[{"month":"01","intvolume":" 99","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"volume":99,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"creator":"dernst","file_size":718857,"date_updated":"2020-07-14T12:45:19Z","file_name":"2018_LIPIcs_Fulek.pdf","date_created":"2018-12-17T12:33:52Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_id":"5701"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-066-8"]},"publication_status":"published","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"_id":"185","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2021-01-12T06:53:36Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"doi":"10.4230/LIPIcs.SoCG.2018.39","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:04Z","day":"01","has_accepted_license":"1","year":"2018","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"article_number":"39","title":"Hanani-Tutte for approximating maps of graphs","publist_id":"7735","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39."}},{"day":"11","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.35","page":"35:1 - 35:13","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35."},"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","publist_id":"7733","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Ziga","full_name":"Virk, Ziga","last_name":"Virk"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","last_name":"Wagner"}],"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5724","checksum":"7509403803b3ac1aee94bbc2ad293d21","date_updated":"2020-07-14T12:45:20Z","file_size":489080,"creator":"dernst","date_created":"2018-12-17T16:31:31Z","file_name":"2018_LIPIcs_Edelsbrunner.pdf"}],"publication_status":"published","volume":99,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"intvolume":" 99","month":"06","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"ddc":["000"],"date_updated":"2021-01-12T06:53:48Z","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"HeEd"}],"_id":"188","status":"public","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference"},{"date_updated":"2021-01-12T06:54:44Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"2015","volume":7,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0366"}],"month":"04","intvolume":" 7","abstract":[{"lang":"eng","text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size."}],"oa_version":"Preprint","publist_id":"5061","author":[{"first_name":"Garvesh","last_name":"Raskutti","full_name":"Raskutti, Garvesh"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1307.0366"]},"article_processing_charge":"No","title":"Learning directed acyclic graphs based on sparsest permutations","citation":{"ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183.","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183.","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” STAT, vol. 7, no. 1. Wiley, 2018.","short":"G. Raskutti, C. Uhler, STAT 7 (2018).","ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. STAT. 2018;7(1). doi:10.1002/sta4.183","apa":"Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e183","doi":"10.1002/sta4.183","date_published":"2018-04-17T00:00:00Z","date_created":"2018-12-11T11:55:13Z","year":"2018","day":"17","publication":"STAT","publisher":"Wiley","quality_controlled":"1","oa":1},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"e00596","author":[{"last_name":"De Martino","full_name":"De Martino, Andrea","first_name":"Andrea"},{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"}],"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","citation":{"ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_published":"2018-04-01T00:00:00Z","doi":"10.1016/j.heliyon.2018.e00596","date_created":"2018-12-11T11:45:44Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Heliyon","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"306","file_date_updated":"2020-07-14T12:45:59Z","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T07:40:46Z","ddc":["530"],"scopus_import":1,"month":"04","intvolume":" 4","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"oa_version":"Published Version","issue":"4","volume":4,"ec_funded":1,"publication_status":"published","file":[{"file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_Heliyon_DeMartino.pdf","date_created":"2019-02-06T07:36:24Z","creator":"dernst","file_size":994490,"date_updated":"2020-07-14T12:45:59Z"}],"language":[{"iso":"eng"}]},{"publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"year":"2018","publication_status":"published","day":"08","language":[{"iso":"eng"}],"page":"XLVIII, 1212","doi":"10.1007/978-3-319-10575-8","date_published":"2018-06-08T00:00:00Z","date_created":"2018-12-11T12:02:32Z","abstract":[{"text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools.","lang":"eng"}],"oa_version":"None","publisher":"Springer Nature","scopus_import":"1","quality_controlled":"1","edition":"1","place":"Cham","month":"06","date_updated":"2021-12-21T10:49:36Z","citation":{"chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Clarke, Edmund M.","last_name":"Clarke","first_name":"Edmund M."},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"publist_id":"3340","article_processing_charge":"No","title":"Handbook of Model Checking","department":[{"_id":"ToHe"}],"_id":"3300","type":"book","status":"public"},{"file_date_updated":"2020-10-13T14:20:37Z","department":[{"_id":"AnKi"}],"ddc":["570"],"date_updated":"2021-01-12T07:49:03Z","status":"public","type":"book_chapter","_id":"37","series_title":"MIMB","volume":1863,"ec_funded":1,"file":[{"file_name":"2018_MIMB_Zagorski.pdf","date_created":"2020-10-13T14:20:37Z","file_size":4906815,"date_updated":"2020-10-13T14:20:37Z","creator":"dernst","success":1,"file_id":"8656","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"publication_status":"published","month":"10","intvolume":" 1863","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"oa_version":"Submitted Version","abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","publist_id":"8018","author":[{"last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4."},"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"date_published":"2018-10-16T00:00:00Z","doi":"10.1007/978-1-4939-8772-6_4","date_created":"2018-12-11T11:44:17Z","page":"47 - 63","day":"16","publication":"Morphogen Gradients ","has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"date_published":"2018-01-01T00:00:00Z","doi":"10.1007/978-1-4939-7792-5_15","date_created":"2018-12-11T11:45:43Z","page":"183 - 202","day":"01","publication":"Methods in Molecular Biology","year":"2018","quality_controlled":"1","publisher":"Springer","acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","title":"Fabrication and operation of microfluidic hanging drop networks","author":[{"last_name":"Misun","full_name":"Misun, Patrick","first_name":"Patrick"},{"full_name":"Birchler, Axel","last_name":"Birchler","first_name":"Axel"},{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang"},{"last_name":"Hierlemann","full_name":"Hierlemann, Andreas","first_name":"Andreas"},{"first_name":"Olivier","last_name":"Frey","full_name":"Frey, Olivier"}],"publist_id":"7574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15"},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":1771,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 1771","scopus_import":1,"alternative_title":["MIMB"],"oa_version":"None","abstract":[{"text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2021-01-12T07:40:42Z","status":"public","type":"journal_article","_id":"305"},{"date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3158122","date_created":"2018-12-11T11:45:50Z","day":"01","year":"2018","publisher":"ACM","quality_controlled":"1","oa":1,"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","publist_id":"7540","author":[{"first_name":"Sheshansh","last_name":"Agrawal","full_name":"Agrawal, Sheshansh"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novotny","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"}],"external_id":{"arxiv":["1709.04037"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"article_number":"34","issue":"POPL","volume":2,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 2","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"oa_version":"Preprint","abstract":[{"text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T07:42:07Z","status":"public","type":"conference","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, USA","start_date":"2018-01-07"},"_id":"325"},{"page":"223 - 228","issue":"1","doi":"10.1021/acs.nanolett.7b03953","volume":18,"date_published":"2018-01-10T00:00:00Z","date_created":"2018-12-11T11:46:13Z","publication_status":"published","year":"2018","day":"10","language":[{"iso":"eng"}],"publication":"Nano Letters","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.07925"}],"month":"01","intvolume":" 18","abstract":[{"lang":"eng","text":"The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. "}],"oa_version":"Submitted Version","publist_id":"7435","author":[{"last_name":"Mahmood","full_name":"Mahmood, Fahad","first_name":"Fahad"},{"orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yi","full_name":"Lee, Yi","last_name":"Lee"},{"last_name":"Kong","full_name":"Kong, Jing","first_name":"Jing"},{"first_name":"Nuh","full_name":"Gedik, Nuh","last_name":"Gedik"}],"external_id":{"arxiv":["1712.07925"]},"title":"Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2","date_updated":"2021-01-12T07:53:20Z","citation":{"ista":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228.","chicago":"Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.","ieee":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.","short":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228.","apa":"Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953","ama":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953","mla":"Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"394"},{"date_updated":"2021-01-12T07:54:21Z","department":[{"_id":"JiFr"}],"_id":"408","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1064-3745"]},"volume":1761,"pmid":1,"oa_version":"None","abstract":[{"text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings.","lang":"eng"}],"intvolume":" 1761","month":"03","alternative_title":["MIMB"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7."},"title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","article_processing_charge":"No","external_id":{"pmid":["29525951"]},"publist_id":"7421","author":[{"first_name":"Hoang","last_name":"Trinh","full_name":"Trinh, Hoang"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"publication":"Root Development ","day":"01","year":"2018","date_created":"2018-12-11T11:46:18Z","doi":"10.1007/978-1-4939-7747-5_7","date_published":"2018-03-01T00:00:00Z","page":"95 - 102","publisher":"Springer Nature","quality_controlled":"1"},{"page":"131 - 143","date_created":"2018-12-11T11:46:20Z","volume":1761,"date_published":"2018-03-11T00:00:00Z","doi":"10.1007/978-1-4939-7747-5_10","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"publication":"Root Development. Methods and Protocols","day":"11","quality_controlled":"1","publisher":"Springer","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"intvolume":" 1761","month":"03","abstract":[{"lang":"eng","text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins."}],"oa_version":"None","publist_id":"7418","author":[{"full_name":"Karampelias, Michael","last_name":"Karampelias","first_name":"Michael"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"editor":[{"first_name":"Daniela","full_name":"Ristova, Daniela","last_name":"Ristova"},{"first_name":"Elke","full_name":"Barbez, Elke","last_name":"Barbez"}],"title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","department":[{"_id":"JiFr"}],"citation":{"mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143."},"date_updated":"2021-01-12T07:54:34Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","status":"public","_id":"411","series_title":"MIMB"},{"_id":"456","article_number":"eaar7514","type":"journal_article","status":"public","citation":{"mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.","short":"G. Novarino, Science Translational Medicine 10 (2018).","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514","chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.","ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514."},"date_updated":"2021-01-12T07:59:42Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"publist_id":"7365","department":[{"_id":"GaNo"}],"title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","abstract":[{"text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. ","lang":"eng"}],"oa_version":"None","publisher":"American Association for the Advancement of Science","scopus_import":1,"quality_controlled":"1","month":"01","intvolume":" 10","publication_status":"published","year":"2018","day":"10","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"volume":10,"doi":"10.1126/scitranslmed.aar7514","issue":"423","date_published":"2018-01-10T00:00:00Z","date_created":"2018-12-11T11:46:34Z"},{"author":[{"last_name":"Petritsch","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Porsche","full_name":"Porsche, Jana"}],"publist_id":"8001","title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","citation":{"ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"page":"199 - 206","doi":"10.31263/voebm.v71i1.1993","date_published":"2018-10-01T00:00:00Z","date_created":"2018-12-11T11:44:22Z","has_accepted_license":"1","year":"2018","day":"01","publication":"VÖB Mitteilungen","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"53","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"E-Lib"}],"date_updated":"2021-01-12T08:01:26Z","ddc":["020"],"scopus_import":1,"month":"10","intvolume":" 71","abstract":[{"text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.","lang":"eng"}],"oa_version":"Published Version","volume":71,"issue":"1","publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:38Z","file_size":509434,"creator":"dernst","date_created":"2018-12-17T12:40:27Z","file_name":"2018_VOEB_Petritsch.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5702","checksum":"7ac61bade5f37db011ca435ebcf86797"}],"language":[{"iso":"eng"}]},{"_id":"536","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["000"],"date_updated":"2023-02-23T12:23:25Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:46:38Z","oa_version":"Published Version","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."}],"intvolume":" 31","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_size":595707,"date_updated":"2020-07-14T12:46:38Z","creator":"dernst","file_name":"2017_DistribComp_Alistarh.pdf","date_created":"2019-01-22T07:25:51Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"69b46e537acdcac745237ddb853fcbb5","file_id":"5867"}],"publication_status":"published","publication_identifier":{"issn":["01782770"]},"volume":31,"issue":"6","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 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.","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.","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 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."},"title":"Communication-efficient randomized consensus","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"first_name":"Valerie","last_name":"King","full_name":"King, Valerie"},{"full_name":"Saia, Jared","last_name":"Saia","first_name":"Jared"}],"publist_id":"7281","oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Distributed Computing","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:47:01Z","date_published":"2018-11-01T00:00:00Z","doi":"10.1007/s00446-017-0315-1","page":"489-501"},{"publication_identifier":{"issn":["00103616"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":360,"issue":"1","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"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"month":"05","intvolume":" 360","date_updated":"2021-01-12T08:02:35Z","department":[{"_id":"RoSe"}],"_id":"554","type":"journal_article","status":"public","year":"2018","day":"01","publication":"Communications in Mathematical Physics","page":"347-403","doi":"10.1007/s00220-017-3064-x","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:47:09Z","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"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.","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.","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.","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.","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","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. 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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","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. 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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."}],"pmid":1,"oa_version":"Submitted Version","volume":1727,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-19T07:47:43Z","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","date_updated":"2020-07-14T12:47:09Z","file_size":787407,"creator":"dernst","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","file_id":"7046","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}]},{"citation":{"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.","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 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.","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.","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.","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. 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Springer. https://doi.org/10.1007/978-3-319-10575-8_27"},"date_updated":"2021-01-12T08:05:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Barbara","last_name":"Jobstmann","full_name":"Jobstmann, Barbara"}],"publist_id":"7995","title":"Graph games and reactive synthesis","editor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Clarke, Edmund M.","last_name":"Clarke","first_name":"Edmund M."},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"department":[{"_id":"KrCh"}],"_id":"59","type":"book_chapter","status":"public","publication_status":"published","year":"2018","publication_identifier":{"isbn":["978-3-319-10574-1"]},"language":[{"iso":"eng"}],"publication":"Handbook of Model Checking","day":"19","page":"921 - 962","date_created":"2018-12-11T11:44:24Z","date_published":"2018-05-19T00:00:00Z","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"}],"oa_version":"None","edition":"1","quality_controlled":"1","publisher":"Springer","scopus_import":1,"month":"05"},{"type":"book_chapter","status":"public","_id":"60","series_title":"Handbook of Model Checking","publist_id":"7994","author":[{"first_name":"Edmund","full_name":"Clarke, Edmund","last_name":"Clarke"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"editor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"}],"title":"Introduction to model checking","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T08:05:35Z","citation":{"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.","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","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.","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","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","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.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","scopus_import":1,"quality_controlled":"1","month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"None","page":"1 - 26","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_1","date_created":"2018-12-11T11:44:25Z","publication_status":"published","year":"2018","day":"19","publication":"Handbook of Model Checking","language":[{"iso":"eng"}]},{"month":"05","quality_controlled":"1","publisher":"Springer","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06286"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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. "}],"doi":"10.1007/978-3-319-72456-0_7","date_published":"2018-05-23T00:00:00Z","date_created":"2018-12-11T11:44:25Z","page":"131 - 134","day":"23","publication":"Contemporary Computational Mathematics","language":[{"iso":"eng"}],"publication_status":"published","year":"2018","status":"public","type":"book_chapter","_id":"61","title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","department":[{"_id":"TaHa"}],"author":[{"first_name":"Andriy","full_name":"Bondarenko, Andriy","last_name":"Bondarenko"},{"full_name":"Mellit, Anton","last_name":"Mellit","first_name":"Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prymak","full_name":"Prymak, Andriy","first_name":"Andriy"},{"first_name":"Danylo","full_name":"Radchenko, Danylo","last_name":"Radchenko"},{"full_name":"Viazovska, Maryna","last_name":"Viazovska","first_name":"Maryna"}],"publist_id":"7993","article_processing_charge":"No","external_id":{"arxiv":["1509.06286"]},"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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). 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Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","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."},"date_updated":"2021-01-12T08:06:06Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (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","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","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.","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.","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."},"title":"A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism","author":[{"full_name":"McLachlan, Ian G.","last_name":"McLachlan","first_name":"Ian G."},{"last_name":"Beets","full_name":"Beets, Isabel","first_name":"Isabel"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"},{"last_name":"Heiman","full_name":"Heiman, Maxwell G.","first_name":"Maxwell G."}],"external_id":{"pmid":["29879119"]},"article_number":"e1007435","day":"07","publication":"PLOS Genetics","has_accepted_license":"1","year":"2018","doi":"10.1371/journal.pgen.1007435","date_published":"2018-06-07T00:00:00Z","date_created":"2019-03-19T13:09:28Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"extern":"1","ddc":["570"],"date_updated":"2021-01-12T08:06:11Z","file_date_updated":"2020-07-14T12:47:19Z","_id":"6111","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:19Z","file_size":13011506,"date_created":"2019-03-19T13:18:01Z","file_name":"2018_PLOS_McLachlan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"622036b945365dbc575bea2768aa9bc8","file_id":"6112"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7404"]},"publication_status":"published","volume":14,"issue":"6","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"06","intvolume":" 14"}]