--- _id: '185' abstract: - lang: eng 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. alternative_title: - Leibniz International Proceedings in Information, LIPIcs article_number: '39' author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl 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' 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. 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.' 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.' 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. short: R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2018.39 file: - access_level: open_access checksum: f1b94f1a75b37c414a1f61d59fb2cd4c content_type: application/pdf creator: dernst date_created: 2018-12-17T12:33:52Z date_updated: 2020-07-14T12:45:19Z file_id: '5701' file_name: 2018_LIPIcs_Fulek.pdf file_size: 718857 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication_identifier: isbn: - 978-3-95977-066-8 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7735' quality_controlled: '1' scopus_import: 1 status: public title: Hanani-Tutte for approximating maps of graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '188' 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. 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 alternative_title: - Leibniz International Proceedings in Information, LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ziga full_name: Virk, Ziga last_name: Virk - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: 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' 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' 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.' 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.' 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. short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:05Z date_published: 2018-06-11T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '11' ddc: - '000' department: - _id: HeEd doi: 10.4230/LIPIcs.SoCG.2018.35 file: - access_level: open_access checksum: 7509403803b3ac1aee94bbc2ad293d21 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:31:31Z date_updated: 2020-07-14T12:45:20Z file_id: '5724' file_name: 2018_LIPIcs_Edelsbrunner.pdf file_size: 489080 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 35:1 - 35:13 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7733' quality_controlled: '1' scopus_import: 1 status: public title: Smallest enclosing spheres and Chernoff points in Bregman geometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '306' 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. article_number: e00596 author: - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: 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 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 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. 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. 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. 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. short: A. De Martino, D. De Martino, Heliyon 4 (2018). date_created: 2018-12-11T11:45:44Z date_published: 2018-04-01T00:00:00Z date_updated: 2021-01-12T07:40:46Z day: '01' ddc: - '530' department: - _id: GaTk doi: 10.1016/j.heliyon.2018.e00596 ec_funded: 1 file: - access_level: open_access checksum: 67010cf5e3b3e0637c659371714a715a content_type: application/pdf creator: dernst date_created: 2019-02-06T07:36:24Z date_updated: 2020-07-14T12:45:59Z file_id: '5929' file_name: 2018_Heliyon_DeMartino.pdf file_size: 994490 relation: main_file file_date_updated: 2020-07-14T12:45:59Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Heliyon publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: 1 status: public title: An introduction to the maximum entropy approach and its application to inference problems in biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2018' ... --- _id: '3300' abstract: - lang: eng 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." article_processing_charge: No author: - first_name: Edmund M. full_name: Clarke, Edmund M. last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem citation: 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' 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.' ieee: 'E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.' 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. short: E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018. date_created: 2018-12-11T12:02:32Z date_published: 2018-06-08T00:00:00Z date_updated: 2021-12-21T10:49:36Z day: '08' department: - _id: ToHe doi: 10.1007/978-3-319-10575-8 edition: '1' language: - iso: eng month: '06' oa_version: None page: XLVIII, 1212 place: Cham publication_identifier: eisbn: - 978-3-319-10575-8 isbn: - 978-3-319-10574-1 publication_status: published publisher: Springer Nature publist_id: '3340' quality_controlled: '1' scopus_import: '1' status: public title: Handbook of Model Checking type: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2018' ... --- _id: '37' abstract: - lang: eng 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. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: 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' 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 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. 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. 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.' 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. short: M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63. date_created: 2018-12-11T11:44:17Z date_published: 2018-10-16T00:00:00Z date_updated: 2021-01-12T07:49:03Z day: '16' ddc: - '570' department: - _id: AnKi doi: 10.1007/978-1-4939-8772-6_4 ec_funded: 1 file: - access_level: open_access checksum: 2a97d0649fdcfcf1bdca7c8ad1dce71b content_type: application/pdf creator: dernst date_created: 2020-10-13T14:20:37Z date_updated: 2020-10-13T14:20:37Z file_id: '8656' file_name: 2018_MIMB_Zagorski.pdf file_size: 4906815 relation: main_file success: 1 file_date_updated: 2020-10-13T14:20:37Z has_accepted_license: '1' intvolume: ' 1863' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 47 - 63 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: 'Morphogen Gradients ' publication_identifier: isbn: - 978-1-4939-8771-9 issn: - 1064-3745 publication_status: published publisher: Springer Nature publist_id: '8018' quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1863 year: '2018' ... --- _id: '305' abstract: - lang: eng 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. 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. alternative_title: - MIMB author: - first_name: Patrick full_name: Misun, Patrick last_name: Misun - first_name: Axel full_name: Birchler, Axel last_name: Birchler - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Andreas full_name: Hierlemann, Andreas last_name: Hierlemann - first_name: Olivier full_name: Frey, Olivier last_name: Frey citation: 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 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. 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. 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. short: P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202. date_created: 2018-12-11T11:45:43Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T07:40:42Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1007/978-1-4939-7792-5_15 ec_funded: 1 intvolume: ' 1771' language: - iso: eng month: '01' oa_version: None page: 183 - 202 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Methods in Molecular Biology publication_status: published publisher: Springer publist_id: '7574' quality_controlled: '1' scopus_import: 1 status: public title: Fabrication and operation of microfluidic hanging drop networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1771 year: '2018' ... --- _id: '325' abstract: - lang: eng 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. article_number: '34' author: - first_name: Sheshansh full_name: Agrawal, Sheshansh last_name: Agrawal - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: 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' 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' 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.' 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.' 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.' 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.' short: S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018. conference: end_date: 2018-01-13 location: Los Angeles, CA, USA name: 'POPL: Principles of Programming Languages' start_date: 2018-01-07 date_created: 2018-12-11T11:45:50Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T07:42:07Z day: '01' department: - _id: KrCh doi: 10.1145/3158122 external_id: arxiv: - '1709.04037' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.04037 month: '01' oa: 1 oa_version: Preprint project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: ACM publist_id: '7540' quality_controlled: '1' status: public title: 'Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '408' abstract: - lang: eng 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. alternative_title: - MIMB article_processing_charge: No author: - first_name: Hoang full_name: Trinh, Hoang last_name: Trinh - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Danny full_name: Geelen, Danny last_name: Geelen citation: 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' 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 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. 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. 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.' 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. short: H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102. date_created: 2018-12-11T11:46:18Z date_published: 2018-03-01T00:00:00Z date_updated: 2021-01-12T07:54:21Z day: '01' department: - _id: JiFr doi: 10.1007/978-1-4939-7747-5_7 external_id: pmid: - '29525951' intvolume: ' 1761' language: - iso: eng month: '03' oa_version: None page: 95 - 102 pmid: 1 publication: 'Root Development ' publication_identifier: issn: - 1064-3745 publication_status: published publisher: Springer Nature publist_id: '7421' quality_controlled: '1' scopus_import: '1' status: public title: In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1761 year: '2018' ... --- _id: '411' 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. alternative_title: - Methods in Molecular Biology author: - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: 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 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. 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. 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.' 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. 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. date_created: 2018-12-11T11:46:20Z date_published: 2018-03-11T00:00:00Z date_updated: 2021-01-12T07:54:34Z day: '11' department: - _id: JiFr doi: 10.1007/978-1-4939-7747-5_10 editor: - first_name: Daniela full_name: Ristova, Daniela last_name: Ristova - first_name: Elke full_name: Barbez, Elke last_name: Barbez intvolume: ' 1761' language: - iso: eng month: '03' oa_version: None page: 131 - 143 publication: Root Development. Methods and Protocols publication_status: published publisher: Springer publist_id: '7418' quality_controlled: '1' scopus_import: 1 series_title: MIMB status: public title: Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1761 year: '2018' ... --- _id: '456' abstract: - lang: eng text: 'Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. ' article_number: eaar7514 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: 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.' 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.' ista: 'Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.' 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). date_created: 2018-12-11T11:46:34Z date_published: 2018-01-10T00:00:00Z date_updated: 2021-01-12T07:59:42Z day: '10' department: - _id: GaNo doi: 10.1126/scitranslmed.aar7514 intvolume: ' 10' issue: '423' language: - iso: eng month: '01' oa_version: None publication: Science Translational Medicine publication_status: published publisher: American Association for the Advancement of Science publist_id: '7365' quality_controlled: '1' scopus_import: 1 status: public title: 'Zika-associated microcephaly: Reduce the stress and race for the treatment' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ...