--- _id: '2012' abstract: - lang: eng text: The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice. acknowledgement: We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper. The second author has been supported by the Max Planck Center for Visual Computing and Communication article_number: '1401.0468' article_processing_charge: No author: - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham - first_name: Michael full_name: Kerber, Michael last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv. doi:10.48550/arXiv.1401.0468 apa: Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468 chicago: Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468. ieee: M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” arXiv. . ista: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468. mla: Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv, 1401.0468, doi:10.48550/arXiv.1401.0468. short: M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.). date_created: 2018-12-11T11:55:12Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-10-18T08:06:45Z day: '01' department: - _id: HeEd - _id: CaUh doi: 10.48550/arXiv.1401.0468 external_id: arxiv: - '1401.0468' language: - iso: eng main_file_link: - open_access: '1' url: http://cccg.ca/proceedings/2014/papers/paper23.pdf month: '01' oa: 1 oa_version: Submitted Version publication: arXiv publication_status: submitted publist_id: '5064' status: public title: Sphere packing with limited overlap type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2209' abstract: - lang: eng text: "A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985.\r\n" alternative_title: - '2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) ' author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 citation: ama: 'Biedl T, Held M, Huber S. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. In: IEEE; 2013:37-46. doi:10.1109/ISVD.2013.11' apa: 'Biedl, T., Held, M., & Huber, S. (2013). Recognizing straight skeletons and Voronoi diagrams and reconstructing their input (pp. 37–46). Presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia: IEEE. https://doi.org/10.1109/ISVD.2013.11' chicago: Biedl, Therese, Martin Held, and Stefan Huber. “Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input,” 37–46. IEEE, 2013. https://doi.org/10.1109/ISVD.2013.11. ieee: 'T. Biedl, M. Held, and S. Huber, “Recognizing straight skeletons and Voronoi diagrams and reconstructing their input,” presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia, 2013, pp. 37–46.' ista: 'Biedl T, Held M, Huber S. 2013. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. ISVD: Voronoi Diagrams in Science and Engineering, 2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) , , 37–46.' mla: Biedl, Therese, et al. Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input. IEEE, 2013, pp. 37–46, doi:10.1109/ISVD.2013.11. short: T. Biedl, M. Held, S. Huber, in:, IEEE, 2013, pp. 37–46. conference: end_date: 2013-07-10 location: St. Petersburg, Russia name: 'ISVD: Voronoi Diagrams in Science and Engineering' start_date: 2013-07-08 date_created: 2018-12-11T11:56:20Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:00Z day: '01' department: - _id: HeEd doi: 10.1109/ISVD.2013.11 language: - iso: eng month: '12' oa_version: None page: 37 - 46 publication_identifier: eisbn: - '978-0-7695-5037-4 ' publication_status: published publisher: IEEE publist_id: '4763' quality_controlled: '1' scopus_import: 1 status: public title: Recognizing straight skeletons and Voronoi diagrams and reconstructing their input type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2210' abstract: - lang: eng text: 'A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model.' author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 citation: ama: 'Biedl T, Held M, Huber S. Reconstructing polygons from embedded straight skeletons. In: 29th European Workshop on Computational Geometry. TU Braunschweig; 2013:95-98.' apa: 'Biedl, T., Held, M., & Huber, S. (2013). Reconstructing polygons from embedded straight skeletons. In 29th European Workshop on Computational Geometry (pp. 95–98). Braunschweig, Germany: TU Braunschweig.' chicago: Biedl, Therese, Martin Held, and Stefan Huber. “Reconstructing Polygons from Embedded Straight Skeletons.” In 29th European Workshop on Computational Geometry, 95–98. TU Braunschweig, 2013. ieee: T. Biedl, M. Held, and S. Huber, “Reconstructing polygons from embedded straight skeletons,” in 29th European Workshop on Computational Geometry, Braunschweig, Germany, 2013, pp. 95–98. ista: 'Biedl T, Held M, Huber S. 2013. Reconstructing polygons from embedded straight skeletons. 29th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 95–98.' mla: Biedl, Therese, et al. “Reconstructing Polygons from Embedded Straight Skeletons.” 29th European Workshop on Computational Geometry, TU Braunschweig, 2013, pp. 95–98. short: T. Biedl, M. Held, S. Huber, in:, 29th European Workshop on Computational Geometry, TU Braunschweig, 2013, pp. 95–98. conference: end_date: 2013-03-20 location: Braunschweig, Germany name: 'EuroCG: European Workshop on Computational Geometry' start_date: 2013-03-17 date_created: 2018-12-11T11:56:21Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:56:00Z day: '01' department: - _id: HeEd language: - iso: eng main_file_link: - open_access: '1' url: http://www.ibr.cs.tu-bs.de/alg/eurocg13/booklet_eurocg13.pdf month: '03' oa: 1 oa_version: Submitted Version page: 95 - 98 publication: 29th European Workshop on Computational Geometry publication_status: published publisher: TU Braunschweig publist_id: '4762' status: public title: Reconstructing polygons from embedded straight skeletons type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2304' abstract: - lang: eng text: This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter. acknowledgement: This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria). author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Pausinger F. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 2013;43:43-50. doi:10.1016/j.endm.2013.07.008 apa: Pausinger, F. (2013). Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2013.07.008 chicago: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics. Elsevier, 2013. https://doi.org/10.1016/j.endm.2013.07.008. ieee: F. Pausinger, “Van der Corput sequences and linear permutations,” Electronic Notes in Discrete Mathematics, vol. 43. Elsevier, pp. 43–50, 2013. ista: Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50. mla: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics, vol. 43, Elsevier, 2013, pp. 43–50, doi:10.1016/j.endm.2013.07.008. short: F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50. date_created: 2018-12-11T11:56:53Z date_published: 2013-09-05T00:00:00Z date_updated: 2021-01-12T06:56:39Z day: '05' department: - _id: HeEd doi: 10.1016/j.endm.2013.07.008 intvolume: ' 43' language: - iso: eng month: '09' oa_version: None page: 43 - 50 publication: Electronic Notes in Discrete Mathematics publication_status: published publisher: Elsevier publist_id: '4623' quality_controlled: '1' scopus_import: 1 status: public title: Van der Corput sequences and linear permutations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2013' ... --- _id: '2807' abstract: - lang: eng text: 'We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov''s result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. ' author: - first_name: Martin full_name: Čadek, Martin last_name: Čadek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Lukáš full_name: Vokřínek, Lukáš last_name: Vokřínek - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683' apa: 'Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In 45th Annual ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United States: ACM. https://doi.org/10.1145/2488608.2488683' chicago: 'Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683.' ieee: 'M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory of computing, Palo Alto, CA, United States, 2013, pp. 595–604.' ista: 'Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.' mla: 'Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604, doi:10.1145/2488608.2488683.' short: M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604. conference: end_date: 2013-06-04 location: Palo Alto, CA, United States name: 'STOC: Symposium on the Theory of Computing' start_date: 2013-06-01 date_created: 2018-12-11T11:59:42Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:59:51Z day: '01' ddc: - '510' department: - _id: UlWa - _id: HeEd doi: 10.1145/2488608.2488683 file: - access_level: open_access checksum: 06c2ce5c1135fbc1f71ca15eeb242dcf content_type: application/pdf creator: system date_created: 2018-12-12T10:14:29Z date_updated: 2020-07-14T12:45:48Z file_id: '5081' file_name: IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf file_size: 447945 relation: main_file file_date_updated: 2020-07-14T12:45:48Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 595 - 604 publication: 45th Annual ACM Symposium on theory of computing publication_status: published publisher: ACM publist_id: '4078' pubrep_id: '533' quality_controlled: '1' scopus_import: 1 status: public title: 'Extending continuous maps: Polynomiality and undecidability' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2812' abstract: - lang: eng text: 'We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.' acknowledgement: Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827). author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Olivier full_name: Devillers, Olivier last_name: Devillers - first_name: Marc full_name: Glisse, Marc last_name: Glisse - first_name: André full_name: Lieutier, André last_name: Lieutier citation: ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373' apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013). Homological reconstruction and simplification in R3. In Proceedings of the 29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro, Brazil: ACM. https://doi.org/10.1145/2462356.2462373' chicago: Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013. https://doi.org/10.1145/2462356.2462373. ieee: D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in Proceedings of the 29th annual symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125. ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.' mla: Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373. short: D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125. conference: end_date: 2013-06-20 location: Rio de Janeiro, Brazil name: 'SoCG: Symposium on Computational Geometry' start_date: 2013-06-17 date_created: 2018-12-11T11:59:44Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T10:15:15Z day: '01' department: - _id: HeEd doi: 10.1145/2462356.2462373 language: - iso: eng main_file_link: - open_access: '1' url: http://hal.archives-ouvertes.fr/hal-00833791/ month: '06' oa: 1 oa_version: Submitted Version page: 117 - 125 publication: Proceedings of the 29th annual symposium on Computational Geometry publication_status: published publisher: ACM publist_id: '4072' quality_controlled: '1' related_material: record: - id: '1805' relation: later_version status: public scopus_import: 1 status: public title: Homological reconstruction and simplification in R3 type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2822' abstract: - lang: eng text: Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops. author: - first_name: Christopher full_name: Topp, Christopher last_name: Topp - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Jill full_name: Anderson, Jill last_name: Anderson - first_name: Cheng full_name: Lee, Cheng last_name: Lee - first_name: Paul full_name: Zurek, Paul last_name: Zurek - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Alexander full_name: Bucksch, Alexander last_name: Bucksch - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Taras full_name: Galkovskyi, Taras last_name: Galkovskyi - first_name: Brad full_name: Moore, Brad last_name: Moore - first_name: John full_name: Harer, John last_name: Harer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Thomas full_name: Mitchell Olds, Thomas last_name: Mitchell Olds - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110 apa: Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110 chicago: Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110. ieee: C. Topp et al., “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” PNAS, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013. ista: Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704. mla: Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110. short: C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '30' department: - _id: MaJö - _id: HeEd doi: 10.1073/pnas.1304354110 external_id: pmid: - '25673779' intvolume: ' 110' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/ month: '04' oa: 1 oa_version: Submitted Version page: E1695 - E1704 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3979' quality_controlled: '1' scopus_import: 1 status: public title: 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2843' abstract: - lang: eng text: 'Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes.' alternative_title: - LNCS author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: 'Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery. Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0' apa: 'Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like shapes. In 17th IAPR International Conference on Discrete Geometry for Computer Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0' chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0. ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” in 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Seville, Spain, 2013, vol. 7749, pp. XV–XIX. ista: 'Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes. 17th IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.' mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0. short: H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX. conference: end_date: 2013-03-22 location: Seville, Spain name: 'DGCI: Discrete Geometry for Computer Imagery' start_date: 2013-03-20 date_created: 2018-12-11T11:59:53Z date_published: 2013-02-21T00:00:00Z date_updated: 2023-02-23T10:35:00Z day: '21' department: - _id: HeEd doi: 10.1007/978-3-642-37067-0 intvolume: ' 7749' language: - iso: eng month: '02' oa_version: None page: XV - XIX publication: 17th IAPR International Conference on Discrete Geometry for Computer Imagery publication_status: published publisher: Springer publist_id: '3952' quality_controlled: '1' related_material: record: - id: '2255' relation: later_version status: public scopus_import: 1 status: public title: Stable length estimates of tube-like shapes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7749 year: '2013' ... --- _id: '2859' abstract: - lang: eng text: Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Amit full_name: Patel, Amit id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 2013;15(1):51-72. doi:10.4310/HHA.2013.v15.n1.a3 apa: Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2013). Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2013.v15.n1.a3 chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications. International Press, 2013. https://doi.org/10.4310/HHA.2013.v15.n1.a3. ieee: P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” Homology, Homotopy and Applications, vol. 15, no. 1. International Press, pp. 51–72, 2013. ista: Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72. mla: Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” Homology, Homotopy and Applications, vol. 15, no. 1, International Press, 2013, pp. 51–72, doi:10.4310/HHA.2013.v15.n1.a3. short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72. date_created: 2018-12-11T11:59:58Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T07:00:18Z day: '01' department: - _id: HeEd doi: 10.4310/HHA.2013.v15.n1.a3 external_id: arxiv: - '1102.3389' intvolume: ' 15' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1102.3389v1 month: '05' oa: 1 oa_version: Preprint page: 51 - 72 publication: Homology, Homotopy and Applications publication_status: published publisher: International Press publist_id: '3930' quality_controlled: '1' scopus_import: 1 status: public title: Homology and robustness of level and interlevel sets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2887' abstract: - lang: eng text: 'Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.' article_processing_charge: No article_type: original author: - first_name: Suqin full_name: Fang, Suqin last_name: Fang - first_name: Randy full_name: Clark, Randy last_name: Clark - first_name: Ying full_name: Zheng, Ying last_name: Zheng - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz - first_name: Leon full_name: Kochian, Leon last_name: Kochian - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Hong full_name: Liao, Hong last_name: Liao - first_name: Philip full_name: Benfey, Philip last_name: Benfey citation: ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110 apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110 chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1222821110. ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013. ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675. mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:10.1073/pnas.1222821110. short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675. date_created: 2018-12-11T12:00:09Z date_published: 2013-02-12T00:00:00Z date_updated: 2021-01-12T07:00:29Z day: '12' department: - _id: HeEd doi: 10.1073/pnas.1222821110 external_id: pmid: - '23362379' intvolume: ' 110' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/ month: '02' oa: 1 oa_version: Published Version page: 2670 - 2675 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3872' quality_controlled: '1' scopus_import: 1 status: public title: Genotypic recognition and spatial responses by rice roots type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ...