":"12","type":"journal_article","oa_version":"None","_id":"7146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","intvolume":" 3"},{"oa_version":"Published Version","title":"Defying gravity: a plant's quest for moisture","status":"public","intvolume":" 29","_id":"7143","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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"}],"type":"journal_article","date_published":"2019-12-01T00:00:00Z","article_type":"original","page":"965-966","publication":"Cell Research","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","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.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","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","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.","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."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_created":"2019-12-02T12:30:48Z","date_updated":"2023-09-06T11:20:58Z","volume":29,"author":[{"full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","first_name":"Scott A"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2019","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41422-019-0254-4","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41422-019-0254-4"}],"oa":1,"external_id":{"pmid":["31745287"],"isi":["000500749600001"]},"month":"12","publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]}},{"type":"journal_article","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."}],"status":"public","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","ddc":["530"],"intvolume":" 5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7156","oa_version":"Published Version","file":[{"file_id":"7157","relation":"main_file","date_created":"2019-12-09T08:25:06Z","date_updated":"2020-07-14T12:47:50Z","checksum":"13e0ea1d4f9b5f5710780d9473364f58","file_name":"2019_NPJ_Rueda.pdf","access_level":"open_access","creator":"dernst","file_size":1580132,"content_type":"application/pdf"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"npj Quantum Information","citation":{"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","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","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.","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.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","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.","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."},"date_published":"2019-12-01T00:00:00Z","article_number":"108","file_date_updated":"2020-07-14T12:47:50Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"year":"2019","date_created":"2019-12-09T08:18:56Z","date_updated":"2023-09-06T11:22:39Z","volume":5,"author":[{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","last_name":"Hease","first_name":"William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"month":"12","publication_identifier":{"issn":["2056-6387"]},"quality_controlled":"1","isi":1,"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1909.01470"],"isi":["000502996200003"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41534-019-0220-5"},{"date_published":"2019-12-04T00:00:00Z","article_type":"original","citation":{"ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297."},"publication":"Development","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2019_Development_Guerrero.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":7797881,"file_id":"7177","relation":"main_file","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-13T07:34:06Z","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a"}],"intvolume":" 146","ddc":["570"],"status":"public","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7165","issue":"23","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1242/dev.176297","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"12","volume":146,"date_created":"2019-12-10T14:39:50Z","date_updated":"2023-09-06T11:26:36Z","author":[{"first_name":"Pilar","last_name":"Guerrero","full_name":"Guerrero, Pilar"},{"full_name":"Perez-Carrasco, Ruben","first_name":"Ruben","last_name":"Perez-Carrasco"},{"orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"last_name":"Page","first_name":"Karen M.","full_name":"Page, Karen M."}],"department":[{"_id":"AnKi"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","article_number":"dev176297"},{"abstract":[{"lang":"eng","text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. "}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7159","title":"Shape expressions for specifying and extracting signal features","status":"public","intvolume":" 11757","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","publication":"19th International Conference on Runtime Verification","citation":{"chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.","mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17"},"page":"292-309","author":[{"full_name":"Ničković, Dejan","last_name":"Ničković","first_name":"Dejan"},{"full_name":"Qin, Xin","last_name":"Qin","first_name":"Xin"},{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mateis","first_name":"Cristinel","full_name":"Mateis, Cristinel"},{"full_name":"Deshmukh, Jyotirmoy","last_name":"Deshmukh","first_name":"Jyotirmoy"}],"date_updated":"2023-09-06T11:24:10Z","date_created":"2019-12-09T08:47:55Z","volume":11757,"year":"2019","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","month":"10","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030320782","9783030320799"]},"conference":{"start_date":"2019-10-08","location":"Porto, Portugal","end_date":"2019-10-11","name":"RV: Runtime Verification"},"doi":"10.1007/978-3-030-32079-9_17","language":[{"iso":"eng"}],"external_id":{"isi":["000570006300017"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}]},{"oa_version":"Preprint","title":"Deciding fast termination for probabilistic VASS with nondeterminism","status":"public","intvolume":" 11781","_id":"7183","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2019-10-21T00:00:00Z","page":"462-478","publication":"International Symposium on Automated Technology for Verification and Analysis","citation":{"ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27."},"day":"21","article_processing_charge":"No","scopus_import":"1","date_created":"2019-12-15T23:00:44Z","date_updated":"2023-09-06T12:40:58Z","volume":11781,"author":[{"full_name":"Brázdil, Tomás","last_name":"Brázdil","first_name":"Tomás"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kucera, Antonín","first_name":"Antonín","last_name":"Kucera"},{"full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velan, Dominik","first_name":"Dominik","last_name":"Velan"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2019","language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","end_date":"2019-10-31","location":"Taipei, Taiwan","start_date":"2019-10-28"},"doi":"10.1007/978-3-030-31784-3_27","isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"oa":1,"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11010","open_access":"1"}],"month":"10","publication_identifier":{"isbn":["9783030317836"],"eissn":["16113349"],"issn":["03029743"]}},{"volume":10,"date_created":"2019-12-15T23:00:43Z","date_updated":"2023-09-06T14:33:46Z","author":[{"last_name":"Alcântara","first_name":"André","full_name":"Alcântara, André"},{"full_name":"Bosch, Jason","last_name":"Bosch","first_name":"Jason"},{"last_name":"Nazari","first_name":"Fahimeh","full_name":"Nazari, Fahimeh"},{"first_name":"Gesa","last_name":"Hoffmann","full_name":"Hoffmann, Gesa"},{"first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"first_name":"Martin A.","last_name":"Darino","full_name":"Darino, Martin A."},{"first_name":"Toluwase","last_name":"Olukayode","full_name":"Olukayode, Toluwase"},{"full_name":"Reumann, Daniel","first_name":"Daniel","last_name":"Reumann"},{"first_name":"Laura","last_name":"Baggaley","full_name":"Baggaley, Laura"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"publisher":"Frontiers","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:52Z","article_number":"1437","language":[{"iso":"eng"}],"doi":"10.3389/fpls.2019.01437","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"publication_identifier":{"eissn":["1664462X"]},"month":"11","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:58:43Z","checksum":"995aa838aec2064d93550de82b40bbd1","file_id":"7185","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1532505,"file_name":"2019_FrontiersPlant_Alcantara.pdf","access_level":"open_access"}],"intvolume":" 10","ddc":["580"],"status":"public","title":"Systematic Y2H screening reveals extensive effector-complex formation","_id":"7182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"11","abstract":[{"lang":"eng","text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome."}],"type":"journal_article","date_published":"2019-11-14T00:00:00Z","article_type":"original","citation":{"ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019)."},"publication":"Frontiers in Plant Science","article_processing_charge":"No","has_accepted_license":"1","day":"14","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7184","relation":"main_file","checksum":"77e8720a8e0f3091b98159f85be40893","date_created":"2019-12-16T07:37:50Z","date_updated":"2020-07-14T12:47:52Z","access_level":"open_access","file_name":"2019_NatureComm_Retzer.pdf","creator":"dernst","file_size":5156533,"content_type":"application/pdf"}],"_id":"7180","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 10","ddc":["570"],"status":"public","title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","citation":{"ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019)."},"publication":"Nature Communications","article_type":"original","file_date_updated":"2020-07-14T12:47:52Z","article_number":"5516","author":[{"full_name":"Retzer, Katarzyna","first_name":"Katarzyna","last_name":"Retzer"},{"full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162"},{"full_name":"Konstantinova, Nataliia","first_name":"Nataliia","last_name":"Konstantinova"},{"last_name":"Malínská","first_name":"Kateřina","full_name":"Malínská, Kateřina"},{"last_name":"Leitner","first_name":"Johannes","full_name":"Leitner, Johannes"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"}],"volume":10,"date_updated":"2023-09-06T14:08:21Z","date_created":"2019-12-15T23:00:43Z","pmid":1,"year":"2019","department":[{"_id":"DaSi"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"month":"12","doi":"10.1038/s41467-019-13543-1","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000500508100001"],"pmid":["31797871"]},"project":[{"call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379"}],"quality_controlled":"1","isi":1},{"_id":"7181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Large multiple sequence alignments with a root-to-leaf regressive method","status":"public","intvolume":" 37","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.","lang":"eng"}],"issue":"12","publication":"Nature Biotechnology","citation":{"apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6."},"article_type":"original","page":"1466-1470","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"full_name":"Di Tommaso, Paolo","first_name":"Paolo","last_name":"Di Tommaso"},{"full_name":"Magis, Cedrik","first_name":"Cedrik","last_name":"Magis"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Evan","last_name":"Floden","full_name":"Floden, Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"related_material":{"record":[{"id":"13059","status":"public","relation":"research_data"}]},"date_updated":"2023-09-06T14:32:52Z","date_created":"2019-12-15T23:00:43Z","volume":37,"ec_funded":1,"oa":1,"external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"doi":"10.1038/s41587-019-0333-6","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]}},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.51381","isi":1,"quality_controlled":"1","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11","publication_identifier":{"eissn":["2050084X"]},"date_created":"2019-12-22T23:00:42Z","date_updated":"2023-09-06T14:38:39Z","volume":8,"author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong Kuan","first_name":"Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou-Pouliou, Eleni","last_name":"Serafeimidou-Pouliou","first_name":"Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"SiHi"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_number":"e51381","date_published":"2019-11-18T00:00:00Z","article_type":"original","publication":"eLife","citation":{"ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019)."},"day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_name":"2019_eLife_Llorca.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2960543,"creator":"dernst","relation":"main_file","file_id":"7503","date_created":"2020-02-18T15:19:26Z","date_updated":"2020-07-14T12:47:53Z","checksum":"b460ecc33e1a68265e7adea775021f3a"}],"oa_version":"Published Version","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","ddc":["570"],"status":"public","intvolume":" 8","_id":"7202","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas.","lang":"eng"}],"type":"journal_article"},{"date_updated":"2023-09-06T14:34:36Z","date_created":"2019-12-15T23:00:42Z","volume":33,"author":[{"last_name":"Klotz","first_name":"Lisa","full_name":"Klotz, Lisa"},{"last_name":"Wendler","first_name":"Olaf","full_name":"Wendler, Olaf"},{"full_name":"Frischknecht, Renato","last_name":"Frischknecht","first_name":"Renato"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Schulze, Holger","last_name":"Schulze","first_name":"Holger"},{"first_name":"Ralf","last_name":"Enz","full_name":"Enz, Ralf"}],"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"FASEB","year":"2019","pmid":1,"file_date_updated":"2020-12-06T17:30:09Z","language":[{"iso":"eng"}],"doi":"10.1096/fj.201901543R","quality_controlled":"1","isi":1,"external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"oa":1,"month":"12","publication_identifier":{"eissn":["15306860"]},"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8922","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"date_updated":"2020-12-06T17:30:09Z","date_created":"2020-12-06T17:30:09Z","access_level":"open_access","file_name":"Klotz et al 2019 EMBO Reports.pdf","content_type":"application/pdf","file_size":4766789,"creator":"shigemot"}],"ddc":["571","599"],"status":"public","title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","intvolume":" 33","_id":"7179","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"issue":"12","type":"journal_article","date_published":"2019-12-01T00:00:00Z","article_type":"original","page":"13734-13746","publication":"FASEB Journal","citation":{"mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"day":"17","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-17T00:00:00Z","publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","citation":{"ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019."},"abstract":[{"text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks.","lang":"eng"}],"type":"conference","oa_version":"Preprint","status":"public","title":"SparCML: High-performance sparse communication for machine learning","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7201","month":"11","publication_identifier":{"eissn":["21674337"],"isbn":["9781450362290"],"issn":["21674329"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-11-19","location":"Denver, CO, Unites States","start_date":"2019-11-17","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"doi":"10.1145/3295500.3356222","isi":1,"quality_controlled":"1","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"ec_funded":1,"article_number":"a11","date_updated":"2023-09-06T14:37:55Z","date_created":"2019-12-22T23:00:42Z","author":[{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"},{"last_name":"Ashkboos","first_name":"Saleh","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","full_name":"Ashkboos, Saleh"},{"full_name":"Aghagolzadeh, Mehdi","first_name":"Mehdi","last_name":"Aghagolzadeh"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"DaAl"}],"year":"2019"},{"department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13067","year":"2019","oa_version":"Published Version","date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","related_material":{"record":[{"id":"7205","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"type":"research_data_reference","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","article_processing_charge":"No","month":"12","day":"02"},{"abstract":[{"lang":"eng","text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7221","relation":"main_file","checksum":"7a30357efdcf8f66587ed495c0927724","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-02T16:10:58Z","access_level":"open_access","file_name":"2019_BMCBioinfo_Aganezov.pdf","creator":"dernst","content_type":"application/pdf","file_size":1917374}],"ddc":["570"],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","status":"public","intvolume":" 20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7214","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-17T00:00:00Z","article_type":"original","publication":"BMC Bioinformatics","citation":{"chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4"},"file_date_updated":"2020-07-14T12:47:54Z","article_number":"641","date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","volume":20,"author":[{"full_name":"Aganezov, Sergey","first_name":"Sergey","last_name":"Aganezov"},{"last_name":"Zban","first_name":"Ilya","full_name":"Zban, Ilya"},{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","last_name":"Aksenov","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alexeev, Nikita","first_name":"Nikita","last_name":"Alexeev"},{"first_name":"Michael C.","last_name":"Schatz","full_name":"Schatz, Michael C."}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"BMC","year":"2019","month":"12","publication_identifier":{"eissn":["14712105"]},"language":[{"iso":"eng"}],"doi":"10.1186/s12859-019-3208-4","isi":1,"quality_controlled":"1","external_id":{"isi":["000511618800007"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"issue":"4","abstract":[{"text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"80f1499e2a4caccdf3aa54b137fd99a0","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z","relation":"main_file","file_id":"7243","content_type":"application/pdf","file_size":2660780,"creator":"dernst","access_level":"open_access","file_name":"2019_Bioengineering_Merrin.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7225","intvolume":" 6","status":"public","ddc":["620"],"title":"Frontiers in microfluidics, a teaching resource review","has_accepted_license":"1","article_processing_charge":"Yes","day":"03","scopus_import":"1","date_published":"2019-12-03T00:00:00Z","citation":{"short":"J. Merrin, Bioengineering 6 (2019).","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering, vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.","ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering. 2019;6(4). doi:10.3390/bioengineering6040109","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering, vol. 6, no. 4. MDPI, 2019.","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109."},"publication":"Bioengineering","article_type":"review","file_date_updated":"2020-07-14T12:47:54Z","article_number":"109","author":[{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"}],"volume":6,"date_created":"2020-01-05T23:00:45Z","date_updated":"2023-09-06T14:52:49Z","pmid":1,"year":"2019","publisher":"MDPI","department":[{"_id":"NanoFab"}],"publication_status":"published","publication_identifier":{"eissn":["23065354"]},"month":"12","doi":"10.3390/bioengineering6040109","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31816954"],"isi":["000505590000024"]},"oa":1,"isi":1,"quality_controlled":"1"},{"_id":"7228","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11725","title":"Scalable FIFO channels for programming via communicating sequential processes","status":"public","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. "}],"citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23"},"publication":"25th Anniversary of Euro-Par","page":"317-333","date_published":"2019-08-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"13","year":"2019","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"volume":11725,"date_created":"2020-01-05T23:00:46Z","date_updated":"2023-09-06T14:53:59Z","external_id":{"isi":["000851061400023"]},"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-030-29400-7_23","conference":{"name":"Euro-Par: European Conference on Parallel Processing","location":"Göttingen, Germany","start_date":"2019-08-26","end_date":"2019-08-30"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-0302-9399-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"08"},{"abstract":[{"text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.","lang":"eng"}],"article_number":"8917514","type":"conference","date_updated":"2023-09-06T14:50:28Z","date_created":"2019-12-29T23:00:47Z","oa_version":"None","author":[{"last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"},{"last_name":"Cook","first_name":"James","full_name":"Cook, James"},{"last_name":"Fabrikant","first_name":"Alex","full_name":"Fabrikant, Alex"},{"last_name":"Gruteser","first_name":"Marco","full_name":"Gruteser, Marco"}],"title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","publication_status":"published","status":"public","department":[{"_id":"HeEd"}],"publisher":"IEEE","_id":"7216","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","month":"11","day":"28","article_processing_charge":"No","publication_identifier":{"isbn":["9781538670248"]},"scopus_import":"1","language":[{"iso":"eng"}],"conference":{"location":"Auckland, New Zealand","start_date":"2019-10-27","end_date":"2019-10-30","name":"ITSC: Intelligent Transportation Systems Conference"},"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","quality_controlled":"1","isi":1,"publication":"2019 IEEE Intelligent Transportation Systems Conference","external_id":{"isi":["000521238102050"]},"citation":{"chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.","apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514.","ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514"}},{"author":[{"last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"date_updated":"2023-09-06T14:55:15Z","date_created":"2020-01-05T23:00:47Z","volume":11750,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"conference":{"end_date":"2019-08-29","location":"Amsterdam, The Netherlands","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"doi":"10.1007/978-3-030-29662-9_8","language":[{"iso":"eng"}],"external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11514"}],"isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"oa_version":"Preprint","_id":"7231","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","status":"public","intvolume":" 11750","abstract":[{"text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2019-08-13T00:00:00Z","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141."},"page":"123-141","day":"13","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.50793","isi":1,"quality_controlled":"1","external_id":{"isi":["000512303700001"],"pmid":["31873072"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["2050084X"]},"month":"12","volume":8,"date_updated":"2023-09-06T14:58:02Z","date_created":"2020-01-19T23:00:39Z","author":[{"last_name":"Amin-Wetzel","first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","full_name":"Amin-Wetzel, Niko Paresh"},{"last_name":"Neidhardt","first_name":"Lisa","full_name":"Neidhardt, Lisa"},{"full_name":"Yan, Yahui","first_name":"Yahui","last_name":"Yan"},{"full_name":"Mayer, Matthias P.","first_name":"Matthias P.","last_name":"Mayer"},{"full_name":"Ron, David","last_name":"Ron","first_name":"David"}],"department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","file_date_updated":"2020-11-19T11:37:41Z","article_number":"e50793","date_published":"2019-12-24T00:00:00Z","article_type":"original","citation":{"chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793"},"publication":"eLife","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8777","date_updated":"2020-11-19T11:37:41Z","date_created":"2020-11-19T11:37:41Z","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","success":1,"file_name":"2019_eLife_AminWetzel.pdf","access_level":"open_access","file_size":4817384,"content_type":"application/pdf","creator":"dernst"}],"intvolume":" 8","status":"public","ddc":["570"],"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7340","abstract":[{"text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.","lang":"eng"}],"type":"journal_article"},{"issue":"5","abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7422","intvolume":" 150","title":"eGFRD in all dimensions","status":"public","article_processing_charge":"No","day":"07","date_published":"2019-02-07T00:00:00Z","citation":{"chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867"},"publication":"The Journal of Chemical Physics","article_type":"original","article_number":"054108","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R"},{"first_name":"Joris","last_name":"Paijmans","full_name":"Paijmans, Joris"},{"full_name":"Bossen, Laurens","last_name":"Bossen","first_name":"Laurens"},{"last_name":"Miedema","first_name":"Thomas","full_name":"Miedema, Thomas"},{"first_name":"Martijn","last_name":"Wehrens","full_name":"Wehrens, Martijn"},{"full_name":"Becker, Nils B.","last_name":"Becker","first_name":"Nils B."},{"first_name":"Kazunari","last_name":"Kaizu","full_name":"Kaizu, Kazunari"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"last_name":"Dogterom","first_name":"Marileen","full_name":"Dogterom, Marileen"},{"full_name":"ten Wolde, Pieter Rein","first_name":"Pieter Rein","last_name":"ten Wolde"}],"volume":150,"date_updated":"2023-09-06T14:59:28Z","date_created":"2020-01-30T10:34:36Z","year":"2019","publisher":"AIP Publishing","department":[{"_id":"GaTk"}],"publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"02","doi":"10.1063/1.5064867","language":[{"iso":"eng"}],"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"isi":1,"quality_controlled":"1"},{"page":"230-243","citation":{"chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18"},"publication":"27th International Symposium on Graph Drawing and Network Visualization","date_published":"2019-11-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","intvolume":" 11904","title":"Extending simple drawings","status":"public","_id":"7230","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.","lang":"eng"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-35802-0_18","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2019-09-20","start_date":"2019-09-17","location":"Prague, Czech Republic"},"publication_identifier":{"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"11","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","volume":11904,"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:56:00Z","author":[{"full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","first_name":"Alan M","last_name":"Arroyo Guevara"},{"full_name":"Derka, Martin","first_name":"Martin","last_name":"Derka"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"}],"ec_funded":1},{"day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","page":"59-75","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75."},"abstract":[{"text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","status":"public","title":"Mixed-time signal temporal logic","intvolume":" 11750","_id":"7232","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"language":[{"iso":"eng"}],"conference":{"name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","end_date":"2019-08-29","start_date":"2019-08-27","location":"Amsterdam, The Netherlands"},"doi":"10.1007/978-3-030-29662-9_4","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"external_id":{"isi":["000611677700004"]},"date_created":"2020-01-05T23:00:48Z","date_updated":"2023-09-06T14:57:17Z","volume":11750,"author":[{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","year":"2019"},{"date_created":"2020-01-30T10:31:42Z","date_updated":"2023-09-06T15:01:00Z","volume":132,"author":[{"first_name":"Pranshu","last_name":"Sahgal","full_name":"Sahgal, Pranshu"},{"full_name":"Alanko, Jonna H","first_name":"Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061"},{"full_name":"Icha, Jaroslav","first_name":"Jaroslav","last_name":"Icha"},{"first_name":"Ilkka","last_name":"Paatero","full_name":"Paatero, Ilkka"},{"first_name":"Hellyeh","last_name":"Hamidi","full_name":"Hamidi, Hellyeh"},{"full_name":"Arjonen, Antti","first_name":"Antti","last_name":"Arjonen"},{"first_name":"Mika","last_name":"Pietilä","full_name":"Pietilä, Mika"},{"full_name":"Rokka, Anne","last_name":"Rokka","first_name":"Anne"},{"full_name":"Ivaska, Johanna","first_name":"Johanna","last_name":"Ivaska"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"The Company of Biologists","year":"2019","pmid":1,"article_number":"jcs233387","language":[{"iso":"eng"}],"doi":"10.1242/jcs.233387","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.233387"}],"oa":1,"external_id":{"pmid":["31076515"],"isi":["000473327900017"]},"month":"06","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"oa_version":"Published Version","status":"public","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","intvolume":" 132","_id":"7420","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2019-06-07T00:00:00Z","article_type":"original","publication":"Journal of Cell Science","citation":{"short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387.","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387."},"day":"07","article_processing_charge":"No"},{"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"year":"2019","date_created":"2020-01-30T10:36:50Z","date_updated":"2023-09-06T14:58:39Z","volume":55,"author":[{"full_name":"Akemann, Gernot","first_name":"Gernot","last_name":"Akemann"},{"last_name":"Checinski","first_name":"Tomasz","full_name":"Checinski, Tomasz"},{"full_name":"Liu, Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87","first_name":"Dangzheng","last_name":"Liu"},{"full_name":"Strahov, Eugene","last_name":"Strahov","first_name":"Eugene"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.05224"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/18-aihp888","month":"02","publication_identifier":{"issn":["0246-0203"]},"title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","status":"public","intvolume":" 55","_id":"7423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.","lang":"eng"}],"issue":"1","article_type":"original","page":"441-479","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","citation":{"chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.","mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.","short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479.","ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.","apa":"Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888","ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888"},"date_published":"2019-02-01T00:00:00Z","day":"01","article_processing_charge":"No"},{"type":"journal_article","abstract":[{"text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.","lang":"eng"}],"issue":"8","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","status":"public","intvolume":" 28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7421","oa_version":"None","day":"01","article_processing_charge":"No","article_type":"original","page":"1877-1889","publication":"Molecular Ecology","citation":{"mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:10.1111/mec.14990.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14990.","ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 2019;28(8):1877-1889. doi:10.1111/mec.14990","ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","apa":"Toups, M. A., Rodrigues, N., Perrin, N., & Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14990","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” Molecular Ecology, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019."},"date_published":"2019-04-01T00:00:00Z","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Wiley","year":"2019","pmid":1,"date_created":"2020-01-30T10:33:05Z","date_updated":"2023-09-06T15:00:13Z","volume":28,"author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"last_name":"Perrin","first_name":"Nicolas","full_name":"Perrin, Nicolas"},{"full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick","first_name":"Mark"}],"month":"04","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"quality_controlled":"1","isi":1,"external_id":{"pmid":["30576024"],"isi":["000468200800004"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.14990"},{"author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Walter","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"date_created":"2020-01-30T09:26:14Z","date_updated":"2023-09-06T15:26:06Z","volume":11477,"year":"2019","publication_status":"published","publisher":"Springer International Publishing","department":[{"_id":"KrPi"}],"ec_funded":1,"conference":{"end_date":"2019-05-23","location":"Darmstadt, Germany","start_date":"2019-05-19","name":"International Conference on the Theory and Applications of Cryptographic Techniques"},"doi":"10.1007/978-3-030-17656-3_10","language":[{"iso":"eng"}],"external_id":{"isi":["000483516200010"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/252"}],"isi":1,"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030176556","9783030176563"],"eissn":["1611-3349"]},"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7411","status":"public","title":"Reversible proofs of sequential work","intvolume":" 11477","abstract":[{"lang":"eng","text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at)."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2019-04-24T00:00:00Z","publication":"Advances in Cryptology – EUROCRYPT 2019","citation":{"ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2019). Reversible proofs of sequential work. In Advances in Cryptology – EUROCRYPT 2019 (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. https://doi.org/10.1007/978-3-030-17656-3_10","ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in Advances in Cryptology – EUROCRYPT 2019, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: Advances in Cryptology – EUROCRYPT 2019. Vol 11477. Springer International Publishing; 2019:277-291. doi:10.1007/978-3-030-17656-3_10","chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In Advances in Cryptology – EUROCRYPT 2019, 11477:277–91. Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-17656-3_10.","mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” Advances in Cryptology – EUROCRYPT 2019, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:10.1007/978-3-030-17656-3_10.","short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291."},"page":"277-291","day":"24","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"issn":["0165-0270"]},"month":"01","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["30496761"],"isi":["000456220900013"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"doi":"10.1016/j.jneumeth.2018.11.018","ec_funded":1,"publisher":"Elsevier","department":[{"_id":"HaJa"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2019","volume":312,"date_created":"2020-01-30T09:12:19Z","date_updated":"2023-09-06T15:27:29Z","author":[{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Spanova, Miroslava","id":"44A924DC-F248-11E8-B48F-1D18A9856A87","last_name":"Spanova","first_name":"Miroslava"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa"},{"full_name":"Sitte, Harald H.","first_name":"Harald H.","last_name":"Sitte"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"scopus_import":"1","article_processing_charge":"No","day":"15","page":"114-121","article_type":"original","citation":{"mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods, vol. 312, Elsevier, 2019, pp. 114–21, doi:10.1016/j.jneumeth.2018.11.018.","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods. Elsevier, 2019. https://doi.org/10.1016/j.jneumeth.2018.11.018.","ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 2019;312:114-121. doi:10.1016/j.jneumeth.2018.11.018","ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121.","ieee":"C. Mckenzie et al., “Isolation of synaptic vesicles from genetically engineered cultured neurons,” Journal of Neuroscience Methods, vol. 312. Elsevier, pp. 114–121, 2019.","apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., & Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2018.11.018"},"publication":"Journal of Neuroscience Methods","date_published":"2019-01-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts."}],"intvolume":" 312","title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","status":"public","_id":"7406","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None"},{"conference":{"end_date":"2019-06-15","start_date":"2019-06-10","location":"Long Beach, CA, United States","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07766"}],"external_id":{"arxiv":["1810.07766"],"isi":["000684034307036"]},"oa":1,"isi":1,"quality_controlled":"1","month":"06","publication_identifier":{"isbn":["9781510886988"]},"author":[{"first_name":"Chen","last_name":"Yu","full_name":"Yu, Chen"},{"full_name":"Tang, Hanlin","first_name":"Hanlin","last_name":"Tang"},{"full_name":"Renggli, Cedric","last_name":"Renggli","first_name":"Cedric"},{"full_name":"Kassing, Simon","first_name":"Simon","last_name":"Kassing"},{"last_name":"Singla","first_name":"Ankit","full_name":"Singla, Ankit"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"last_name":"Zhang","first_name":"Ce","full_name":"Zhang, Ce"},{"full_name":"Liu, Ji","last_name":"Liu","first_name":"Ji"}],"date_created":"2020-02-02T23:01:06Z","date_updated":"2023-09-06T15:21:48Z","volume":"2019-June","year":"2019","publication_status":"published","publisher":"IMLS","department":[{"_id":"DaAl"}],"date_published":"2019-06-01T00:00:00Z","publication":"36th International Conference on Machine Learning, ICML 2019","citation":{"chicago":"Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512. IMLS, 2019.","mla":"Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp. 12481–512.","short":"C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512.","ista":"Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.","apa":"Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In 36th International Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.","ieee":"C. Yu et al., “Distributed learning over unreliable networks,” in 36th International Conference on Machine Learning, ICML 2019, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512.","ama":"Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June. IMLS; 2019:12481-12512."},"page":"12481-12512","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7437","title":"Distributed learning over unreliable networks","status":"public","abstract":[{"text":"Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.","lang":"eng"}],"type":"conference"},{"year":"2019","department":[{"_id":"VlKo"}],"publisher":"SIAM","publication_status":"published","author":[{"full_name":"Achlioptas, Dimitris","last_name":"Achlioptas","first_name":"Dimitris"},{"full_name":"Iliopoulos, Fotis","first_name":"Fotis","last_name":"Iliopoulos"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"volume":48,"date_created":"2020-01-30T09:27:32Z","date_updated":"2023-09-06T15:25:29Z","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1809.01537"],"isi":["000493900200005"]},"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1137/16m109332x","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"month":"10","_id":"7412","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 48","title":"A local lemma for focused stochastical algorithms","status":"public","oa_version":"Preprint","type":"journal_article","issue":"5","abstract":[{"text":"We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure.","lang":"eng"}],"citation":{"ieee":"D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” SIAM Journal on Computing, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019.","apa":"Achlioptas, D., Iliopoulos, F., & Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16m109332x","ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","ama":"Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 2019;48(5):1583-1602. doi:10.1137/16m109332x","chicago":"Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing. SIAM, 2019. https://doi.org/10.1137/16m109332x.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602.","mla":"Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:10.1137/16m109332x."},"publication":"SIAM Journal on Computing","page":"1583-1602","article_type":"original","date_published":"2019-10-31T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"31"},{"issue":"6","abstract":[{"text":"Multiple importance sampling (MIS) has become an indispensable tool in Monte Carlo rendering, widely accepted as a near-optimal solution for combining different sampling techniques. But an MIS combination, using the common balance or power heuristics, often results in an overly defensive estimator, leading to high variance. We show that by generalizing the MIS framework, variance can be substantially reduced. Specifically, we optimize one of the combined sampling techniques so as to decrease the overall variance of the resulting MIS estimator. We apply the approach to the computation of direct illumination due to an HDR environment map and to the computation of global illumination using a path guiding algorithm. The implementation can be as simple as subtracting a constant value from the tabulated sampling density done entirely in a preprocessing step. This produces a consistent noise reduction in all our tests with no negative influence on run time, no artifacts or bias, and no failure cases.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 38","title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7418","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","citation":{"short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019).","mla":"Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 6, 151, ACM, 2019, doi:10.1145/3355089.3356565.","chicago":"Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356565.","ama":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356565","apa":"Karlík, O., Šik, M., Vévoda, P., Skrivan, T., & Křivánek, J. (2019). MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356565","ieee":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation: Optimizing sampling techniques in multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","ista":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 38(6), 151."},"publication":"ACM Transactions on Graphics","article_number":"151","volume":38,"date_updated":"2023-09-06T15:22:23Z","date_created":"2020-01-30T10:19:43Z","author":[{"full_name":"Karlík, Ondřej","last_name":"Karlík","first_name":"Ondřej"},{"first_name":"Martin","last_name":"Šik","full_name":"Šik, Martin"},{"last_name":"Vévoda","first_name":"Petr","full_name":"Vévoda, Petr"},{"first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","year":"2019","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1145/3355089.3356565","isi":1,"quality_controlled":"1","external_id":{"isi":["000498397300001"]}},{"_id":"7413","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 222","status":"public","title":"Bogoliubov theory in the Gross–Pitaevskii limit","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions."}],"citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 2019;222(2):219-335. doi:10.4310/acta.2019.v222.n2.a1","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. International Press of Boston. https://doi.org/10.4310/acta.2019.v222.n2.a1","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” Acta Mathematica, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019.","mla":"Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:10.4310/acta.2019.v222.n2.a1.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica. International Press of Boston, 2019. https://doi.org/10.4310/acta.2019.v222.n2.a1."},"publication":"Acta Mathematica","page":"219-335","article_type":"original","date_published":"2019-06-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"07","year":"2019","department":[{"_id":"RoSe"}],"publisher":"International Press of Boston","publication_status":"published","author":[{"full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"}],"volume":222,"date_created":"2020-01-30T09:30:41Z","date_updated":"2023-09-06T15:24:31Z","external_id":{"isi":["000495865300001"],"arxiv":["1801.01389"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.01389"}],"quality_controlled":"1","isi":1,"doi":"10.4310/acta.2019.v222.n2.a1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0001-5962"],"eissn":["1871-2509"]},"month":"06"},{"intvolume":" 5","ddc":["570"],"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7393","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1869449,"access_level":"open_access","file_name":"2019_ScienceAdvances_Morales.pdf","checksum":"af99a5dcdc66c6d6102051faf3be48d8","date_created":"2020-02-03T13:33:25Z","date_updated":"2020-07-14T12:47:57Z","file_id":"7442","relation":"main_file"}],"type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"article_type":"original","citation":{"ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963."},"publication":"Science Advances","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"04","publisher":"AAAS","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019","volume":5,"date_created":"2020-01-29T15:58:27Z","date_updated":"2023-09-06T15:35:56Z","author":[{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"article_number":"eaav9963","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aav9963","publication_identifier":{"issn":["2375-2548"]},"month":"12"},{"author":[{"full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"volume":874,"date_created":"2020-01-29T16:05:19Z","date_updated":"2023-09-06T15:36:36Z","year":"2019","publisher":"CUP","department":[{"_id":"BjHo"}],"publication_status":"published","doi":"10.1017/jfm.2019.486","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1808.04080","open_access":"1"}],"oa":1,"external_id":{"isi":["000475349900001"],"arxiv":["1808.04080"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"month":"09","oa_version":"Preprint","_id":"7397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 874","title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","status":"public","abstract":[{"lang":"eng","text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT)."}],"type":"journal_article","date_published":"2019-09-10T00:00:00Z","citation":{"mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719.","chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.","ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486","ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719.","apa":"Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019."},"publication":"Journal of Fluid Mechanics","page":"699-719","article_type":"original","article_processing_charge":"No","day":"10","scopus_import":"1"}]