[{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":595707,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_DistribComp_Alistarh.pdf","checksum":"69b46e537acdcac745237ddb853fcbb5","date_created":"2019-01-22T07:25:51Z","date_updated":"2020-07-14T12:46:38Z","file_id":"5867","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"536","intvolume":" 31","title":"Communication-efficient randomized consensus","status":"public","ddc":["000"],"issue":"6","abstract":[{"lang":"eng","text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model."}],"type":"journal_article","date_published":"2018-11-01T00:00:00Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1"},"publication":"Distributed Computing","page":"489-501","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"last_name":"King","first_name":"Valerie","full_name":"King, Valerie"},{"first_name":"Jared","last_name":"Saia","full_name":"Saia, Jared"}],"volume":31,"date_updated":"2023-02-23T12:23:25Z","date_created":"2018-12-11T11:47:01Z","year":"2018","department":[{"_id":"DaAl"}],"publisher":"Springer","publication_status":"published","publist_id":"7281","file_date_updated":"2020-07-14T12:46:38Z","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1007/s00446-017-0315-1","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","publication_identifier":{"issn":["01782770"]},"month":"11"},{"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"554","status":"public","title":"The Bogoliubov free energy functional II: The dilute Limit","intvolume":" 360","abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2018-05-01T00:00:00Z","publication":"Communications in Mathematical Physics","citation":{"ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x."},"page":"347-403","day":"01","scopus_import":1,"author":[{"last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"},{"last_name":"Reuvers","first_name":"Robin","full_name":"Reuvers, Robin"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"date_created":"2018-12-11T11:47:09Z","date_updated":"2021-01-12T08:02:35Z","volume":360,"year":"2018","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","publist_id":"7260","doi":"10.1007/s00220-017-3064-x","language":[{"iso":"eng"}],"external_id":{"arxiv":["1511.05953"]},"main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"month":"05","publication_identifier":{"issn":["00103616"]}},{"date_published":"2018-01-01T00:00:00Z","page":"201 - 215","publication":"Neurotrophic Factors","citation":{"ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15.","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"oa_version":"Submitted Version","file":[{"checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-11-19T07:47:43Z","relation":"main_file","file_id":"7046","file_size":787407,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf"}],"title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","status":"public","ddc":["570"],"intvolume":" 1727","_id":"562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-7571-6_15","quality_controlled":"1","external_id":{"pmid":["29222783"]},"oa":1,"month":"01","date_created":"2018-12-11T11:47:11Z","date_updated":"2021-01-12T08:03:05Z","volume":1727,"author":[{"first_name":"Dimitar","last_name":"Dimitrov","full_name":"Dimitrov, Dimitar"},{"first_name":"Laurent","last_name":"Guillaud","full_name":"Guillaud, Laurent"},{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"publication_status":"published","department":[{"_id":"RySh"}],"editor":[{"full_name":"Skaper, Stephen D.","last_name":"Skaper","first_name":"Stephen D."}],"publisher":"Springer","year":"2018","pmid":1,"file_date_updated":"2020-07-14T12:47:09Z","publist_id":"7252"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"59","year":"2018","status":"public","title":"Graph games and reactive synthesis","publication_status":"published","publisher":"Springer","editor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Clarke, Edmund M.","first_name":"Edmund M.","last_name":"Clarke"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"}],"department":[{"_id":"KrCh"}],"author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"edition":"1","date_created":"2018-12-11T11:44:24Z","date_updated":"2021-01-12T08:05:10Z","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches."}],"publist_id":"7995","publication":"Handbook of Model Checking","citation":{"short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962."},"quality_controlled":"1","page":"921 - 962","doi":"10.1007/978-3-319-10575-8_27","date_published":"2018-05-19T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"05","day":"19","publication_identifier":{"isbn":["978-3-319-10574-1"]}},{"day":"19","month":"05","series_title":"Handbook of Model Checking","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-10575-8_1","date_published":"2018-05-19T00:00:00Z","page":"1 - 26","quality_controlled":"1","citation":{"mla":"Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26.","chicago":"Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1.","ama":"Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","ieee":"E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26.","apa":"Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1"},"publication":"Handbook of Model Checking","publist_id":"7994","abstract":[{"lang":"eng","text":"Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking."}],"type":"book_chapter","oa_version":"None","date_created":"2018-12-11T11:44:25Z","date_updated":"2021-01-12T08:05:35Z","author":[{"first_name":"Edmund","last_name":"Clarke","full_name":"Clarke, Edmund"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"editor":[{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"title":"Introduction to model checking","status":"public","publication_status":"published","_id":"60","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018"},{"type":"book_chapter","extern":"1","publist_id":"7993","abstract":[{"text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ","lang":"eng"}],"department":[{"_id":"TaHa"}],"publisher":"Springer","status":"public","publication_status":"published","title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"61","year":"2018","oa_version":"Preprint","date_created":"2018-12-11T11:44:25Z","date_updated":"2021-01-12T08:06:06Z","author":[{"first_name":"Andriy","last_name":"Bondarenko","full_name":"Bondarenko, Andriy"},{"last_name":"Mellit","first_name":"Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","full_name":"Mellit, Anton"},{"full_name":"Prymak, Andriy","last_name":"Prymak","first_name":"Andriy"},{"first_name":"Danylo","last_name":"Radchenko","full_name":"Radchenko, Danylo"},{"full_name":"Viazovska, Maryna","first_name":"Maryna","last_name":"Viazovska"}],"article_processing_charge":"No","month":"05","day":"23","page":"131 - 134","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1509.06286","open_access":"1"}],"external_id":{"arxiv":["1509.06286"]},"oa":1,"citation":{"ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134."},"publication":"Contemporary Computational Mathematics","language":[{"iso":"eng"}],"date_published":"2018-05-23T00:00:00Z","doi":"10.1007/978-3-319-72456-0_7"},{"article_number":"e1007435","file_date_updated":"2020-07-14T12:47:19Z","extern":"1","pmid":1,"year":"2018","publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"McLachlan, Ian G.","first_name":"Ian G.","last_name":"McLachlan"},{"full_name":"Beets, Isabel","last_name":"Beets","first_name":"Isabel"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario"},{"full_name":"Heiman, Maxwell G.","first_name":"Maxwell G.","last_name":"Heiman"}],"volume":14,"date_updated":"2021-01-12T08:06:11Z","date_created":"2019-03-19T13:09:28Z","publication_identifier":{"issn":["1553-7404"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29879119"]},"quality_controlled":"1","doi":"10.1371/journal.pgen.1007435","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending."}],"_id":"6111","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 14","title":"A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"6112","relation":"main_file","checksum":"622036b945365dbc575bea2768aa9bc8","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-19T13:18:01Z","access_level":"open_access","file_name":"2018_PLOS_McLachlan.pdf","creator":"kschuh","content_type":"application/pdf","file_size":13011506}],"has_accepted_license":"1","day":"07","citation":{"chicago":"McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007435.","mla":"McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435.","short":"I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).","ista":"McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435.","apa":"McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435","ieee":"I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of Science, 2018.","ama":"McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435"},"publication":"PLOS Genetics","date_published":"2018-06-07T00:00:00Z"},{"has_accepted_license":"1","day":"17","date_published":"2018-07-17T00:00:00Z","citation":{"chicago":"Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.","short":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899.","mla":"Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115.","apa":"Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115","ieee":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.","ista":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.","ama":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115"},"publication":"Proceedings of the National Academy of Sciences","page":"E6890-E6899","issue":"29","abstract":[{"lang":"eng","text":"Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6110","checksum":"5e81665377441cdd8d99ab952c534319","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-19T13:01:58Z","access_level":"open_access","file_name":"2018_PNAS_Laurent.pdf","content_type":"application/pdf","file_size":1567765,"creator":"kschuh"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6109","intvolume":" 115","status":"public","title":"Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron","ddc":["570"],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"07","doi":"10.1073/pnas.1714610115","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["29959203"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:19Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","author":[{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"},{"first_name":"QueeLim","last_name":"Ch’ng","full_name":"Ch’ng, QueeLim"},{"full_name":"Jospin, Maëlle","first_name":"Maëlle","last_name":"Jospin"},{"last_name":"Chen","first_name":"Changchun","full_name":"Chen, Changchun"},{"full_name":"Lorenzo, Ramiro","first_name":"Ramiro","last_name":"Lorenzo"},{"full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"}],"volume":115,"date_created":"2019-03-19T12:41:33Z","date_updated":"2021-01-12T08:06:09Z","pmid":1,"year":"2018","publisher":"National Academy of Sciences","publication_status":"published"},{"year":"2018","_id":"6164","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 11255","publisher":"Springer","publication_status":"published","title":"Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D","status":"public","author":[{"full_name":"Koshti, Girish","last_name":"Koshti","first_name":"Girish"},{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"first_name":"Gaëlle","last_name":"Largeteau-Skapin","full_name":"Largeteau-Skapin, Gaëlle"},{"last_name":"Zrour","first_name":"Rita","full_name":"Zrour, Rita"},{"last_name":"Andres","first_name":"Eric","full_name":"Andres, Eric"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"volume":11255,"oa_version":"None","date_updated":"2022-01-27T15:26:39Z","date_created":"2019-03-21T12:16:58Z","type":"conference","place":"Cham","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity."}],"extern":"1","citation":{"ieee":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96.","apa":"Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7","ista":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.","ama":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7","chicago":"Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.","short":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96.","mla":"Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7."},"publication":"19th International Workshop","page":"82-96","quality_controlled":"1","doi":"10.1007/978-3-030-05288-1_7","date_published":"2018-11-22T00:00:00Z","conference":{"end_date":"2018-11-24","start_date":"2018-11-22","location":"Porto, Portugal","name":"IWCIA: International Workshop on Combinatorial Image Analysis"},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-3-030-05288-1"],"issn":["0302-9743"],"isbn":["978-3-030-05287-4"],"eissn":["1611-3349"]},"article_processing_charge":"No","day":"22","month":"11"},{"day":"20","has_accepted_license":"1","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"date_published":"2018-09-20T00:00:00Z","publication":"Bio-Protocol","citation":{"short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018."},"abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"issue":"18","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_BioProtocol_Fan.pdf","access_level":"open_access","creator":"dernst","file_size":2928337,"content_type":"application/pdf","file_id":"6360","relation":"main_file","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T08:04:33Z","checksum":"d4588377e789da7f360b553ae02c5119"}],"status":"public","ddc":["570"],"title":"Platelet migration and bacterial trapping assay under flow","intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6354","month":"09","publication_identifier":{"issn":["2331-8325"]},"language":[{"iso":"eng"}],"doi":"10.21769/bioprotoc.3018","quality_controlled":"1","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:47:28Z","ec_funded":1,"article_number":"e3018","date_updated":"2021-01-12T08:07:12Z","date_created":"2019-04-29T09:40:33Z","volume":8,"author":[{"last_name":"Fan","first_name":"Shuxia","full_name":"Fan, Shuxia"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Bio-Protocol","department":[{"_id":"MiSi"}],"year":"2018","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)"}]