[{"_id":"8089","year":"2020","date_created":"2020-07-05T22:00:45Z","abstract":[{"lang":"eng","text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example."}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"article_processing_charge":"No","oa_version":"Preprint","quality_controlled":"1","date_updated":"2025-06-02T08:53:42Z","citation":{"short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687."},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"}],"oa":1,"publication_identifier":{"isbn":["9781450376136"]},"publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","day":"11","title":"Polynomial invariant generation for non-deterministic recursive programs","external_id":{"isi":["000614622300045"],"arxiv":["1902.04373"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"page":"672-687","conference":{"start_date":"2020-06-15","location":"London, United Kingdom","name":"PLDI: Programming Language Design and Implementation","end_date":"2020-06-20"},"arxiv":1,"scopus_import":"1","month":"06","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.04373"}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"date_published":"2020-06-11T00:00:00Z","doi":"10.1145/3385412.3385969"},{"publication":"Journal of Statistical Physics","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"oa":1,"day":"01","citation":{"short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0","ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464."},"date_updated":"2023-08-22T07:51:47Z","author":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"has_accepted_license":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions","external_id":{"arxiv":["2001.07144"],"isi":["000543030000002"]},"year":"2020","_id":"8091","ec_funded":1,"date_created":"2020-07-05T22:00:46Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file":[{"checksum":"5cbeef52caf18d0d952f17fed7b5545a","file_size":404778,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_JourStatPhysics_Seiringer.pdf","success":1,"date_created":"2020-11-25T15:05:04Z","relation":"main_file","file_id":"8812","date_updated":"2020-11-25T15:05:04Z"}],"abstract":[{"lang":"eng","text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level."}],"publication_status":"published","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-11-25T15:05:04Z","volume":181,"type":"journal_article","ddc":["530"],"intvolume":" 181","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1007/s10955-020-02586-0","date_published":"2020-10-01T00:00:00Z","scopus_import":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","page":"448-464","arxiv":1,"license":"https://creativecommons.org/licenses/by/4.0/","isi":1,"department":[{"_id":"RoSe"}],"publisher":"Springer","month":"10"},{"title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","external_id":{"arxiv":["1711.05139"]},"day":"08","publication":"Domain Adaptation for Visual Understanding","publication_identifier":{"isbn":["9783030306717"]},"oa":1,"citation":{"ista":"Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49.","chicago":"Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.","ama":"Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3","ieee":"A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49.","apa":"Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3","mla":"Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3.","short":"A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49."},"author":[{"last_name":"Royer","first_name":"Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"},{"first_name":"Konstantinos","last_name":"Bousmalis","full_name":"Bousmalis, Konstantinos"},{"first_name":"Stephan","last_name":"Gouws","full_name":"Gouws, Stephan"},{"full_name":"Bertsch, Fred","last_name":"Bertsch","first_name":"Fred"},{"full_name":"Mosseri, Inbar","last_name":"Mosseri","first_name":"Inbar"},{"full_name":"Cole, Forrester","last_name":"Cole","first_name":"Forrester"},{"full_name":"Murphy, Kevin","first_name":"Kevin","last_name":"Murphy"}],"date_updated":"2023-09-07T13:16:18Z","quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"deleted","id":"8331"},{"status":"public","id":"8390","relation":"dissertation_contains"}]},"abstract":[{"text":"Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.","lang":"eng"}],"date_created":"2020-07-05T22:00:46Z","year":"2020","_id":"8092","doi":"10.1007/978-3-030-30671-7_3","date_published":"2020-01-08T00:00:00Z","language":[{"iso":"eng"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.05139"}],"publisher":"Springer Nature","department":[{"_id":"ChLa"}],"month":"01","editor":[{"full_name":"Singh, Richa","first_name":"Richa","last_name":"Singh"},{"full_name":"Vatsa, Mayank","last_name":"Vatsa","first_name":"Mayank"},{"last_name":"Patel","first_name":"Vishal M.","full_name":"Patel, Vishal M."},{"full_name":"Ratha, Nalini","last_name":"Ratha","first_name":"Nalini"}],"scopus_import":"1","arxiv":1,"page":"33-49"},{"has_accepted_license":"1","external_id":{"isi":["000544152500001"],"pmid":["32601464"]},"title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","oa":1,"publication":"British Journal of Cancer","publication_identifier":{"eissn":["1532-1827"],"issn":["0007-0920"]},"day":"15","date_updated":"2023-08-22T07:51:12Z","citation":{"ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.","ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954."},"author":[{"full_name":"Hippe, Andreas","last_name":"Hippe","first_name":"Andreas"},{"full_name":"Braun, Stephan Alexander","last_name":"Braun","first_name":"Stephan Alexander"},{"first_name":"Péter","last_name":"Oláh","full_name":"Oláh, Péter"},{"last_name":"Gerber","first_name":"Peter Arne","full_name":"Gerber, Peter Arne"},{"last_name":"Schorr","first_name":"Anne","full_name":"Schorr, Anne"},{"full_name":"Seeliger, Stephan","last_name":"Seeliger","first_name":"Stephan"},{"full_name":"Holtz, Stephanie","first_name":"Stephanie","last_name":"Holtz"},{"full_name":"Jannasch, Katharina","first_name":"Katharina","last_name":"Jannasch"},{"full_name":"Pivarcsi, Andor","last_name":"Pivarcsi","first_name":"Andor"},{"last_name":"Buhren","first_name":"Bettina","full_name":"Buhren, Bettina"},{"last_name":"Schrumpf","first_name":"Holger","full_name":"Schrumpf, Holger"},{"last_name":"Kislat","first_name":"Andreas","full_name":"Kislat, Andreas"},{"first_name":"Erich","last_name":"Bünemann","full_name":"Bünemann, Erich"},{"last_name":"Steinhoff","first_name":"Martin","full_name":"Steinhoff, Martin"},{"last_name":"Fischer","first_name":"Jens","full_name":"Fischer, Jens"},{"full_name":"Lira, Sérgio A.","first_name":"Sérgio A.","last_name":"Lira"},{"full_name":"Boukamp, Petra","last_name":"Boukamp","first_name":"Petra"},{"first_name":"Peter","last_name":"Hevezi","full_name":"Hevezi, Peter"},{"last_name":"Stoecklein","first_name":"Nikolas Hendrik","full_name":"Stoecklein, Nikolas Hendrik"},{"full_name":"Hoffmann, Thomas","last_name":"Hoffmann","first_name":"Thomas"},{"first_name":"Frauke","last_name":"Alves","full_name":"Alves, Frauke"},{"full_name":"Sleeman, Jonathan","last_name":"Sleeman","first_name":"Jonathan"},{"last_name":"Bauer","first_name":"Thomas","full_name":"Bauer, Thomas"},{"first_name":"Jörg","last_name":"Klufa","full_name":"Klufa, Jörg"},{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"full_name":"Sibilia, Maria","first_name":"Maria","last_name":"Sibilia"},{"full_name":"Zlotnik, Albert","first_name":"Albert","last_name":"Zlotnik"},{"full_name":"Müller-Homey, Anja","first_name":"Anja","last_name":"Müller-Homey"},{"first_name":"Bernhard","last_name":"Homey","full_name":"Homey, Bernhard"}],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy."}],"file":[{"creator":"cchlebak","access_level":"open_access","checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","content_type":"application/pdf","file_size":3620691,"date_updated":"2021-12-02T12:35:12Z","file_name":"2020_BrJournalCancer_Hippe.pdf","success":1,"date_created":"2021-12-02T12:35:12Z","relation":"main_file","file_id":"10398"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"deleted","id":"10170"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}]},"article_type":"original","_id":"8093","year":"2020","date_created":"2020-07-05T22:00:46Z","pmid":1,"intvolume":" 123","ddc":["610"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2020-09-15T00:00:00Z","doi":"10.1038/s41416-020-0943-2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-12-02T12:35:12Z","volume":123,"type":"journal_article","isi":1,"month":"09","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"scopus_import":"1","acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","page":"942-954"},{"year":"2020","_id":"8097","date_created":"2020-07-06T20:40:19Z","acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"article_processing_charge":"No","file":[{"access_level":"open_access","creator":"bkavcic","content_type":"application/zip","file_size":255770756,"checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","date_updated":"2020-07-14T12:48:09Z","file_id":"8098","relation":"main_file","date_created":"2020-07-06T20:38:27Z","file_name":"natComm_2020_scripts.zip"}],"abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"contributor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","last_name":"Tkačik","first_name":"Gašper"},{"contributor_type":"research_group","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach"}],"day":"15","file_date_updated":"2020-07-14T12:48:09Z","date_updated":"2024-02-21T12:40:51Z","author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","last_name":"Kavcic"}],"type":"research_data","citation":{"apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","short":"B. Kavcic, (2020)."},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","status":"public","doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_published":"2020-11-01T00:00:00Z","doi":"10.1111/1755-0998.13210","ddc":["570"],"intvolume":" 20","volume":20,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-11-26T11:46:43Z","month":"11","department":[{"_id":"BeVi"}],"publisher":"Wiley","isi":1,"page":"1517-1525","scopus_import":"1","external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"title":"Disagreement in FST estimators: A case study from sex chromosomes","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"issue":"6","has_accepted_license":"1","citation":{"mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525."},"date_updated":"2023-09-05T16:07:08Z","author":[{"first_name":"William J","last_name":"Gammerdinger","orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups"},{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"oa":1,"publication":"Molecular Ecology Resources","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"day":"01","abstract":[{"text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.","lang":"eng"}],"file":[{"access_level":"open_access","creator":"dernst","checksum":"3d87ebb8757dcd504f20c618b72e6575","file_size":820428,"content_type":"application/pdf","date_updated":"2020-11-26T11:46:43Z","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","file_id":"8814","date_created":"2020-11-26T11:46:43Z","relation":"main_file","success":1}],"publication_status":"published","article_type":"original","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","quality_controlled":"1","_id":"8099","year":"2020","date_created":"2020-07-07T08:56:16Z","ec_funded":1,"pmid":1},{"_id":"8101","year":"2020","ec_funded":1,"date_created":"2020-07-07T11:33:54Z","abstract":[{"lang":"eng","text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature."}],"file":[{"date_updated":"2020-08-17T15:54:20Z","file_name":"Grosjean2020.pdf","date_created":"2020-08-17T15:54:20Z","success":1,"relation":"main_file","file_id":"8277","creator":"ggrosjea","access_level":"open_access","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","content_type":"application/pdf","file_size":853753}],"publication_status":"published","article_type":"original","related_material":{"record":[{"id":"12697","status":"public","relation":"popular_science"}]},"keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"article_processing_charge":"Yes","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Grosjean","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X"},{"first_name":"Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian"},{"last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"date_updated":"2023-08-22T08:41:32Z","citation":{"ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602.","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020)."},"oa":1,"publication_identifier":{"issn":["2475-9953"]},"publication":"Physical Review Materials","day":"17","external_id":{"isi":["000561897000001"],"arxiv":["2006.07120"]},"title":"Quantitatively consistent scale-spanning model for same-material tribocharging","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"issue":"8","article_number":"082602","has_accepted_license":"1","arxiv":1,"scopus_import":"1","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","month":"08","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"isi":1,"volume":4,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-08-17T15:54:20Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2020-08-17T00:00:00Z","doi":"10.1103/PhysRevMaterials.4.082602","intvolume":" 4","ddc":["530"]},{"month":"03","publisher":"EDP Sciences","department":[{"_id":"GaTk"}],"type":"journal_article","volume":230,"file_date_updated":"2020-07-22T06:17:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-03-11T00:00:00Z","doi":"10.1051/epjconf/202023000005","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"intvolume":" 230","ddc":["530"],"date_created":"2020-07-12T16:20:33Z","_id":"8105","year":"2020","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality."}],"file":[{"date_updated":"2020-07-22T06:17:11Z","file_name":"2020_EPJWebConf_Lombardi.pdf","file_id":"8144","date_created":"2020-07-22T06:17:11Z","success":1,"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2197543}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2021-01-12T08:16:55Z","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"last_name":"Wang","first_name":"Jilin W.J.L.","full_name":"Wang, Jilin W.J.L."},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"first_name":"Plamen Ch","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch"}],"citation":{"mla":"Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005.","apa":"Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. EDP Sciences. https://doi.org/10.1051/epjconf/202023000005","ieee":"F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality,” EPJ Web of Conferences, vol. 230. EDP Sciences, 2020.","ama":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005","chicago":"Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences. EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.","ista":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 230, 00005.","short":"F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020)."},"day":"11","oa":1,"publication_identifier":{"issn":["2100-014X"]},"publication":"EPJ Web of Conferences","title":"Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality","has_accepted_license":"1","article_number":"00005"},{"publisher":"The Royal Society","department":[{"_id":"NiBa"}],"month":"07","isi":1,"scopus_import":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1098/rstb.2019.0530","date_published":"2020-07-12T00:00:00Z","intvolume":" 375","volume":375,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"letter_note","publication_status":"published","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","year":"2020","_id":"8112","pmid":1,"date_created":"2020-07-13T03:41:39Z","title":"On the completion of speciation","external_id":{"isi":["000552662100002"],"pmid":["32654647"]},"issue":"1806","article_number":"20190530","citation":{"apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.","short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020)."},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-22T07:53:52Z","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","day":"12"},{"citation":{"short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020."},"author":[{"orcid":"0000-0001-7184-7311","full_name":"Agnes, Everton J.","first_name":"Everton J.","last_name":"Agnes"},{"first_name":"Andrea I.","last_name":"Luppi","full_name":"Luppi, Andrea I."},{"first_name":"Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"}],"date_updated":"2023-08-22T07:54:26Z","oa":1,"publication_identifier":{"eissn":["1529-2401"]},"publication":"The Journal of Neuroscience","day":"09","title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","external_id":{"isi":["000606706400009"],"pmid":["33168622"]},"issue":"50","has_accepted_license":"1","_id":"8126","year":"2020","date_created":"2020-07-16T12:25:04Z","pmid":1,"abstract":[{"text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.","lang":"eng"}],"file":[{"creator":"dernst","access_level":"open_access","checksum":"7977e4dd6b89357d1a5cc88babac56da","file_size":2750920,"content_type":"application/pdf","date_updated":"2020-12-28T08:31:47Z","file_name":"2020_JourNeuroscience_Agnes.pdf","relation":"main_file","success":1,"date_created":"2020-12-28T08:31:47Z","file_id":"8977"}],"article_type":"original","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","volume":40,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-12-28T08:31:47Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_published":"2020-12-09T00:00:00Z","doi":"10.1523/JNEUROSCI.0276-20.2020","intvolume":" 40","ddc":["570"],"page":"9634-9649","scopus_import":"1","month":"12","department":[{"_id":"TiVo"}],"publisher":"Society for Neuroscience","isi":1},{"month":"09","department":[{"_id":"TiVo"}],"publisher":"eLife Sciences Publications","isi":1,"acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","scopus_import":"1","date_published":"2020-09-17T00:00:00Z","doi":"10.7554/eLife.56261","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"ddc":["570"],"intvolume":" 9","type":"journal_article","volume":9,"file_date_updated":"2020-10-27T11:37:32Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics."}],"file":[{"date_updated":"2020-10-27T11:37:32Z","file_id":"8709","relation":"main_file","date_created":"2020-10-27T11:37:32Z","success":1,"file_name":"2020_eLife_Gonçalves.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":17355867,"checksum":"c4300ddcd93ed03fc9c6cdf1f77890be"}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","pmid":1,"ec_funded":1,"date_created":"2020-07-16T12:26:04Z","_id":"8127","year":"2020","title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","external_id":{"pmid":["32940606"],"isi":["000584989400001"]},"project":[{"call_identifier":"H2020","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"has_accepted_license":"1","article_number":"e56261","citation":{"mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261.","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020)."},"date_updated":"2023-08-22T07:54:52Z","author":[{"first_name":"Pedro J.","last_name":"Gonçalves","full_name":"Gonçalves, Pedro J.","orcid":"0000-0002-6987-4836"},{"first_name":"Jan-Matthis","last_name":"Lueckmann","full_name":"Lueckmann, Jan-Matthis","orcid":"0000-0003-4320-4663"},{"orcid":"0000-0002-3573-0404","full_name":"Deistler, Michael","last_name":"Deistler","first_name":"Michael"},{"orcid":"0000-0001-6044-6627","full_name":"Nonnenmacher, Marcel","last_name":"Nonnenmacher","first_name":"Marcel"},{"last_name":"Öcal","first_name":"Kaan","full_name":"Öcal, Kaan","orcid":"0000-0002-8528-6858"},{"last_name":"Bassetto","first_name":"Giacomo","full_name":"Bassetto, Giacomo"},{"orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","first_name":"Chaitanya","last_name":"Chintaluri"},{"first_name":"William F.","last_name":"Podlaski","orcid":"0000-0001-6619-7502","full_name":"Podlaski, William F."},{"orcid":"0000-0003-0807-0823","full_name":"Haddad, Sara A.","first_name":"Sara A.","last_name":"Haddad"},{"first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181"},{"first_name":"David S.","last_name":"Greenberg","full_name":"Greenberg, David S."},{"orcid":"0000-0001-5154-8912","full_name":"Macke, Jakob H.","first_name":"Jakob H.","last_name":"Macke"}],"day":"17","oa":1,"publication_identifier":{"eissn":["2050-084X"]},"publication":"eLife"},{"ddc":["510"],"intvolume":" 238","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1007/s00205-020-01548-w","date_published":"2020-11-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-12-02T08:50:38Z","volume":238,"type":"journal_article","isi":1,"publisher":"Springer Nature","department":[{"_id":"RoSe"}],"month":"11","scopus_import":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","page":"541-606","arxiv":1,"issue":"11","has_accepted_license":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"isi":["000550164400001"],"arxiv":["1907.04547"]},"title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","publication":"Archive for Rational Mechanics and Analysis","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"oa":1,"day":"01","citation":{"chicago":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w.","ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w.","ama":"Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606. doi:10.1007/s00205-020-01548-w","apa":"Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01548-w","ieee":"L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020.","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606."},"date_updated":"2023-09-05T14:19:06Z","author":[{"orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","file":[{"date_updated":"2020-12-02T08:50:38Z","file_name":"2020_ArchiveRatMech_Bossmann.pdf","file_id":"8826","date_created":"2020-12-02T08:50:38Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","checksum":"cc67a79a67bef441625fcb1cd031db3d","file_size":942343,"content_type":"application/pdf"}],"abstract":[{"text":"We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.","lang":"eng"}],"article_type":"original","publication_status":"published","year":"2020","_id":"8130","date_created":"2020-07-18T15:06:35Z","ec_funded":1},{"day":"01","oa":1,"publication":"Current Opinion in Genetics and Development","publication_identifier":{"eissn":["18790380"],"issn":["0959437X"]},"citation":{"ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” Current Opinion in Genetics and Development, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137. doi:10.1016/j.gde.2020.06.004","apa":"Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2020.06.004","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.","ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development. Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137."},"author":[{"first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette"},{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"date_updated":"2024-09-10T12:04:25Z","has_accepted_license":"1","issue":"12","title":"Molecular mechanisms for targeted ASD treatments","external_id":{"isi":["000598918900019"],"pmid":["32659636"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"pmid":1,"ec_funded":1,"date_created":"2020-07-19T22:00:58Z","_id":"8131","year":"2020","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","publication_status":"published","article_type":"original","related_material":{"record":[{"id":"8620","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.","lang":"eng"}],"file":[{"file_name":"2020_CurrentOpGenetics_Basilico.pdf","file_id":"8146","relation":"main_file","success":1,"date_created":"2020-07-22T06:47:45Z","date_updated":"2020-07-22T06:47:45Z","content_type":"application/pdf","file_size":1381545,"access_level":"open_access","creator":"dernst"}],"file_date_updated":"2020-07-22T06:47:45Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":65,"ddc":["570"],"intvolume":" 65","date_published":"2020-12-01T00:00:00Z","doi":"10.1016/j.gde.2020.06.004","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"scopus_import":"1","page":"126-137","isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"12","department":[{"_id":"GaNo"}],"publisher":"Elsevier"},{"year":"2020","_id":"8132","date_created":"2020-07-19T22:00:58Z","pmid":1,"oa_version":"None","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.","lang":"eng"}],"article_type":"original","publication_status":"published","publication":"Science Immunology","publication_identifier":{"eissn":["24709468"]},"day":"10","date_updated":"2023-08-22T07:56:04Z","author":[{"full_name":"Salzer, Elisabeth","last_name":"Salzer","first_name":"Elisabeth"},{"full_name":"Zoghi, Samaneh","last_name":"Zoghi","first_name":"Samaneh"},{"first_name":"Máté G.","last_name":"Kiss","full_name":"Kiss, Máté G."},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Rashkova, Christina","first_name":"Christina","last_name":"Rashkova"},{"last_name":"Stahnke","first_name":"Stephanie","full_name":"Stahnke, Stephanie"},{"first_name":"Matthias","last_name":"Haimel","full_name":"Haimel, Matthias"},{"full_name":"Platzer, René","first_name":"René","last_name":"Platzer"},{"last_name":"Caldera","first_name":"Michael","full_name":"Caldera, Michael"},{"last_name":"Ardy","first_name":"Rico Chandra","full_name":"Ardy, Rico Chandra"},{"full_name":"Hoeger, Birgit","first_name":"Birgit","last_name":"Hoeger"},{"first_name":"Jana","last_name":"Block","full_name":"Block, Jana"},{"full_name":"Medgyesi, David","last_name":"Medgyesi","first_name":"David"},{"full_name":"Sin, Celine","first_name":"Celine","last_name":"Sin"},{"full_name":"Shahkarami, Sepideh","last_name":"Shahkarami","first_name":"Sepideh"},{"last_name":"Kain","first_name":"Renate","full_name":"Kain, Renate"},{"last_name":"Ziaee","first_name":"Vahid","full_name":"Ziaee, Vahid"},{"first_name":"Peter","last_name":"Hammerl","full_name":"Hammerl, Peter"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Dupré, Loïc","last_name":"Dupré","first_name":"Loïc"},{"first_name":"Johannes B.","last_name":"Huppa","full_name":"Huppa, Johannes B."},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Lomakin","first_name":"Alexis","full_name":"Lomakin, Alexis"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"last_name":"Binder","first_name":"Christoph J.","full_name":"Binder, Christoph J."},{"last_name":"Stradal","first_name":"Theresia E.B.","full_name":"Stradal, Theresia E.B."},{"last_name":"Rezaei","first_name":"Nima","full_name":"Rezaei, Nima"},{"last_name":"Boztug","first_name":"Kaan","full_name":"Boztug, Kaan"}],"citation":{"ista":"Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 5(49), eabc3979.","chicago":"Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology. AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.","apa":"Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., … Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979","ama":"Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology. 2020;5(49). doi:10.1126/sciimmunol.abc3979","ieee":"E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.","mla":"Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979, AAAS, 2020, doi:10.1126/sciimmunol.abc3979.","short":"E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel, R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S. Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B. Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei, K. Boztug, Science Immunology 5 (2020)."},"article_number":"eabc3979","issue":"49","external_id":{"pmid":["32646852"],"isi":["000546994600004"]},"title":"The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity","scopus_import":"1","isi":1,"department":[{"_id":"MiSi"}],"publisher":"AAAS","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":5,"type":"journal_article","intvolume":" 5","language":[{"iso":"eng"}],"status":"public","doi":"10.1126/sciimmunol.abc3979","date_published":"2020-07-10T00:00:00Z"},{"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","article_type":"original","related_material":{"record":[{"status":"public","id":"9706","relation":"research_data"}]},"publication_status":"published","file":[{"date_updated":"2020-07-22T06:27:38Z","file_id":"8145","date_created":"2020-07-22T06:27:38Z","success":1,"relation":"main_file","file_name":"2020_GenomeMedicine_Hillary.pdf","access_level":"open_access","creator":"dernst","file_size":1136983,"content_type":"application/pdf"}],"abstract":[{"text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.","lang":"eng"}],"date_created":"2020-07-19T22:00:58Z","pmid":1,"year":"2020","_id":"8133","has_accepted_license":"1","issue":"1","article_number":"60","external_id":{"pmid":["32641083"],"isi":["000551778400001"]},"title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","day":"08","publication":"Genome Medicine","publication_identifier":{"eissn":["1756994X"]},"oa":1,"citation":{"mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1","ieee":"R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020)."},"author":[{"full_name":"Hillary, Robert F.","first_name":"Robert F.","last_name":"Hillary"},{"first_name":"Daniel","last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"first_name":"Daniel L.","last_name":"Mccartney","full_name":"Mccartney, Daniel L."},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"full_name":"Stevenson, Anna J.","last_name":"Stevenson","first_name":"Anna J."},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"full_name":"Ojavee, Sven Erik","first_name":"Sven Erik","last_name":"Ojavee"},{"last_name":"Zhang","first_name":"Qian","full_name":"Zhang, Qian"},{"first_name":"David C.","last_name":"Liewald","full_name":"Liewald, David C."},{"full_name":"Ritchie, Craig W.","first_name":"Craig W.","last_name":"Ritchie"},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"first_name":"Elliot M.","last_name":"Tucker-Drob","full_name":"Tucker-Drob, Elliot M."},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"last_name":"Mcrae","first_name":"Allan F.","full_name":"Mcrae, Allan F."},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"}],"date_updated":"2023-08-22T07:55:37Z","isi":1,"department":[{"_id":"MaRo"}],"publisher":"Springer Nature","month":"07","scopus_import":"1","ddc":["570"],"intvolume":" 12","doi":"10.1186/s13073-020-00754-1","date_published":"2020-07-08T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2020-07-22T06:27:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":12},{"year":"2020","_id":"8134","ec_funded":1,"date_created":"2020-07-19T22:00:59Z","abstract":[{"lang":"eng","text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion."}],"article_type":"original","publication_status":"published","oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","citation":{"short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.","chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950."},"date_updated":"2023-08-22T08:12:40Z","author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"publication_identifier":{"issn":["00222488"]},"publication":"Journal of Mathematical Physics","oa":1,"day":"22","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"external_id":{"isi":["000544595100001"],"arxiv":["2002.08281"]},"title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","article_number":"061901","issue":"6","arxiv":1,"scopus_import":"1","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"isi":1,"volume":61,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","doi":"10.1063/5.0005950","date_published":"2020-06-22T00:00:00Z","intvolume":" 61"},{"type":"conference","volume":15,"file_date_updated":"2020-10-08T08:56:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-030-43408-3_8","date_published":"2020-06-22T00:00:00Z","language":[{"iso":"eng"}],"status":"public","alternative_title":["Abel Symposia"],"ddc":["510"],"intvolume":" 15","page":"181-218","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","scopus_import":"1","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"month":"06","citation":{"short":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, P. Synak, in:, Topological Data Analysis, Springer Nature, 2020, pp. 181–218.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, Katharina Ölsböck, and Peter Synak. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” In Topological Data Analysis, 15:181–218. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-43408-3_8.","ista":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. 2020. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. Topological Data Analysis. , Abel Symposia, vol. 15, 181–218.","mla":"Edelsbrunner, Herbert, et al. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” Topological Data Analysis, vol. 15, Springer Nature, 2020, pp. 181–218, doi:10.1007/978-3-030-43408-3_8.","ieee":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, and P. Synak, “Radius functions on Poisson–Delaunay mosaics and related complexes experimentally,” in Topological Data Analysis, 2020, vol. 15, pp. 181–218.","ama":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In: Topological Data Analysis. Vol 15. Springer Nature; 2020:181-218. doi:10.1007/978-3-030-43408-3_8","apa":"Edelsbrunner, H., Nikitenko, A., Ölsböck, K., & Synak, P. (2020). Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In Topological Data Analysis (Vol. 15, pp. 181–218). Springer Nature. https://doi.org/10.1007/978-3-030-43408-3_8"},"date_updated":"2021-01-12T08:17:06Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"},{"id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton","first_name":"Anton","last_name":"Nikitenko"},{"id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","first_name":"Katharina","last_name":"Ölsböck"},{"first_name":"Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter"}],"day":"22","publication_identifier":{"isbn":["9783030434076"],"eissn":["21978549"],"issn":["21932808"]},"publication":"Topological Data Analysis","oa":1,"project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Radius functions on Poisson–Delaunay mosaics and related complexes experimentally","has_accepted_license":"1","ec_funded":1,"date_created":"2020-07-19T22:00:59Z","year":"2020","_id":"8135","publication_status":"published","file":[{"file_name":"2020-B-01-PoissonExperimentalSurvey.pdf","file_id":"8628","relation":"main_file","success":1,"date_created":"2020-10-08T08:56:14Z","date_updated":"2020-10-08T08:56:14Z","checksum":"7b5e0de10675d787a2ddb2091370b8d8","content_type":"application/pdf","file_size":2207071,"access_level":"open_access","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics."}],"quality_controlled":"1","oa_version":"Submitted Version","article_processing_charge":"No"},{"ec_funded":1,"pmid":1,"date_created":"2020-07-21T08:58:07Z","_id":"8138","year":"2020","publication_status":"published","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"}]},"article_type":"original","abstract":[{"lang":"eng","text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration."}],"file":[{"access_level":"open_access","creator":"dernst","file_size":1759490,"content_type":"application/pdf","date_updated":"2020-07-22T08:32:55Z","file_id":"8148","date_created":"2020-07-22T08:32:55Z","relation":"main_file","success":1,"file_name":"2020_NatureComm_Zhang.pdf"}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","author":[{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"last_name":"Mazur","first_name":"E","full_name":"Mazur, E"},{"last_name":"Balla","first_name":"J","full_name":"Balla, J"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"},{"first_name":"P","last_name":"Kalousek","full_name":"Kalousek, P"},{"full_name":"Medveďová, Z","first_name":"Z","last_name":"Medveďová"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"full_name":"Wang, Y","first_name":"Y","last_name":"Wang"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas"},{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K"},{"full_name":"Reinöhl, V","first_name":"V","last_name":"Reinöhl"},{"last_name":"Procházka","first_name":"S","full_name":"Procházka, S"},{"full_name":"Halouzka, R","first_name":"R","last_name":"Halouzka"},{"last_name":"Tarkowski","first_name":"P","full_name":"Tarkowski, P"},{"last_name":"Luschnig","first_name":"C","full_name":"Luschnig, C"},{"full_name":"Brewer, PB","first_name":"PB","last_name":"Brewer"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.","ieee":"J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y"},"date_updated":"2023-08-22T08:13:44Z","day":"14","oa":1,"publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"external_id":{"pmid":["32665554"],"isi":["000550062200004"]},"title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"has_accepted_license":"1","issue":"1","page":"3508","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","scopus_import":"1","month":"07","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","isi":1,"type":"journal_article","volume":11,"file_date_updated":"2020-07-22T08:32:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-07-14T00:00:00Z","doi":"10.1038/s41467-020-17252-y","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"intvolume":" 11","ddc":["580"]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2021-08-08T22:30:03Z","volume":133,"type":"journal_article","ddc":["575"],"intvolume":" 133","status":"public","language":[{"iso":"eng"}],"date_published":"2020-08-06T00:00:00Z","doi":"10.1242/jcs.248062","scopus_import":"1","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","isi":1,"month":"08","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"oa":1,"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"publication":"Journal of Cell Science","day":"06","citation":{"chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020)."},"author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"last_name":"Narasimhan","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"first_name":"G","last_name":"Vert","full_name":"Vert, G"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"date_updated":"2023-12-01T13:51:07Z","issue":"15","article_number":"jcs248062","has_accepted_license":"1","title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"_id":"8139","year":"2020","ec_funded":1,"date_created":"2020-07-21T08:58:19Z","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}],"file":[{"embargo":"2021-08-07","date_updated":"2021-08-08T22:30:03Z","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","file_id":"8815","date_created":"2020-11-26T17:12:51Z","relation":"main_file","access_level":"open_access","creator":"ajohnson","checksum":"2d11f79a0b4e0a380fb002b933da331a","file_size":15150403,"content_type":"application/pdf"}],"publication_status":"published","article_type":"original","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]}},{"date_updated":"2023-09-05T13:05:47Z","author":[{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","first_name":"Juan C","last_name":"Montesinos López"},{"last_name":"Abuzeineh","first_name":"A","full_name":"Abuzeineh, A"},{"first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"first_name":"Alba","last_name":"Juanes Garcia","full_name":"Juanes Garcia, Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1009-9652"},{"first_name":"Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983"},{"full_name":"Petrášek, J","last_name":"Petrášek","first_name":"J"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"citation":{"chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238.","ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238.","mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238.","ieee":"J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” The Embo Journal, vol. 39, no. 17. Embo Press, 2020.","apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020)."},"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"publication":"The Embo Journal","oa":1,"day":"01","project":[{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"},{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"}],"title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","external_id":{"pmid":["32667089"],"isi":["000548311800001"]},"issue":"17","article_number":"e104238","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2020","_id":"8142","pmid":1,"date_created":"2020-07-21T09:08:38Z","file":[{"creator":"dernst","access_level":"open_access","file_size":3497156,"content_type":"application/pdf","checksum":"43d2b36598708e6ab05c69074e191d57","date_updated":"2020-12-02T09:13:23Z","success":1,"date_created":"2020-12-02T09:13:23Z","relation":"main_file","file_id":"8827","file_name":"2020_EMBO_Montesinos.pdf"}],"abstract":[{"text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.","lang":"eng"}],"article_type":"original","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","volume":39,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-12-02T09:13:23Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.15252/embj.2019104238","date_published":"2020-09-01T00:00:00Z","intvolume":" 39","ddc":["580"],"scopus_import":"1","acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","publisher":"Embo Press","department":[{"_id":"MiSi"},{"_id":"EvBe"}],"month":"09","isi":1}]