[{"title":"Algebraic methods in the congested clique","quality_controlled":"1","page":"461-478","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.04963"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00446-016-0270-2","intvolume":"        32","publication_identifier":{"issn":["0178-2770","1432-0452"]},"status":"public","publication":"Distributed Computing","external_id":{"arxiv":["1503.04963"]},"volume":32,"oa_version":"Preprint","arxiv":1,"extern":"1","article_type":"original","article_processing_charge":"No","issue":"6","type":"journal_article","day":"01","publisher":"Springer Nature","citation":{"ista":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic methods in the congested clique. Distributed Computing. 32(6), 461–478.","ieee":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela, “Algebraic methods in the congested clique,” <i>Distributed Computing</i>, vol. 32, no. 6. Springer Nature, pp. 461–478, 2019.","mla":"Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>.","apa":"Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., &#38; Suomela, J. (2019). Algebraic methods in the congested clique. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>","short":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed Computing 32 (2019) 461–478.","ama":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic methods in the congested clique. <i>Distributed Computing</i>. 2019;32(6):461-478. doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>","chicago":"Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen, Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>."},"abstract":[{"lang":"eng","text":"In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:\r\n\r\n1.    triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.\r\n   \r\nIn addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles."}],"month":"12","date_updated":"2021-01-12T08:12:05Z","date_published":"2019-12-01T00:00:00Z","_id":"7150","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2019-12-05T09:49:49Z","year":"2019","author":[{"full_name":"Censor-Hillel, Keren","last_name":"Censor-Hillel","first_name":"Keren"},{"last_name":"Kaski","first_name":"Petteri","full_name":"Kaski, Petteri"},{"full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen","first_name":"Janne"},{"first_name":"Christoph","last_name":"Lenzen","full_name":"Lenzen, Christoph"},{"full_name":"Paz, Ami","first_name":"Ami","last_name":"Paz"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"}]},{"department":[{"_id":"BeBi"}],"article_processing_charge":"No","year":"2019","related_material":{"record":[{"status":"deleted","relation":"used_in_publication","id":"8433"},{"relation":"used_in_publication","id":"7262","status":"public"}]},"has_accepted_license":"1","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","last_name":"Guseinov","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan"}],"day":"06","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_created":"2019-12-09T07:52:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"12","date_updated":"2024-02-21T12:45:03Z","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","ddc":["000"],"contributor":[{"first_name":"Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"McMahan","first_name":"Connor"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Daraio","first_name":"Chiara"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"ec_funded":1,"date_published":"2019-12-06T00:00:00Z","_id":"7154","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>.","short":"R. Guseinov, (2019).","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019."},"file_date_updated":"2020-07-14T12:47:50Z","doi":"10.15479/AT:ISTA:7154","file":[{"file_name":"temporal_morphing_supp_data.zip","checksum":"155133e6e188e85b3c0676a5e70b9341","access_level":"open_access","relation":"main_file","date_created":"2019-12-09T07:52:17Z","file_id":"7155","content_type":"application/x-zip-compressed","file_size":65307107,"creator":"dernst","date_updated":"2020-07-14T12:47:50Z"}]},{"isi":1,"article_processing_charge":"No","day":"01","type":"journal_article","department":[{"_id":"JoFi"}],"article_type":"original","volume":5,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"108","license":"https://creativecommons.org/licenses/by/4.0/","arxiv":1,"oa_version":"Published Version","publication":"npj Quantum Information","external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"ddc":["530"],"project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894"},{"call_identifier":"FWF","grant_number":"F07105","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_identifier":{"issn":["2056-6387"]},"doi":"10.1038/s41534-019-0220-5","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:50Z","creator":"dernst","file_id":"7157","date_created":"2019-12-09T08:25:06Z","content_type":"application/pdf","file_size":1580132,"file_name":"2019_NPJ_Rueda.pdf","checksum":"13e0ea1d4f9b5f5710780d9473364f58","access_level":"open_access","relation":"main_file"}],"intvolume":"         5","quality_controlled":"1","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","oa":1,"has_accepted_license":"1","year":"2019","author":[{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","orcid":"0000-0001-9868-2166","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_created":"2019-12-09T08:18:56Z","date_published":"2019-12-01T00:00:00Z","ec_funded":1,"_id":"7156","date_updated":"2024-08-07T07:11:55Z","scopus_import":"1","month":"12","abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"citation":{"ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” <i>npj Quantum Information</i>, vol. 5. Springer Nature, 2019.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>, vol. 5, 108, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., &#38; Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>npj Quantum Information</i>. 2019;5. doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>","chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>."},"file_date_updated":"2020-07-14T12:47:50Z","publisher":"Springer Nature"},{"file":[{"file_id":"8632","date_created":"2020-10-08T12:58:10Z","content_type":"application/pdf","file_size":667357,"success":1,"file_name":"2019_ACMTransactions_Chatterjee.pdf","checksum":"291cc86a07bd010d4815e177dac57b70","access_level":"open_access","relation":"main_file","date_updated":"2020-10-08T12:58:10Z","creator":"dernst"}],"intvolume":"        41","doi":"10.1145/3363525","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","publication":"ACM Transactions on Programming Languages and Systems","external_id":{"isi":["000564108400004"]},"ddc":["000"],"publication_identifier":{"issn":["0164-0925"]},"status":"public","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"article_type":"original","article_number":"23","oa_version":"Submitted Version","volume":41,"day":"01","type":"journal_article","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"article_processing_charge":"No","isi":1,"issue":"4","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n"}],"citation":{"ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23.","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4. ACM, 2019.","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. <i>ACM Transactions on Programming Languages and Systems</i>. ACM. <a href=\"https://doi.org/10.1145/3363525\">https://doi.org/10.1145/3363525</a>","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4, 23, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3363525\">10.1145/3363525</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” <i>ACM Transactions on Programming Languages and Systems</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3363525\">https://doi.org/10.1145/3363525</a>.","ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. <i>ACM Transactions on Programming Languages and Systems</i>. 2019;41(4). doi:<a href=\"https://doi.org/10.1145/3363525\">10.1145/3363525</a>","short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019)."},"file_date_updated":"2020-10-08T12:58:10Z","publisher":"ACM","_id":"7158","date_published":"2019-11-01T00:00:00Z","ec_funded":1,"date_updated":"2024-03-25T23:30:19Z","scopus_import":"1","month":"11","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-09T08:33:33Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Prateesh","last_name":"Goyal","full_name":"Goyal, Prateesh"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"has_accepted_license":"1","year":"2019"},{"page":"292-309","quality_controlled":"1","title":"Shape expressions for specifying and extracting signal features","intvolume":"     11757","doi":"10.1007/978-3-030-32079-9_17","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030320782","9783030320799"]},"status":"public","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"}],"publication":"19th International Conference on Runtime Verification","external_id":{"isi":["000570006300017"]},"oa_version":"None","volume":11757,"department":[{"_id":"ToHe"}],"conference":{"start_date":"2019-10-08","location":"Porto, Portugal","end_date":"2019-10-11","name":"RV: Runtime Verification"},"day":"01","type":"conference","article_processing_charge":"No","isi":1,"publisher":"Springer Nature","citation":{"mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” <i>19th International Conference on Runtime Verification</i>, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., &#38; Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In <i>19th International Conference on Runtime Verification</i> (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: <i>19th International Conference on Runtime Verification</i>. Vol 11757. Springer Nature; 2019:292-309. doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In <i>19th International Conference on Runtime Verification</i>, 11757:292–309. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>.","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in <i>19th International Conference on Runtime Verification</i>, Porto, Portugal, 2019, vol. 11757, pp. 292–309."},"abstract":[{"lang":"eng","text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. "}],"date_updated":"2023-09-06T11:24:10Z","scopus_import":"1","month":"10","_id":"7159","date_published":"2019-10-01T00:00:00Z","date_created":"2019-12-09T08:47:55Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Ničković, Dejan","last_name":"Ničković","first_name":"Dejan"},{"first_name":"Xin","last_name":"Qin","full_name":"Qin, Xin"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"first_name":"Cristinel","last_name":"Mateis","full_name":"Mateis, Cristinel"},{"first_name":"Jyotirmoy","last_name":"Deshmukh","full_name":"Deshmukh, Jyotirmoy"}],"year":"2019"},{"language":[{"iso":"eng"}],"doi":"10.1242/dev.176297","intvolume":"       146","file":[{"date_updated":"2020-07-14T12:47:50Z","creator":"dernst","file_id":"7177","date_created":"2019-12-13T07:34:06Z","content_type":"application/pdf","file_size":7797881,"checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","file_name":"2019_Development_Guerrero.pdf","relation":"main_file","access_level":"open_access"}],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","quality_controlled":"1","oa":1,"ddc":["570"],"publication":"Development","external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"project":[{"grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"status":"public","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"article_type":"original","volume":146,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","article_number":"dev176297","issue":"23","isi":1,"article_processing_charge":"No","type":"journal_article","day":"04","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:47:50Z","abstract":[{"text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube.","lang":"eng"}],"citation":{"ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ieee":"P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146, no. 23. The Company of Biologists, 2019.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. 2019;146(23). doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>."},"publisher":"The Company of Biologists","ec_funded":1,"date_published":"2019-12-04T00:00:00Z","_id":"7165","month":"12","scopus_import":"1","date_updated":"2023-09-06T11:26:36Z","date_created":"2019-12-10T14:39:50Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","has_accepted_license":"1","author":[{"full_name":"Guerrero, Pilar","last_name":"Guerrero","first_name":"Pilar"},{"last_name":"Perez-Carrasco","first_name":"Ruben","full_name":"Perez-Carrasco, Ruben"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"full_name":"Page, David","last_name":"Page","first_name":"David"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"last_name":"Page","first_name":"Karen M.","full_name":"Page, Karen M."}],"pmid":1},{"doi":"10.1007/978-3-658-26763-6","language":[{"iso":"ger"}],"abstract":[{"lang":"ger","text":"Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!"}],"citation":{"ieee":"K. Kersting, C. Lampert, and C. Rothkopf, Eds., <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>, 1st ed. Wiesbaden: Springer Nature, 2019.","ista":"Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.","chicago":"Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed. Wiesbaden: Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-658-26763-6\">https://doi.org/10.1007/978-3-658-26763-6</a>.","ama":"Kersting K, Lampert C, Rothkopf C, eds. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed. Wiesbaden: Springer Nature; 2019. doi:<a href=\"https://doi.org/10.1007/978-3-658-26763-6\">10.1007/978-3-658-26763-6</a>","short":"K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.","apa":"Kersting, K., Lampert, C., &#38; Rothkopf, C. (Eds.). (2019). <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i> (1st ed.). Wiesbaden: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-658-26763-6\">https://doi.org/10.1007/978-3-658-26763-6</a>","mla":"Kersting, Kristian, et al., editors. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed., Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/978-3-658-26763-6\">10.1007/978-3-658-26763-6</a>."},"quality_controlled":"1","place":"Wiesbaden","title":"Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt","publisher":"Springer Nature","page":"XIV, 245","date_published":"2019-10-30T00:00:00Z","_id":"7171","edition":"1","date_updated":"2021-12-22T14:40:58Z","month":"10","status":"public","publication_identifier":{"eisbn":["978-3-658-26763-6"],"isbn":["978-3-658-26762-9"]},"date_created":"2019-12-11T14:15:56Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","oa_version":"None","related_material":{"link":[{"url":"https://ist.ac.at/en/news/book-release-how-machines-learn/","relation":"press_release","description":"News on IST Website"}]},"year":"2019","article_processing_charge":"No","type":"book_editor","day":"30","editor":[{"first_name":"Kristian","last_name":"Kersting","full_name":"Kersting, Kristian"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Rothkopf, Constantin","first_name":"Constantin","last_name":"Rothkopf"}],"department":[{"_id":"ChLa"}]},{"page":"192","oa":1,"title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","file":[{"relation":"source_file","access_level":"closed","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_name":"Thesis_Mina_final_upload_7.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20454014,"file_id":"7175","date_created":"2019-12-12T09:32:36Z","creator":"mvasilev","date_updated":"2020-07-14T12:47:51Z"},{"date_updated":"2020-07-14T12:47:51Z","creator":"mvasilev","content_type":"application/pdf","file_size":11565025,"file_id":"7176","date_created":"2019-12-12T09:33:10Z","relation":"main_file","access_level":"open_access","checksum":"3882c4585e46c9cfb486e4225cad54ab","file_name":"Thesis_Mina_final_upload_7.pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:7172","publication_identifier":{"eissn":["2663-337X"]},"status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["570"],"oa_version":"Published Version","department":[{"_id":"JiFr"}],"day":"12","type":"dissertation","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"6377","relation":"part_of_dissertation"},{"id":"449","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1346","relation":"part_of_dissertation"}]},"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. <i>Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>.","apa":"Vasileva, M. K. (2019). <i>Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>."},"file_date_updated":"2020-07-14T12:47:51Z","abstract":[{"text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes.","lang":"eng"}],"month":"12","date_updated":"2025-05-07T11:12:29Z","_id":"7172","date_published":"2019-12-12T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-11T21:24:39Z","publication_status":"published","degree_awarded":"PhD","author":[{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K"}],"year":"2019","has_accepted_license":"1"},{"abstract":[{"text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity.","lang":"eng"}],"file_date_updated":"2020-12-06T17:30:09Z","citation":{"ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. 2019;33(12):13734-13746. doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>. FASEB, 2019. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>.","mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., &#38; Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” <i>FASEB Journal</i>, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746."},"publisher":"FASEB","_id":"7179","date_published":"2019-12-01T00:00:00Z","month":"12","date_updated":"2023-09-06T14:34:36Z","scopus_import":"1","date_created":"2019-12-15T23:00:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","author":[{"full_name":"Klotz, Lisa","first_name":"Lisa","last_name":"Klotz"},{"first_name":"Olaf","last_name":"Wendler","full_name":"Wendler, Olaf"},{"full_name":"Frischknecht, Renato","last_name":"Frischknecht","first_name":"Renato"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Schulze, Holger","first_name":"Holger","last_name":"Schulze"},{"last_name":"Enz","first_name":"Ralf","full_name":"Enz, Ralf"}],"year":"2019","has_accepted_license":"1","pmid":1,"intvolume":"        33","file":[{"creator":"shigemot","date_updated":"2020-12-06T17:30:09Z","success":1,"file_name":"Klotz et al 2019 EMBO Reports.pdf","checksum":"79e3b72481dc32489911121cf3b7d8d0","access_level":"open_access","relation":"main_file","date_created":"2020-12-06T17:30:09Z","file_id":"8922","content_type":"application/pdf","file_size":4766789}],"language":[{"iso":"eng"}],"doi":"10.1096/fj.201901543R","page":"13734-13746","oa":1,"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","quality_controlled":"1","ddc":["571","599"],"publication":"FASEB Journal","external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"publication_identifier":{"eissn":["15306860"]},"status":"public","article_type":"original","oa_version":"Submitted Version","volume":33,"day":"01","type":"journal_article","article_processing_charge":"No","issue":"12","isi":1,"department":[{"_id":"RySh"}]},{"doi":"10.1038/s41467-019-13543-1","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:52Z","creator":"dernst","file_size":5156533,"content_type":"application/pdf","date_created":"2019-12-16T07:37:50Z","file_id":"7184","relation":"main_file","access_level":"open_access","checksum":"77e8720a8e0f3091b98159f85be40893","file_name":"2019_NatureComm_Retzer.pdf"}],"intvolume":"        10","quality_controlled":"1","title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","oa":1,"external_id":{"isi":["000500508100001"],"pmid":["31797871"]},"publication":"Nature Communications","ddc":["570"],"project":[{"call_identifier":"FWF","grant_number":"M02379","name":"Modeling epithelial tissue mechanics during cell invasion","_id":"264CBBAC-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["20411723"]},"status":"public","article_type":"original","volume":10,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"5516","oa_version":"Published Version","isi":1,"article_processing_charge":"No","day":"01","type":"journal_article","department":[{"_id":"DaSi"}],"abstract":[{"lang":"eng","text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation."}],"citation":{"chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., &#38; Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>, vol. 10, 5516, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>.","ieee":"K. Retzer <i>et al.</i>, “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516."},"file_date_updated":"2020-07-14T12:47:52Z","publisher":"Springer Nature","date_published":"2019-12-01T00:00:00Z","_id":"7180","date_updated":"2023-09-06T14:08:21Z","scopus_import":"1","month":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-15T23:00:43Z","publication_status":"published","has_accepted_license":"1","year":"2019","author":[{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0003-1522-3162","last_name":"Akhmanova"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Malínská, Kateřina","first_name":"Kateřina","last_name":"Malínská"},{"full_name":"Leitner, Johannes","first_name":"Johannes","last_name":"Leitner"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"}],"pmid":1},{"status":"public","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"project":[{"grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales"}],"external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"publication":"Nature Biotechnology","page":"1466-1470","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/"}],"oa":1,"title":"Large multiple sequence alignments with a root-to-leaf regressive method","quality_controlled":"1","intvolume":"        37","language":[{"iso":"eng"}],"doi":"10.1038/s41587-019-0333-6","department":[{"_id":"FyKo"}],"type":"journal_article","day":"01","issue":"12","article_processing_charge":"No","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"13059"}]},"oa_version":"Submitted Version","volume":37,"article_type":"original","month":"12","scopus_import":"1","date_updated":"2023-09-06T14:32:52Z","_id":"7181","ec_funded":1,"date_published":"2019-12-01T00:00:00Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"citation":{"ieee":"E. Garriga <i>et al.</i>, “Large multiple sequence alignments with a root-to-leaf regressive method,” <i>Nature Biotechnology</i>, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. 2019;37(12):1466-1470. doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>"},"pmid":1,"author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"last_name":"Di Tommaso","first_name":"Paolo","full_name":"Di Tommaso, Paolo"},{"full_name":"Magis, Cedrik","first_name":"Cedrik","last_name":"Magis"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"full_name":"Notredame, Cedric","first_name":"Cedric","last_name":"Notredame"}],"year":"2019","date_created":"2019-12-15T23:00:43Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_type":"original","article_number":"1437","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"type":"journal_article","day":"14","issue":"11","article_processing_charge":"No","isi":1,"department":[{"_id":"JiFr"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:52Z","checksum":"995aa838aec2064d93550de82b40bbd1","file_name":"2019_FrontiersPlant_Alcantara.pdf","relation":"main_file","access_level":"open_access","file_id":"7185","date_created":"2019-12-16T07:58:43Z","content_type":"application/pdf","file_size":1532505}],"intvolume":"        10","doi":"10.3389/fpls.2019.01437","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","title":"Systematic Y2H screening reveals extensive effector-complex formation","external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"publication":"Frontiers in Plant Science","ddc":["580"],"publication_identifier":{"eissn":["1664462X"]},"status":"public","publication_status":"published","date_created":"2019-12-15T23:00:43Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Alcântara, André","first_name":"André","last_name":"Alcântara"},{"full_name":"Bosch, Jason","last_name":"Bosch","first_name":"Jason"},{"first_name":"Fahimeh","last_name":"Nazari","full_name":"Nazari, Fahimeh"},{"full_name":"Hoffmann, Gesa","last_name":"Hoffmann","first_name":"Gesa"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"first_name":"Martin A.","last_name":"Darino","full_name":"Darino, Martin A."},{"full_name":"Olukayode, Toluwase","first_name":"Toluwase","last_name":"Olukayode"},{"full_name":"Reumann, Daniel","first_name":"Daniel","last_name":"Reumann"},{"full_name":"Baggaley, Laura","first_name":"Laura","last_name":"Baggaley"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"has_accepted_license":"1","year":"2019","pmid":1,"abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"citation":{"apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>, vol. 10, no. 11, 1437, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>.","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. 2019;10(11). doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","ieee":"A. Alcântara <i>et al.</i>, “Systematic Y2H screening reveals extensive effector-complex formation,” <i>Frontiers in Plant Science</i>, vol. 10, no. 11. Frontiers, 2019."},"file_date_updated":"2020-07-14T12:47:52Z","publisher":"Frontiers","_id":"7182","date_published":"2019-11-14T00:00:00Z","date_updated":"2023-09-06T14:33:46Z","scopus_import":"1","month":"11"},{"publisher":"Springer Nature","citation":{"short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: <i>International Symposium on Automated Technology for Verification and Analysis</i>. Vol 11781. Springer Nature; 2019:462-478. doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In <i>International Symposium on Automated Technology for Verification and Analysis</i>, 11781:462–78. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” <i>International Symposium on Automated Technology for Verification and Analysis</i>, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., &#38; Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In <i>International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in <i>International Symposium on Automated Technology for Verification and Analysis</i>, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478."},"abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"scopus_import":"1","date_updated":"2023-09-06T12:40:58Z","month":"10","_id":"7183","date_published":"2019-10-21T00:00:00Z","date_created":"2019-12-15T23:00:44Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","author":[{"full_name":"Brázdil, Tomás","first_name":"Tomás","last_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kucera","first_name":"Antonín","full_name":"Kucera, Antonín"},{"first_name":"Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"}],"year":"2019","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"page":"462-478","quality_controlled":"1","title":"Deciding fast termination for probabilistic VASS with nondeterminism","intvolume":"     11781","doi":"10.1007/978-3-030-31784-3_27","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"status":"public","publication_identifier":{"isbn":["9783030317836"],"issn":["03029743"],"eissn":["16113349"]},"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"external_id":{"arxiv":["1907.11010"],"isi":["000723515700027"]},"publication":"International Symposium on Automated Technology for Verification and Analysis","arxiv":1,"oa_version":"Preprint","volume":11781,"department":[{"_id":"KrCh"}],"day":"21","type":"conference","conference":{"start_date":"2019-10-28","location":"Taipei, Taiwan","end_date":"2019-10-31","name":"ATVA: Automated TEchnology for Verification and Analysis"},"isi":1,"article_processing_charge":"No"},{"department":[{"_id":"CaHe"}],"article_processing_charge":"No","related_material":{"record":[{"id":"1096","relation":"dissertation_contains","status":"public"},{"relation":"part_of_dissertation","id":"7001","status":"public"}]},"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"16","oa_version":"Published Version","status":"public","publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","page":"107","oa":1,"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:7186","file":[{"creator":"cschwayer","date_updated":"2020-07-14T12:47:52Z","checksum":"585583c1c875c5d9525703a539668a7c","file_name":"DocumentSourceFiles.zip","relation":"source_file","access_level":"closed","date_created":"2019-12-19T15:18:11Z","file_id":"7194","file_size":19431292,"content_type":"application/zip"},{"date_updated":"2020-07-14T12:47:52Z","creator":"cschwayer","content_type":"application/pdf","file_size":19226428,"date_created":"2019-12-19T15:19:21Z","file_id":"7195","relation":"main_file","access_level":"open_access","checksum":"9b9b24351514948d27cec659e632e2cd","file_name":"Thesis_CS_final.pdf"}],"year":"2019","has_accepted_license":"1","author":[{"full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","first_name":"Cornelia","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-16T14:26:14Z","degree_awarded":"PhD","month":"12","date_updated":"2023-09-07T12:56:42Z","date_published":"2019-12-16T00:00:00Z","_id":"7186","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing."}],"citation":{"ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>.","mla":"Schwayer, Cornelia. <i>Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>.","apa":"Schwayer, C. (2019). <i>Mechanosensation of tight junctions depends on ZO-1 phase separation and flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>"},"file_date_updated":"2020-07-14T12:47:52Z"},{"date_published":"2019-12-16T00:00:00Z","ec_funded":1,"_id":"7190","date_updated":"2024-02-28T13:11:40Z","month":"12","citation":{"chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>.","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. 2019;1(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","apa":"Huber, D., Hammer, H.-W., &#38; Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>.","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” <i>Physical Review Research</i>, vol. 1, no. 3. American Physical Society, 2019.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177."},"file_date_updated":"2020-07-14T12:47:52Z","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"publisher":"American Physical Society","has_accepted_license":"1","year":"2019","author":[{"full_name":"Huber, D.","first_name":"D.","last_name":"Huber"},{"full_name":"Hammer, H.-W.","first_name":"H.-W.","last_name":"Hammer"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2019-12-17T13:03:41Z","external_id":{"arxiv":["1908.02483"]},"publication":"Physical Review Research","ddc":["530"],"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_identifier":{"issn":["2643-1564"]},"doi":"10.1103/physrevresearch.1.033177","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:52Z","creator":"dernst","date_created":"2019-12-18T07:13:14Z","file_id":"7193","content_type":"application/pdf","file_size":1370022,"file_name":"2019_PhysRevResearch_Huber.pdf","checksum":"382eb67e62a77052a23887332d363f96","access_level":"open_access","relation":"main_file"}],"intvolume":"         1","quality_controlled":"1","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","oa":1,"issue":"3","article_processing_charge":"No","day":"16","type":"journal_article","department":[{"_id":"MiLe"}],"article_type":"original","volume":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"033177","arxiv":1,"oa_version":"Published Version"},{"status":"public","publication_identifier":{"issn":["2041-1723"]},"project":[{"grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"external_id":{"isi":["000503009300001"]},"publication":"Nature Communications","ddc":["570"],"oa":1,"quality_controlled":"1","title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","file":[{"relation":"main_file","access_level":"open_access","checksum":"a1b44b427ba341383197790d0e8789fa","file_name":"2019_NatureComm_Caldas.pdf","file_size":8488733,"content_type":"application/pdf","file_id":"7208","date_created":"2019-12-23T07:34:56Z","creator":"dernst","date_updated":"2020-07-14T12:47:53Z"}],"intvolume":"        10","doi":"10.1038/s41467-019-13702-4","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"},{"_id":"BjHo"}],"day":"17","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"8358","status":"public"}]},"article_processing_charge":"No","isi":1,"article_number":"5744","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":10,"article_type":"original","scopus_import":"1","date_updated":"2023-09-07T13:18:51Z","month":"12","_id":"7197","date_published":"2019-12-17T00:00:00Z","ec_funded":1,"publisher":"Springer Nature","citation":{"mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>, vol. 10, 5744, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>.","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., &#38; Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>.","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.","ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019."},"file_date_updated":"2020-07-14T12:47:53Z","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner."}],"author":[{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel J. G.","last_name":"Pearce","full_name":"Pearce, Daniel J. G."},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"has_accepted_license":"1","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-20T12:22:57Z","publication_status":"published"},{"quality_controlled":"1","title":"Limit law of a second class particle in TASEP with non-random initial condition","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"oa":1,"page":"1203-1225","doi":"10.1214/18-AIHP916","language":[{"iso":"eng"}],"intvolume":"        55","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"},{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"}],"status":"public","publication_identifier":{"issn":["0246-0203"]},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","external_id":{"arxiv":["1710.02323"],"isi":["000487763200001"]},"volume":55,"arxiv":1,"oa_version":"Preprint","article_type":"original","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"issue":"3","article_processing_charge":"No","isi":1,"day":"25","type":"journal_article","publisher":"Institute of Mathematical Statistics","abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ&lt;λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t."}],"citation":{"ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>.","apa":"Ferrari, P., Ghosal, P., &#38; Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2019;55(3):1203-1225. doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>."},"date_updated":"2023-10-17T08:53:45Z","scopus_import":"1","month":"09","date_published":"2019-09-25T00:00:00Z","ec_funded":1,"_id":"72","publication_status":"published","date_created":"2018-12-11T11:44:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","author":[{"last_name":"Ferrari","first_name":"Patrick","full_name":"Ferrari, Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","last_name":"Nejjar","first_name":"Peter","full_name":"Nejjar, Peter"}]},{"publication_status":"published","date_created":"2019-12-22T23:00:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Brighi","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro"},{"full_name":"Grilli, Marco","last_name":"Grilli","first_name":"Marco"},{"full_name":"Leridon, Brigitte","last_name":"Leridon","first_name":"Brigitte"},{"full_name":"Caprara, Sergio","last_name":"Caprara","first_name":"Sergio"}],"year":"2019","abstract":[{"text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).","lang":"eng"}],"citation":{"apa":"Brighi, P., Grilli, M., Leridon, B., &#38; Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>","mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>.","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. 2019;100(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” <i>Physical Review B</i>, vol. 100, no. 17. American Physical Society, 2019."},"publisher":"American Physical Society","_id":"7200","date_published":"2019-11-25T00:00:00Z","month":"11","date_updated":"2024-02-28T13:14:08Z","scopus_import":"1","article_type":"original","arxiv":1,"oa_version":"Preprint","article_number":"174518","volume":100,"day":"25","type":"journal_article","article_processing_charge":"No","isi":1,"issue":"17","department":[{"_id":"MaSe"}],"intvolume":"       100","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.100.174518","main_file_link":[{"url":"https://arxiv.org/abs/1907.13579","open_access":"1"}],"oa":1,"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","quality_controlled":"1","external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"publication":"Physical Review B","status":"public","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]}},{"abstract":[{"lang":"eng","text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks."}],"citation":{"chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., &#38; Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. Denver, CO, Unites States: ACM. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, a11, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, Denver, CO, Unites States, 2019.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11."},"publisher":"ACM","ec_funded":1,"date_published":"2019-11-17T00:00:00Z","_id":"7201","month":"11","scopus_import":"1","date_updated":"2023-09-06T14:37:55Z","publication_status":"published","date_created":"2019-12-22T23:00:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","author":[{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"},{"full_name":"Ashkboos, Saleh","first_name":"Saleh","last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A"},{"last_name":"Aghagolzadeh","first_name":"Mehdi","full_name":"Aghagolzadeh, Mehdi"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"}],"language":[{"iso":"eng"}],"doi":"10.1145/3295500.3356222","title":"SparCML: High-performance sparse communication for machine learning","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.08021","open_access":"1"}],"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["21674329"],"isbn":["9781450362290"],"eissn":["21674337"]},"status":"public","arxiv":1,"oa_version":"Preprint","article_number":"a11","isi":1,"article_processing_charge":"No","conference":{"start_date":"2019-11-17","location":"Denver, CO, Unites States","end_date":"2019-11-19","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"day":"17","type":"conference","department":[{"_id":"DaAl"}]},{"has_accepted_license":"1","year":"2019","author":[{"last_name":"Llorca","first_name":"Alfredo","full_name":"Llorca, Alfredo"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","last_name":"Beattie","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong Kuan","first_name":"Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou-Pouliou","full_name":"Serafeimidou-Pouliou, Eleni"},{"full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero","first_name":"Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Arnold","first_name":"Sebastian J.","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","last_name":"Meyer","full_name":"Meyer, Martin"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"pmid":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-12-22T23:00:42Z","date_published":"2019-11-18T00:00:00Z","ec_funded":1,"_id":"7202","scopus_import":"1","date_updated":"2023-09-06T14:38:39Z","month":"11","abstract":[{"text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas.","lang":"eng"}],"citation":{"short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>, vol. 8, e51381, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>","ieee":"A. Llorca <i>et al.</i>, “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381."},"file_date_updated":"2020-07-14T12:47:53Z","publisher":"eLife Sciences Publications","isi":1,"article_processing_charge":"No","type":"journal_article","day":"18","department":[{"_id":"SiHi"}],"article_type":"original","volume":8,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"e51381","oa_version":"Published Version","publication":"eLife","external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"ddc":["570"],"project":[{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF"}],"status":"public","publication_identifier":{"eissn":["2050084X"]},"doi":"10.7554/eLife.51381","language":[{"iso":"eng"}],"file":[{"file_name":"2019_eLife_Llorca.pdf","checksum":"b460ecc33e1a68265e7adea775021f3a","access_level":"open_access","relation":"main_file","file_id":"7503","date_created":"2020-02-18T15:19:26Z","file_size":2960543,"content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:53Z"}],"intvolume":"         8","quality_controlled":"1","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","oa":1}]