--- _id: '9483' abstract: - lang: eng text: Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development. article_processing_charge: No article_type: original author: - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Juhyun full_name: Shin, Juhyun last_name: Shin - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Stephanie full_name: Cohen, Stephanie last_name: Cohen - first_name: Matthew J. full_name: Bauer, Matthew J. last_name: Bauer - first_name: Meryl full_name: Hashimoto, Meryl last_name: Hashimoto - first_name: Ryan C. full_name: Kirkbride, Ryan C. last_name: Kirkbride - first_name: John J. full_name: Harada, John J. last_name: Harada - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108 apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1019273108 chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108. ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis endosperm,” Proceedings of the National Academy of Sciences, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011. ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762. mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108. short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762. date_created: 2021-06-07T07:40:38Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-12-14T08:33:49Z day: '01' department: - _id: DaZi doi: 10.1073/pnas.1019273108 extern: '1' external_id: pmid: - '21257907' intvolume: ' 108' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1019273108 month: '02' oa: 1 oa_version: Published Version page: 1755-1762 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Regulation of imprinted gene expression in Arabidopsis endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 108 year: '2011' ... --- _id: '967' abstract: - lang: eng text: Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Senthil T, Lee P. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2011;84(18). doi:10.1103/PhysRevB.84.180403 apa: Serbyn, M., Senthil, T., & Lee, P. (2011). Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.180403 chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.180403. ieee: M. Serbyn, T. Senthil, and P. Lee, “Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18. American Physical Society, 2011. ista: Serbyn M, Senthil T, Lee P. 2011. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 84(18). mla: Serbyn, Maksym, et al. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18, American Physical Society, 2011, doi:10.1103/PhysRevB.84.180403. short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 84 (2011). date_created: 2018-12-11T11:49:27Z date_published: 2011-11-03T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '03' doi: 10.1103/PhysRevB.84.180403 extern: 1 intvolume: ' 84' issue: '18' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1108.3070 month: '11' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6432' quality_controlled: 0 status: public title: Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice type: journal_article volume: 84 year: '2011' ... --- _id: '969' abstract: - lang: eng text: We investigate the isotope effect on the London penetration depth of a superconductor which measures n S/m*, the ratio of superfluid density to effective mass. We use a simplified model of electrons weakly coupled to a single phonon frequency ω E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless, we find an isotope effect for n S/m* which is significant if Δ is sufficiently large that it becomes comparable to ω E, a regime of interest to high-T c cuprate superconductors and possibly other families of unconventional superconductors with relatively high T c. Our model is too simple to describe the cuprates and it gives the wrong sign of the isotope effect when compared with experiment, but it is a proof of principle that the isotope effect exists for n S/m* in materials where the pairing gap and T c are not of phonon origin and have no isotope effect. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Lee P. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 2011;83(2). doi:10.1103/PhysRevB.83.024506 apa: Serbyn, M., & Lee, P. (2011). Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.83.024506 chicago: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.83.024506. ieee: M. Serbyn and P. Lee, “Isotope effect on the superfluid density in conventional and high-temperature superconductors,” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2. American Physical Society, 2011. ista: Serbyn M, Lee P. 2011. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 83(2). mla: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2, American Physical Society, 2011, doi:10.1103/PhysRevB.83.024506. short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 83 (2011). date_created: 2018-12-11T11:49:28Z date_published: 2011-01-19T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '19' doi: 10.1103/PhysRevB.83.024506 extern: 1 intvolume: ' 83' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1009.2429 month: '01' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6434' quality_controlled: 0 status: public title: Isotope effect on the superfluid density in conventional and high-temperature superconductors type: journal_article volume: 83 year: '2011' ... --- _id: '8471' abstract: - lang: eng text: Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general. article_processing_charge: No article_type: original author: - first_name: Hélène full_name: Van Melckebeke, Hélène last_name: Van Melckebeke - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Julia full_name: Gath, Julia last_name: Gath - first_name: Christian full_name: Wasmer, Christian last_name: Wasmer - first_name: René full_name: Verel, René last_name: Verel - first_name: Adam full_name: Lange, Adam last_name: Lange - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Anja full_name: Böckmann, Anja last_name: Böckmann citation: ama: Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 2011;405(3):765-772. doi:10.1016/j.jmb.2010.11.004 apa: Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A., … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2010.11.004 chicago: Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology. Elsevier, 2011. https://doi.org/10.1016/j.jmb.2010.11.004. ieee: H. Van Melckebeke et al., “Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR,” Journal of Molecular Biology, vol. 405, no. 3. Elsevier, pp. 765–772, 2011. ista: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772. mla: Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology, vol. 405, no. 3, Elsevier, 2011, pp. 765–72, doi:10.1016/j.jmb.2010.11.004. short: H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H. Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772. date_created: 2020-09-18T10:11:03Z date_published: 2011-01-21T00:00:00Z date_updated: 2021-01-12T08:19:30Z day: '21' doi: 10.1016/j.jmb.2010.11.004 extern: '1' intvolume: ' 405' issue: '3' language: - iso: eng month: '01' oa_version: None page: 765-772 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 405 year: '2011' ... --- _id: '8505' abstract: - lang: eng text: The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity. article_processing_charge: No article_type: original author: - first_name: Joseph full_name: Galante, Joseph last_name: Galante - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Galante J, Kaloshin V. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 2011;159(2):275-327. doi:10.1215/00127094-1415878 apa: Galante, J., & Kaloshin, V. (2011). Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1415878 chicago: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1415878. ieee: J. Galante and V. Kaloshin, “Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action,” Duke Mathematical Journal, vol. 159, no. 2. Duke University Press, pp. 275–327, 2011. ista: Galante J, Kaloshin V. 2011. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 159(2), 275–327. mla: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal, vol. 159, no. 2, Duke University Press, 2011, pp. 275–327, doi:10.1215/00127094-1415878. short: J. Galante, V. Kaloshin, Duke Mathematical Journal 159 (2011) 275–327. date_created: 2020-09-18T10:47:41Z date_published: 2011-08-04T00:00:00Z date_updated: 2021-01-12T08:19:45Z day: '04' doi: 10.1215/00127094-1415878 extern: '1' intvolume: ' 159' issue: '2' keyword: - General Mathematics language: - iso: eng month: '08' oa_version: None page: 275-327 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' status: public title: Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2011' ... --- _id: '881' author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4' apa: Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4 chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4. ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76.' mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4. short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. date_created: 2018-12-11T11:49:00Z date_published: 2011-03-14T00:00:00Z date_updated: 2021-01-12T08:21:08Z day: '14' doi: 10.1002/9780470619902.ch4 extern: 1 month: '03' page: 57 - 76 publication: Evolution after Gene Duplication publication_status: published publisher: Wiley-Blackwell publist_id: '6766' quality_controlled: 0 status: public title: Gene Dosage and Duplication type: book_chapter year: '2011' ... --- _id: '919' abstract: - lang: eng text: Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition. author: - first_name: Thomas full_name: Angelini, Thomas last_name: Angelini - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Xavier full_name: Trepatc, Xavier last_name: Trepatc - first_name: Manuel full_name: Marquez, Manuel last_name: Marquez - first_name: Jeffrey full_name: Fredberg, Jeffrey last_name: Fredberg - first_name: David full_name: Weitz, David last_name: Weitz citation: ama: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(12):4714-4719. doi:10.1073/pnas.1010059108 apa: Angelini, T., Hannezo, E. B., Trepatc, X., Marquez, M., Fredberg, J., & Weitz, D. (2011). Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. PNAS. https://doi.org/10.1073/pnas.1010059108 chicago: Angelini, Thomas, Edouard B Hannezo, Xavier Trepatc, Manuel Marquez, Jeffrey Fredberg, and David Weitz. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America. PNAS, 2011. https://doi.org/10.1073/pnas.1010059108. ieee: T. Angelini, E. B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, and D. Weitz, “Glass-like dynamics of collective cell migration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12. PNAS, pp. 4714–4719, 2011. ista: Angelini T, Hannezo EB, Trepatc X, Marquez M, Fredberg J, Weitz D. 2011. Glass-like dynamics of collective cell migration. Proceedings of the National Academy of Sciences of the United States of America. 108(12), 4714–4719. mla: Angelini, Thomas, et al. “Glass-like Dynamics of Collective Cell Migration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 12, PNAS, 2011, pp. 4714–19, doi:10.1073/pnas.1010059108. short: T. Angelini, E.B. Hannezo, X. Trepatc, M. Marquez, J. Fredberg, D. Weitz, Proceedings of the National Academy of Sciences of the United States of America 108 (2011) 4714–4719. date_created: 2018-12-11T11:49:12Z date_published: 2011-03-22T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '22' doi: 10.1073/pnas.1010059108 extern: '1' intvolume: ' 108' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4714 - 4719 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: PNAS publist_id: '6522' quality_controlled: '1' status: public title: Glass-like dynamics of collective cell migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2011' ... --- _id: '918' abstract: - lang: eng text: We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon. acknowledgement: We thank S. Fre and M. Huygue for discussion and for showing us in vivo samples and A. Bergès for help with the manuscript. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 2011;107(7). doi:10.1103/PhysRevLett.107.078104 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2011). Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.078104 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.078104. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Instabilities of monolayered epithelia Shape and structure of villi and crypts,” Physical Review Letters, vol. 107, no. 7. American Physical Society, 2011. ista: Hannezo EB, Prost J, Joanny J. 2011. Instabilities of monolayered epithelia Shape and structure of villi and crypts. Physical Review Letters. 107(7). mla: Hannezo, Edouard B., et al. “Instabilities of Monolayered Epithelia Shape and Structure of Villi and Crypts.” Physical Review Letters, vol. 107, no. 7, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.078104. short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:49:11Z date_published: 2011-08-11T00:00:00Z date_updated: 2021-01-12T08:21:54Z day: '11' doi: 10.1103/PhysRevLett.107.078104 extern: '1' intvolume: ' 107' issue: '7' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6521' status: public title: Instabilities of monolayered epithelia Shape and structure of villi and crypts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2011' ... --- _id: '9522' abstract: - lang: eng text: Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo. article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018 apa: Zilberman, D. (2011). Balancing parental contributions in plant embryonic gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier. https://doi.org/10.1016/j.devcel.2011.05.018 chicago: Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018. ieee: D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736. ista: Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p. mla: Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:10.1016/j.devcel.2011.05.018. short: D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011. date_created: 2021-06-08T06:23:39Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-12-14T08:34:37Z day: '14' department: - _id: DaZi doi: 10.1016/j.devcel.2011.05.018 extern: '1' external_id: pmid: - '21664571' intvolume: ' 20' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2011.05.018 month: '06' oa: 1 oa_version: Published Version page: 735-736 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Balancing parental contributions in plant embryonic gene activation type: other_academic_publication user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2011' ... --- _id: '9648' abstract: - lang: eng text: In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation. alternative_title: - LNCS article_processing_charge: No author: - first_name: Rocio full_name: Gonzalez-Diaz, Rocio last_name: Gonzalez-Diaz - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Maria Jose full_name: Jimenez, Maria Jose last_name: Jimenez - first_name: Regina full_name: Poyatos, Regina last_name: Poyatos citation: ama: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: Computer Analysis of Images and Patterns. Vol 6854. Springer Nature; 2011:286-293. doi:10.1007/978-3-642-23672-3_35' apa: 'Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., & Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In Computer Analysis of Images and Patterns (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. https://doi.org/10.1007/978-3-642-23672-3_35' chicago: Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In Computer Analysis of Images and Patterns, 6854:286–93. Springer Nature, 2011. https://doi.org/10.1007/978-3-642-23672-3_35. ieee: R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in Computer Analysis of Images and Patterns, Seville, Spain, 2011, vol. 6854, pp. 286–293. ista: 'Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.' mla: Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” Computer Analysis of Images and Patterns, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:10.1007/978-3-642-23672-3_35. short: R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293. conference: end_date: 2011-08-31 location: Seville, Spain name: 'CAIP: International Conference on Computer Analysis of Images and Patterns' start_date: 2011-08-29 date_created: 2021-07-11T22:01:19Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-08-12T13:53:17Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-23672-3_35 intvolume: ' 6854' language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/11441/30766 month: '08' oa: 1 oa_version: Published Version page: 286-293 publication: Computer Analysis of Images and Patterns publication_identifier: eissn: - '16113349' isbn: - '9783642236716' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Incremental-decremental algorithm for computing AT-models and persistent homology type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 6854 year: '2011' ... --- _id: '968' abstract: - lang: eng text: A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Mikhail full_name: Skvortsov, Mikhail A last_name: Skvortsov - first_name: Andrei full_name: Varlamov, Andrei A last_name: Varlamov - first_name: Victor full_name: Galitski, Victor M last_name: Galitski citation: ama: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. Serbyn et al. Reply: Physical Review Letters. 2011;106(13). doi:10.1103/PhysRevLett.106.139702' apa: 'Serbyn, M., Skvortsov, M., Varlamov, A., & Galitski, V. (2011). Serbyn et al. Reply: Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.139702' chicago: Serbyn, Maksym, Mikhail Skvortsov, Andrei Varlamov, and Victor Galitski. “Serbyn et Al. Reply:” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.139702. ieee: M. Serbyn, M. Skvortsov, A. Varlamov, and V. Galitski, “Serbyn et al. Reply:,” Physical Review Letters, vol. 106, no. 13. American Physical Society, 2011. ista: 'Serbyn M, Skvortsov M, Varlamov A, Galitski V. 2011. Serbyn et al. Reply: Physical Review Letters. 106(13).' mla: Serbyn, Maksym, et al. “Serbyn et Al. Reply:” Physical Review Letters, vol. 106, no. 13, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.139702. short: M. Serbyn, M. Skvortsov, A. Varlamov, V. Galitski, Physical Review Letters 106 (2011). date_created: 2018-12-11T11:49:27Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '01' doi: 10.1103/PhysRevLett.106.139702 extern: 1 intvolume: ' 106' issue: '13' month: '04' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6433' quality_controlled: 0 status: public title: 'Serbyn et al. Reply:' type: journal_article volume: 106 year: '2011' ... --- _id: '3395' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data. acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474). article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418. doi:10.1111/j.1095-8312.2011.01728.x apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x. ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas,” Biological Journal of the Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011. ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2), 407–418. mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell, 2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x. short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological Journal of the Linnean Society 104 (2011) 407–418. date_created: 2018-12-11T12:03:06Z date_published: 2011-09-14T00:00:00Z date_updated: 2023-02-23T14:07:31Z day: '14' department: - _id: NiBa doi: 10.1111/j.1095-8312.2011.01728.x intvolume: ' 104' issue: '2' language: - iso: eng month: '09' oa_version: None page: 407 - 418 publication: Biological Journal of the Linnean Society publication_status: published publisher: Wiley-Blackwell publist_id: '3212' quality_controlled: '1' related_material: record: - id: '9762' relation: research_data status: public scopus_import: '1' status: public title: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 104 year: '2011' ... --- _id: '9762' abstract: - lang: eng text: Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data. article_processing_charge: No author: - first_name: Ferran full_name: Palero, Ferran id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87 last_name: Palero orcid: 0000-0002-0343-8329 - first_name: Pere full_name: Abello, Pere last_name: Abello - first_name: Enrique full_name: Macpherson, Enrique last_name: Macpherson - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Marta full_name: Pascual, Marta last_name: Pascual citation: ama: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:10.5061/dryad.299h8' apa: 'Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. https://doi.org/10.5061/dryad.299h8' chicago: 'Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. https://doi.org/10.5061/dryad.299h8.' ieee: 'F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.' ista: 'Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, 10.5061/dryad.299h8.' mla: 'Palero, Ferran, et al. Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas). IST Austria, 2011, doi:10.5061/dryad.299h8.' short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011). date_created: 2021-08-02T07:11:19Z date_published: 2011-05-12T00:00:00Z date_updated: 2023-02-23T11:25:25Z day: '12' department: - _id: NiBa doi: 10.5061/dryad.299h8 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.299h8 month: '05' oa: 1 oa_version: Published Version publisher: IST Austria related_material: record: - id: '3395' relation: used_in_publication status: public status: public title: 'Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2011' ... --- _id: '9943' abstract: - lang: eng text: Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org. article_processing_charge: No author: - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Christoph full_name: Straehle, Christoph last_name: Straehle - first_name: Ullrich full_name: Köthe, Ullrich last_name: Köthe - first_name: Fred A. full_name: Hamprecht, Fred A. last_name: Hamprecht citation: ama: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers; 2011. doi:10.1109/isbi.2011.5872394' apa: 'Sommer, C. M., Straehle, C., Köthe, U., & Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/isbi.2011.5872394' chicago: 'Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro. Institute of Electrical and Electronics Engineers, 2011. https://doi.org/10.1109/isbi.2011.5872394.' ieee: 'C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro, Chicago, Illinois, USA, 2011.' ista: 'Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.' mla: 'Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011, doi:10.1109/isbi.2011.5872394.' short: 'C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.' conference: end_date: 2011-04-02 location: Chicago, Illinois, USA name: 'ISBI: International Symposium on Biomedical Imaging' start_date: 2011-03-30 date_created: 2021-08-19T11:49:58Z date_published: 2011-06-09T00:00:00Z date_updated: 2023-02-23T14:13:38Z day: '09' department: - _id: Bio doi: 10.1109/isbi.2011.5872394 extern: '1' keyword: - image segmentation - biomedical imaging - three dimensional displays - neurons - retina - observers - image color analysis language: - iso: eng main_file_link: - open_access: '1' url: https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit month: '06' oa: 1 oa_version: Preprint publication: '2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro' publication_identifier: eissn: - 1945-8452 isbn: - 978-1-4244-4127-3 issn: - 1945-7928 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' status: public title: 'Ilastik: Interactive learning and segmentation toolkit' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2011' ... --- _id: '10907' abstract: - lang: eng text: This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts. acknowledgement: This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13. alternative_title: - LNCS article_processing_charge: No author: - first_name: Nicole M. full_name: Artner, Nicole M. last_name: Artner - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Walter G. full_name: Kropatsch, Walter G. last_name: Kropatsch citation: ama: 'Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22' apa: 'Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22' chicago: 'Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.' ieee: N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in Graph-Based Representations in Pattern Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224. ista: 'Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224.' mla: Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22. short: N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224. conference: end_date: 2011-05-20 location: Münster, Germany name: 'GbRPR: Graph-based Representations in Pattern Recognition' start_date: 2011-05-18 date_created: 2022-03-21T08:08:35Z date_published: 2011-06-01T00:00:00Z date_updated: 2023-09-05T14:10:15Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-20844-7_22 editor: - first_name: Xiaoyi full_name: Jiang, Xiaoyi last_name: Jiang - first_name: Miquel full_name: Ferrer, Miquel last_name: Ferrer - first_name: Andrea full_name: Torsello, Andrea last_name: Torsello intvolume: ' 6658' language: - iso: eng month: '06' oa_version: None page: 215-224 place: Berlin, Heidelberg publication: Graph-Based Representations in Pattern Recognition publication_identifier: eisbn: - '9783642208447' eissn: - 1611-3349 isbn: - '9783642208430' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNIP status: public title: Spatio-temporal extraction of articulated models in a graph pyramid type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6658 year: '2011' ... --- _id: '3275' abstract: - lang: eng text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. ' acknowledgement: "I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Schumann, Kathrin id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F last_name: Schumann citation: ama: Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011. apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria. chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011. ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011. ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria. mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration. Institute of Science and Technology Austria, 2011. short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011. date_created: 2018-12-11T12:02:24Z date_published: 2011-03-01T00:00:00Z date_updated: 2023-09-07T11:31:48Z day: '01' ddc: - '570' - '579' degree_awarded: PhD department: - _id: MiSi file: - access_level: closed checksum: e69eee6252660f0b694a2ea8923ddc72 content_type: application/pdf creator: dernst date_created: 2019-03-26T08:12:21Z date_updated: 2020-07-14T12:46:06Z file_id: '6177' file_name: 2011_Thesis_Kathrin_Schumann.pdf file_size: 4487708 relation: main_file - access_level: open_access checksum: 71727d63f424b5b446f68f4b87ecadc0 content_type: application/pdf creator: dernst date_created: 2021-02-22T11:24:30Z date_updated: 2021-02-22T11:24:30Z file_id: '9175' file_name: 2011_Thesis_Schumann_noS.pdf file_size: 4313127 relation: main_file success: 1 file_date_updated: 2021-02-22T11:24:30Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '141' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '3371' pubrep_id: '11' status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: The role of chemotactic gradients in dendritic cell migration type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2011' ... --- _id: '3273' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 citation: ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011. apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria. chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011. ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011. ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria. mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors. Institute of Science and Technology Austria, 2011. short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011. date_created: 2018-12-11T12:02:23Z date_published: 2011-12-12T00:00:00Z date_updated: 2023-09-07T11:30:16Z day: '12' degree_awarded: PhD department: - _id: CaHe language: - iso: eng month: '12' oa_version: None publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '3373' status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2011' ... --- _id: '3238' abstract: - lang: eng text: We construct efficient authentication protocols and message-authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work - starting with the HB protocol of Hopper and Blum in 2001 - until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle (MIM) attacks. A MAC implies such a (two-round) protocol. © 2011 International Association for Cryptologic Research acknowledgement: The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: David full_name: Cash, David last_name: Cash - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain - first_name: Daniele full_name: Venturi, Daniele last_name: Venturi citation: ama: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:10.1007/978-3-642-20465-4_3' apa: 'Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., & Venturi, D. (2011). Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia: Springer. https://doi.org/10.1007/978-3-642-20465-4_3' chicago: Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer, 2011. https://doi.org/10.1007/978-3-642-20465-4_3. ieee: 'E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication from hard learning problems,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26.' ista: 'Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 6632, 7–26.' mla: Kiltz, Eike, et al. Efficient Authentication from Hard Learning Problems. Vol. 6632, Springer, 2011, pp. 7–26, doi:10.1007/978-3-642-20465-4_3. short: E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011, pp. 7–26. conference: end_date: 2011-05-19 location: Tallinn, Estonia name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2011-05-15 date_created: 2018-12-11T12:02:11Z date_published: 2011-05-01T00:00:00Z date_updated: 2023-09-20T11:20:57Z day: '01' doi: 10.1007/978-3-642-20465-4_3 extern: '1' intvolume: ' 6632' language: - iso: eng month: '05' oa_version: None page: 7 - 26 publication_status: published publisher: Springer publist_id: '3442' quality_controlled: '1' related_material: record: - id: '1187' relation: later_version status: public status: public title: Efficient authentication from hard learning problems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6632 year: '2011' ... --- _id: '3392' abstract: - lang: eng text: Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation. article_processing_charge: No article_type: original author: - first_name: Silvia full_name: Soriano, Silvia last_name: Soriano - first_name: Miroslav full_name: Hons, Miroslav last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Kathrin full_name: Schumann, Kathrin last_name: Schumann - first_name: Varsha full_name: Kumar, Varsha last_name: Kumar - first_name: Timo full_name: Dennier, Timo last_name: Dennier - first_name: Ruth full_name: Lyck, Ruth last_name: Lyck - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Jens full_name: Stein, Jens last_name: Stein citation: ama: Soriano S, Hons M, Schumann K, et al. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 2011;187(5):2356-2364. doi:10.4049/jimmunol.1100935 apa: Soriano, S., Hons, M., Schumann, K., Kumar, V., Dennier, T., Lyck, R., … Stein, J. (2011). In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. American Association of Immunologists. https://doi.org/10.4049/jimmunol.1100935 chicago: Soriano, Silvia, Miroslav Hons, Kathrin Schumann, Varsha Kumar, Timo Dennier, Ruth Lyck, Michael K Sixt, and Jens Stein. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology. American Association of Immunologists, 2011. https://doi.org/10.4049/jimmunol.1100935. ieee: S. Soriano et al., “In vivo analysis of uropod function during physiological T cell trafficking,” Journal of Immunology, vol. 187, no. 5. American Association of Immunologists, pp. 2356–2364, 2011. ista: Soriano S, Hons M, Schumann K, Kumar V, Dennier T, Lyck R, Sixt MK, Stein J. 2011. In vivo analysis of uropod function during physiological T cell trafficking. Journal of Immunology. 187(5), 2356–2364. mla: Soriano, Silvia, et al. “In Vivo Analysis of Uropod Function during Physiological T Cell Trafficking.” Journal of Immunology, vol. 187, no. 5, American Association of Immunologists, 2011, pp. 2356–64, doi:10.4049/jimmunol.1100935. short: S. Soriano, M. Hons, K. Schumann, V. Kumar, T. Dennier, R. Lyck, M.K. Sixt, J. Stein, Journal of Immunology 187 (2011) 2356–2364. date_created: 2018-12-11T12:03:04Z date_published: 2011-09-01T00:00:00Z date_updated: 2023-10-10T13:14:59Z day: '01' department: - _id: MiSi doi: 10.4049/jimmunol.1100935 intvolume: ' 187' issue: '5' language: - iso: eng month: '09' oa_version: None page: 2356 - 2364 publication: Journal of Immunology publication_identifier: eissn: - 1550-6606 issn: - 0022-1767 publication_status: published publisher: American Association of Immunologists publist_id: '3215' quality_controlled: '1' scopus_import: '1' status: public title: In vivo analysis of uropod function during physiological T cell trafficking type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 187 year: '2011' ... --- _id: '3163' abstract: - lang: eng text: We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds. author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.' apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems.' chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011. ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.' ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.' mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction. Neural Information Processing Systems, 2011. short: C. Lampert, in:, Neural Information Processing Systems, 2011. conference: end_date: 2011-12-14 location: Granada, Spain name: 'NIPS: Neural Information Processing Systems' start_date: 2011-12-12 date_created: 2018-12-11T12:01:45Z date_published: 2011-12-01T00:00:00Z date_updated: 2023-10-17T11:47:35Z day: '01' department: - _id: ChLa language: - iso: eng month: '12' oa_version: None publication_status: published publisher: Neural Information Processing Systems publist_id: '3522' quality_controlled: '1' related_material: record: - id: '3322' relation: later_version status: public scopus_import: 1 status: public title: Maximum margin multi-label structured prediction type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ...