[{"publisher":"Wiley","intvolume":" 60","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-12-09T00:00:00Z","external_id":{"isi":["000453555100002"]},"date_created":"2018-12-30T22:59:14Z","scopus_import":"1","publication":"Development Growth and Differentiation","date_updated":"2023-09-19T09:32:49Z","page":"512-521","oa":1,"year":"2018","file":[{"file_id":"5933","date_created":"2019-02-06T10:40:46Z","file_name":"2018_DevGrowh_Hannezo.pdf","file_size":1313606,"creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a6d30b0785db902c734a84fecb2eadd9","date_updated":"2020-07-14T12:47:11Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":60,"article_processing_charge":"No","citation":{"mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521."},"day":"09","month":"12","ddc":["570"],"file_date_updated":"2020-07-14T12:47:11Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","publication_identifier":{"issn":["00121592"]},"status":"public","title":"Statistical theory of branching morphogenesis","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"}],"_id":"5787","abstract":[{"lang":"eng","text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications."}],"issue":"9","doi":"10.1111/dgd.12570"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"date_created":"2018-12-30T22:59:14Z","scopus_import":"1","external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"date_published":"2018-11-21T00:00:00Z","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04372"}],"intvolume":" 11316","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"oa":1,"year":"2018","alternative_title":["LNCS"],"date_updated":"2023-09-12T07:44:01Z","page":"21-36","month":"11","citation":{"ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.","mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2."},"day":"21","oa_version":"Preprint","conference":{"name":"14th International Conference on Web and Internet Economics, WINE","location":"Oxford, UK","start_date":"2018-12-15","end_date":"2018-12-17"},"arxiv":1,"volume":11316,"article_processing_charge":"No","_id":"5788","title":"Infinite-duration poorman-bidding games","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"}],"doi":"10.1007/978-3-030-04612-5_2","abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games."}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"UlWa"}],"date_created":"2018-12-30T22:59:15Z","scopus_import":"1","date_published":"2018-12-18T00:00:00Z","external_id":{"arxiv":["1808.07608"],"isi":["000672802500016"]},"publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1808.07608","open_access":"1"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"oa":1,"alternative_title":["LNCS"],"year":"2018","date_updated":"2023-09-11T12:49:55Z","page":"229-241","month":"12","citation":{"chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241."},"day":"18","oa_version":"Preprint","conference":{"end_date":"2018-09-28","location":"Barcelona, Spain","start_date":"2018-09-26","name":"Graph Drawing and Network Visualization"},"arxiv":1,"article_processing_charge":"No","volume":"11282 ","_id":"5791","title":"Crossing minimization in perturbed drawings","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Tóth, Csaba D.","last_name":"Tóth","first_name":"Csaba D."}],"doi":"10.1007/978-3-030-04414-5_16","abstract":[{"lang":"eng","text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths."}],"publication_identifier":{"isbn":["9783030044138"]},"status":"public","publication_status":"published"},{"oa_version":"Preprint","day":"17","citation":{"ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018.","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302."},"month":"12","volume":121,"article_processing_charge":"No","arxiv":1,"issue":"25","abstract":[{"lang":"eng","text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems."}],"doi":"10.1103/PhysRevLett.121.255302","author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874"},{"orcid":"0000-0002-4310-178X","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"title":"Quantum groups as hidden symmetries of quantum impurities","_id":"5794","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["00319007"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000454178600009"],"arxiv":["1809.00222"]},"date_published":"2018-12-17T00:00:00Z","scopus_import":"1","date_created":"2019-01-06T22:59:12Z","department":[{"_id":"MiLe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"intvolume":" 121","publisher":"American Physical Society","year":"2018","oa":1,"article_type":"original","article_number":"255302","publication":"Physical Review Letters","date_updated":"2023-09-15T12:09:06Z"},{"article_processing_charge":"No","volume":32,"arxiv":1,"oa_version":"Preprint","citation":{"mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.","chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257.","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X"},"day":"06","month":"09","status":"public","publication_status":"published","ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"abstract":[{"text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.","lang":"eng"}],"issue":"3","doi":"10.1137/16M110407X","title":"Counting blanks in polygonal arrangements","author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Segal Halevi","full_name":"Segal Halevi, Erel","first_name":"Erel"}],"_id":"58","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","intvolume":" 32","main_file_link":[{"url":"https://arxiv.org/abs/1604.00960","open_access":"1"}],"external_id":{"arxiv":["1604.00960"],"isi":["000450810500036"]},"date_published":"2018-09-06T00:00:00Z","date_created":"2018-12-11T11:44:24Z","scopus_import":"1","department":[{"_id":"HeEd"}],"publist_id":"7996","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2242 - 2257","publication":"SIAM Journal on Discrete Mathematics","date_updated":"2023-09-11T12:48:39Z","year":"2018","oa":1},{"publication_status":"published","status":"public","publication_identifier":{"issn":["00346748"]},"issue":"11","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"doi":"10.1063/1.5038258","author":[{"last_name":"Hollmann","full_name":"Hollmann, Arne","first_name":"Arne"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801"},{"first_name":"Maciej","last_name":"Kucharski","full_name":"Kucharski, Maciej"},{"first_name":"Dietmar","full_name":"Kissinger, Dietmar","last_name":"Kissinger"},{"last_name":"Fischer","full_name":"Fischer, Gunter","first_name":"Gunter"},{"full_name":"Schreiber, Lars R.","last_name":"Schreiber","first_name":"Lars R."}],"title":"30 GHz-voltage controlled oscillator operating at 4 K","_id":"5816","article_processing_charge":"No","volume":89,"arxiv":1,"oa_version":"Preprint","day":"01","citation":{"short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701.","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258."},"month":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10058"}]},"article_number":"114701","publication":"Review of Scientific Instruments","date_updated":"2024-03-25T23:30:14Z","year":"2018","oa":1,"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"intvolume":" 89","publisher":"AIP Publishing","date_published":"2018-11-01T00:00:00Z","external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"scopus_import":"1","date_created":"2019-01-10T14:22:23Z","department":[{"_id":"GeKa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","pmid":1,"citation":{"ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475."},"department":[{"_id":"JiFr"}],"day":"31","date_created":"2019-01-13T22:59:11Z","oa_version":"Published Version","scopus_import":"1","date_published":"2018-10-31T00:00:00Z","external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"publisher":"Wiley","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"article_processing_charge":"No","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"_id":"5830","title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","oa":1,"author":[{"last_name":"Zhang","full_name":"Zhang, Luosha","first_name":"Luosha"},{"last_name":"Shi","full_name":"Shi, Xiong","first_name":"Xiong"},{"first_name":"Yutao","full_name":"Zhang, Yutao","last_name":"Zhang"},{"last_name":"Wang","full_name":"Wang, Jiajing","first_name":"Jiajing"},{"last_name":"Yang","full_name":"Yang, Jingwei","first_name":"Jingwei"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"full_name":"Jiang, Wenqian","last_name":"Jiang","first_name":"Wenqian"},{"first_name":"Xiangyu","last_name":"Han","full_name":"Han, Xiangyu"},{"last_name":"Kang","full_name":"Kang, Jingke","first_name":"Jingke"},{"last_name":"Wang","full_name":"Wang, Xuening","first_name":"Xuening"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"last_name":"Lv","full_name":"Lv, Shuo","first_name":"Shuo"},{"last_name":"Cao","full_name":"Cao, Bing","first_name":"Bing"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"first_name":"Jinbin","full_name":"Wu, Jinbin","last_name":"Wu"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Hu, Zhubing","last_name":"Hu","first_name":"Zhubing"},{"last_name":"Cui","full_name":"Cui, Langjun","first_name":"Langjun"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"last_name":"He","full_name":"He, Junmin","first_name":"Junmin"},{"last_name":"Wang","full_name":"Wang, Guodong","first_name":"Guodong"}],"doi":"10.1111/pce.13475","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"year":"2018","date_updated":"2023-09-11T12:43:31Z","publication":"Plant Cell and Environment","publication_identifier":{"issn":["01407791"]},"status":"public","publication_status":"epub_ahead"},{"publication_status":"published","status":"public","publication_identifier":{"issn":["17425689"]},"doi":"10.1098/rsif.2018.0600","abstract":[{"text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.","lang":"eng"}],"issue":"149","_id":"5858","title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","author":[{"first_name":"Sabrina","last_name":"Hross","full_name":"Hross, Sabrina"},{"first_name":"Fabian J.","last_name":"Theis","full_name":"Theis, Fabian J."},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Hasenauer, Jan","last_name":"Hasenauer"}],"article_processing_charge":"No","volume":15,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2018_Interface_Hross.pdf","creator":"dernst","relation":"main_file","file_size":1464288,"access_level":"open_access","checksum":"56eb4308a15b7190bff938fab1f780e8","content_type":"application/pdf","date_updated":"2020-07-14T12:47:13Z","file_id":"5925","date_created":"2019-02-05T14:46:44Z"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:13Z","ddc":["570"],"month":"12","citation":{"chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600.","mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600.","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600"},"day":"05","article_number":"20180600","date_updated":"2023-09-13T08:55:05Z","publication":"Journal of the Royal Society Interface","year":"2018","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Royal Society Publishing","intvolume":" 15","date_created":"2019-01-20T22:59:18Z","scopus_import":"1","date_published":"2018-12-05T00:00:00Z","external_id":{"isi":["000456783800011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"}]},{"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643"},{"full_name":"Fibla, Martí Sànchez","last_name":"Fibla","first_name":"Martí Sànchez"},{"first_name":"Sergi","full_name":"Valverde, Sergi","last_name":"Valverde"},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"title":"Chromatic transitions in the emergence of syntax networks","_id":"5859","issue":"12","abstract":[{"lang":"eng","text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations."}],"doi":"10.1098/rsos.181286","publication_identifier":{"issn":["2054-5703"]},"status":"public","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","publication_status":"published","day":"12","citation":{"chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018)."},"pmid":1,"month":"12","file_date_updated":"2020-07-14T12:47:13Z","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"9664d4417f6b792242e31eea77ce9501","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:13Z","file_size":646732,"creator":"dernst","relation":"main_file","file_name":"2018_RoyalSocOS_Corominas.pdf","date_created":"2019-02-05T14:38:09Z","file_id":"5924"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":5,"article_processing_charge":"No","oa":1,"year":"2018","publication":"Royal Society Open Science","date_updated":"2023-10-18T06:41:12Z","article_type":"original","article_number":"181286","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"date_published":"2018-12-12T00:00:00Z","scopus_import":"1","date_created":"2019-01-20T22:59:18Z","intvolume":" 5","publisher":"The Royal Society","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"},{"date_updated":"2023-09-19T10:40:38Z","publication":"Journal of the Royal Society Interface","article_number":"20180395","oa":1,"year":"2018","publisher":"Royal Society Publishing","main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"intvolume":" 15","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"EdHa"}],"date_created":"2019-01-20T22:59:19Z","scopus_import":"1","date_published":"2018-12-12T00:00:00Z","external_id":{"isi":["000456783800002"],"arxiv":["1612.01605"]},"publication_identifier":{"issn":["17425689"]},"publication_status":"published","status":"public","_id":"5860","title":"Zipf's Law, unbounded complexity and open-ended evolution","author":[{"orcid":"0000-0001-9806-5643","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Luís F.","last_name":"Seoane","full_name":"Seoane, Luís F."},{"last_name":"Solé","full_name":"Solé, Ricard","first_name":"Ricard"}],"doi":"10.1098/rsif.2018.0395","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"issue":"149","arxiv":1,"volume":15,"article_processing_charge":"No","month":"12","citation":{"chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395"},"day":"12","oa_version":"Preprint"},{"oa":1,"year":"2018","date_updated":"2023-09-19T10:01:39Z","publication":"eLife","article_type":"original","article_number":"e37888","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"}],"scopus_import":"1","date_created":"2019-01-20T22:59:19Z","date_published":"2018-06-06T00:00:00Z","external_id":{"isi":["000434375000001"]},"intvolume":" 7","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"_id":"5861","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","full_name":"Alanko, Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"title":"The cell sets the tone","doi":"10.7554/eLife.37888","abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"publication_identifier":{"issn":["2050084X"]},"publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:47:13Z","month":"06","ddc":["570"],"day":"06","citation":{"apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888."},"oa_version":"Published Version","file":[{"file_name":"2018_eLife_Alanko.pdf","creator":"dernst","file_size":358141,"relation":"main_file","access_level":"open_access","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","content_type":"application/pdf","date_updated":"2020-07-14T12:47:13Z","file_id":"5973","date_created":"2019-02-13T10:52:11Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":7,"article_processing_charge":"No","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice."}],"issue":"8","doi":"10.1038/s12276-018-0129-7","title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","author":[{"last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia"}],"_id":"5888","status":"public","publication_status":"published","publication_identifier":{"issn":["2092-6413"]},"oa_version":"Published Version","citation":{"ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7","short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018).","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7."},"day":"07","pmid":1,"file_date_updated":"2020-07-14T12:47:13Z","ddc":["570"],"month":"08","has_accepted_license":"1","volume":50,"article_processing_charge":"No","file":[{"date_created":"2019-01-28T15:18:02Z","file_id":"5893","date_updated":"2020-07-14T12:47:13Z","checksum":"4498301c8c53097c9a1a8ef990936eb5","content_type":"application/pdf","access_level":"open_access","file_size":1237482,"relation":"main_file","creator":"dernst","file_name":"2018_EMM_Tarlungeanu.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","oa":1,"article_number":"100","publication":"Experimental & Molecular Medicine","date_updated":"2023-09-11T14:04:41Z","external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"date_published":"2018-08-07T00:00:00Z","date_created":"2019-01-27T22:59:11Z","scopus_import":"1","department":[{"_id":"GaNo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Springer Nature","intvolume":" 50"},{"month":"05","publist_id":"7995","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.","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.","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","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.","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."},"day":"19","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:44:24Z","oa_version":"None","scopus_import":1,"date_published":"2018-05-19T00:00:00Z","publisher":"Springer","language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_chapter","_id":"59","editor":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"title":"Graph games and reactive synthesis","author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"}],"doi":"10.1007/978-3-319-10575-8_27","abstract":[{"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.","lang":"eng"}],"year":"2018","date_updated":"2021-01-12T08:05:10Z","edition":"1","publication":"Handbook of Model Checking","publication_identifier":{"isbn":["978-3-319-10574-1"]},"page":"921 - 962","publication_status":"published","status":"public"},{"ec_funded":1,"publication_status":"published","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27","call_identifier":"FWF","name":"Interneuron plasticity during spatial learning"}],"doi":"10.1523/ENEURO.0087-18.2018","abstract":[{"lang":"eng","text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task."}],"issue":"4","_id":"5914","title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","author":[{"orcid":"0000-0002-8602-4374","first_name":"Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","last_name":"Rangel Guerrero","full_name":"Rangel Guerrero, Dámaris K"},{"full_name":"Donnett, James G.","last_name":"Donnett","first_name":"James G."},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","full_name":"Kovács, Krisztián","last_name":"Kovács","orcid":"0000-0001-6251-1007"}],"article_processing_charge":"No","volume":5,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2019-02-05T12:48:36Z","file_id":"5921","file_size":3746884,"relation":"main_file","creator":"dernst","file_name":"2018_ENeuro_Guerrero.pdf","date_updated":"2020-07-14T12:47:13Z","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","content_type":"application/pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["570"],"month":"07","file_date_updated":"2020-07-14T12:47:13Z","citation":{"chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018"},"day":"27","article_number":"e0087","related_material":{"record":[{"id":"6849","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-25T23:30:06Z","publication":"eNeuro","year":"2018","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Society of Neuroscience","intvolume":" 5","date_created":"2019-02-03T22:59:16Z","scopus_import":"1","external_id":{"isi":["000443994700007"]},"date_published":"2018-07-27T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JoCs"}]},{"publication_identifier":{"isbn":["9781538655603"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"status":"public","publication_status":"published","title":"Keynote: The first-order logic of signals","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"orcid":"0000-0001-5199-3143","last_name":"Ferrere","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Nickovicl","full_name":"Nickovicl, Deian","first_name":"Deian"}],"_id":"5959","abstract":[{"text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain.","lang":"eng"}],"doi":"10.1109/emsoft.2018.8537203","file":[{"creator":"dernst","file_size":338006,"relation":"main_file","file_name":"2018_EMSOFT_Bakhirkin.pdf","date_updated":"2020-07-14T12:47:13Z","content_type":"application/pdf","checksum":"234a33ad9055b3458fcdda6af251b33a","access_level":"open_access","date_created":"2020-05-14T16:01:29Z","file_id":"7839"}],"has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10."},"day":"30","ddc":["000"],"file_date_updated":"2020-07-14T12:47:13Z","month":"09","oa_version":"Published Version","conference":{"end_date":"2018-10-05","location":"Turin, Italy","start_date":"2018-09-30","name":"EMSOFT: International Conference on Embedded Software"},"publication":"2018 International Conference on Embedded Software","date_updated":"2023-09-19T10:41:29Z","page":"1-10","oa":1,"year":"2018","publisher":"IEEE","isi":1,"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000492828500005"]},"date_published":"2018-09-30T00:00:00Z","date_created":"2019-02-13T09:19:28Z","scopus_import":"1"},{"publication_identifier":{"eissn":["1741-3176"],"issn":["0278-3649"]},"publication_status":"published","status":"public","title":"Proving the existence of loops in robot trajectories","author":[{"first_name":"Simon","last_name":"Rohou","full_name":"Rohou, Simon"},{"full_name":"Franek, Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-8878-8397"},{"first_name":"Clément","full_name":"Aubry, Clément","last_name":"Aubry"},{"first_name":"Luc","last_name":"Jaulin","full_name":"Jaulin, Luc"}],"_id":"5960","abstract":[{"lang":"eng","text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion."}],"issue":"12","doi":"10.1177/0278364918808367","arxiv":1,"article_processing_charge":"No","volume":37,"citation":{"ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516.","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367."},"day":"24","month":"10","oa_version":"Preprint","publication":"The International Journal of Robotics Research","date_updated":"2023-09-19T10:41:59Z","page":"1500-1516","oa":1,"year":"2018","publisher":"SAGE Publications","intvolume":" 37","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.01341"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"UlWa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1712.01341"],"isi":["000456881100004"]},"date_published":"2018-10-24T00:00:00Z","date_created":"2019-02-13T09:36:20Z","scopus_import":"1"},{"external_id":{"isi":["000458186900063"]},"date_published":"2018-07-27T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom"},"scopus_import":"1","oa_version":"None","date_created":"2019-02-13T09:48:55Z","day":"27","department":[{"_id":"DaAl"}],"citation":{"chicago":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798.","mla":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798.","ieee":"D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 487–488.","apa":"Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798","ama":"Alistarh D-A. A brief tutorial on distributed and concurrent machine learning. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798","short":"D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–488.","ista":"Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 487–488."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","isi":1,"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publisher":"ACM Press","year":"2018","abstract":[{"lang":"eng","text":"The area of machine learning has made considerable progress over the past decade, enabled by the widespread availability of large datasets, as well as by improved algorithms and models. Given the large computational demands of machine learning workloads, parallelism, implemented either through single-node concurrency or through multi-node distribution, has been a third key ingredient to advances in machine learning.\r\nThe goal of this tutorial is to provide the audience with an overview of standard distribution techniques in machine learning, with an eye towards the intriguing trade-offs between synchronization and communication costs of distributed machine learning algorithms, on the one hand, and their convergence, on the other.The tutorial will focus on parallelization strategies for the fundamental stochastic gradient descent (SGD) algorithm, which is a key tool when training machine learning models, from classical instances such as linear regression, to state-of-the-art neural network architectures.\r\nThe tutorial will describe the guarantees provided by this algorithm in the sequential case, and then move on to cover both shared-memory and message-passing parallelization strategies, together with the guarantees they provide, and corresponding trade-offs. The presentation will conclude with a broad overview of ongoing research in distributed and concurrent machine learning. The tutorial will assume no prior knowledge beyond familiarity with basic concepts in algebra and analysis.\r\n"}],"doi":"10.1145/3212734.3212798","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"title":"A brief tutorial on distributed and concurrent machine learning","_id":"5961","publication_status":"published","status":"public","page":"487-488","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","publication_identifier":{"isbn":["9781450357951"]},"date_updated":"2023-09-19T10:42:28Z"},{"oa":1,"year":"2018","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","date_updated":"2023-09-19T10:42:53Z","page":"169-178","department":[{"_id":"DaAl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-23T00:00:00Z","external_id":{"isi":["000458186900022"],"arxiv":["1803.08841"]},"scopus_import":"1","date_created":"2019-02-13T09:58:58Z","main_file_link":[{"url":"https://arxiv.org/abs/1803.08841","open_access":"1"}],"publisher":"ACM Press","isi":1,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Christopher","last_name":"De Sa","full_name":"De Sa, Christopher"},{"first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"}],"title":"The convergence of stochastic gradient descent in asynchronous shared memory","_id":"5962","abstract":[{"text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently.","lang":"eng"}],"doi":"10.1145/3212734.3212763","publication_identifier":{"isbn":["9781450357951"]},"publication_status":"published","status":"public","day":"23","citation":{"mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178."},"month":"07","conference":{"name":"PODC: Principles of Distributed Computing","location":"Egham, United Kingdom","start_date":"2018-07-23","end_date":"2018-07-27"},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04155"}],"publisher":"ACM Press","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"scopus_import":"1","date_created":"2019-02-13T10:03:25Z","external_id":{"arxiv":["1808.04155"],"isi":["000458186900048"]},"date_published":"2018-07-23T00:00:00Z","date_updated":"2023-09-19T10:43:21Z","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","page":"377-386","oa":1,"year":"2018","arxiv":1,"article_processing_charge":"No","month":"07","day":"23","citation":{"apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386.","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756.","mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756."},"conference":{"end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom","name":"PODC: Principles of Distributed Computing"},"oa_version":"Preprint","publication_identifier":{"isbn":["9781450357951"]},"publication_status":"published","status":"public","_id":"5963","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Justin","last_name":"Kopinsky","full_name":"Kopinsky, Justin"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi"}],"title":"Relaxed schedulers can efficiently parallelize iterative algorithms","doi":"10.1145/3212734.3212756","abstract":[{"text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion.","lang":"eng"}]},{"date_updated":"2023-09-19T10:43:45Z","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","page":"411-413","oa":1,"year":"2018","publisher":"ACM Press","main_file_link":[{"open_access":"1","url":"https://hal-univ-lyon3.archives-ouvertes.fr/INRIA/hal-01887733v1"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"date_created":"2019-02-13T10:08:19Z","scopus_import":"1","date_published":"2018-07-23T00:00:00Z","external_id":{"isi":["000458186900052"]},"publication_identifier":{"isbn":["9781450357951"]},"status":"public","publication_status":"published","_id":"5964","title":"Brief Announcement: Performance prediction for coarse-grained locking","author":[{"last_name":"Aksenov","full_name":"Aksenov, Vitaly","first_name":"Vitaly"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"last_name":"Kuznetsov","full_name":"Kuznetsov, Petr","first_name":"Petr"}],"doi":"10.1145/3212734.3212785","abstract":[{"text":"A standard design pattern found in many concurrent data structures, such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarse-grained lock-based algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc.","lang":"eng"}],"article_processing_charge":"No","month":"07","citation":{"apa":"Aksenov, V., Alistarh, D.-A., & Kuznetsov, P. (2018). Brief Announcement: Performance prediction for coarse-grained locking. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 411–413). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212785","ieee":"V. Aksenov, D.-A. Alistarh, and P. Kuznetsov, “Brief Announcement: Performance prediction for coarse-grained locking,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 411–413.","ama":"Aksenov V, Alistarh D-A, Kuznetsov P. Brief Announcement: Performance prediction for coarse-grained locking. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:411-413. doi:10.1145/3212734.3212785","ista":"Aksenov V, Alistarh D-A, Kuznetsov P. 2018. Brief Announcement: Performance prediction for coarse-grained locking. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 411–413.","short":"V. Aksenov, D.-A. Alistarh, P. Kuznetsov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–413.","mla":"Aksenov, Vitaly, et al. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–13, doi:10.1145/3212734.3212785.","chicago":"Aksenov, Vitaly, Dan-Adrian Alistarh, and Petr Kuznetsov. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 411–13. ACM Press, 2018. https://doi.org/10.1145/3212734.3212785."},"day":"23","oa_version":"Submitted Version","conference":{"end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom","name":"PODC: Principles of Distributed Computing"}}]