--- _id: '2270' abstract: - lang: eng text: "Representation languages for coalitional games are a key research area in algorithmic game theory. There is an inher-\r\nent tradeoff between how general a language is, allowing it to capture more elaborate games, and how hard \ it is computationally to optimize and solve such games. One prominent such \ language is the simple yet expressive\r\nWeighted Graph Games (WGGs) representation (Deng and Papadimitriou 1994), which maintains knowledge about synergies between agents in the form of an edge weighted graph. We consider the problem of finding \ the optimal coalition structure in WGGs. The agents in such games are vertices in a graph, and the value of a coalition is the sum of the weights of the edges present between coalition members. The optimal coalition structure is a partition of the agents to coalitions, that maximizes the sum of utilities obtained by the coalitions. We show that finding the optimal coalition structure is not only hard for general graphs, but is also intractable for restricted families such as planar graphs which are amenable for many other combinatorial problems. \ We then provide algorithms with constant factor approximations for planar, minorfree and bounded degree graphs." author: - first_name: Yoram full_name: Bachrach, Yoram last_name: Bachrach - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Morteza full_name: Zadimoghaddam, Morteza last_name: Zadimoghaddam citation: ama: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. Optimal Coalition Structures in Cooperative Graph Games. In: AAAI Press; 2013:81-87.' apa: 'Bachrach, Y., Kohli, P., Kolmogorov, V., & Zadimoghaddam, M. (2013). Optimal Coalition Structures in Cooperative Graph Games (pp. 81–87). Presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States: AAAI Press.' chicago: Bachrach, Yoram, Pushmeet Kohli, Vladimir Kolmogorov, and Morteza Zadimoghaddam. “Optimal Coalition Structures in Cooperative Graph Games,” 81–87. AAAI Press, 2013. ieee: 'Y. Bachrach, P. Kohli, V. Kolmogorov, and M. Zadimoghaddam, “Optimal Coalition Structures in Cooperative Graph Games,” presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States, 2013, pp. 81–87.' ista: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. 2013. Optimal Coalition Structures in Cooperative Graph Games. AAAI: Conference on Artificial Intelligence, 81–87.' mla: Bachrach, Yoram, et al. Optimal Coalition Structures in Cooperative Graph Games. AAAI Press, 2013, pp. 81–87. short: Y. Bachrach, P. Kohli, V. Kolmogorov, M. Zadimoghaddam, in:, AAAI Press, 2013, pp. 81–87. conference: end_date: 2013-07-18 location: Bellevue, WA, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2013-07-14 date_created: 2018-12-11T11:56:41Z date_published: 2013-12-31T00:00:00Z date_updated: 2021-01-12T06:56:25Z day: '31' department: - _id: VlKo external_id: arxiv: - '1108.5248' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1108.5248 month: '12' oa: 1 oa_version: None page: 81-87 publication_status: published publisher: AAAI Press publist_id: '4674' quality_controlled: '1' status: public title: Optimal Coalition Structures in Cooperative Graph Games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2273' abstract: - lang: eng text: We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. We present such a generalization for the case of higher-order graphical models, and test it on several real-world problems with promising results. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Reweighted Message Passing Revisited. IST Austria; 2013. apa: Kolmogorov, V. (2013). Reweighted message passing revisited. IST Austria. chicago: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013. ieee: V. Kolmogorov, Reweighted message passing revisited. IST Austria, 2013. ista: Kolmogorov V. 2013. Reweighted message passing revisited, IST Austria,p. mla: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013. short: V. Kolmogorov, Reweighted Message Passing Revisited, IST Austria, 2013. date_created: 2018-12-11T11:56:42Z date_published: 2013-09-22T00:00:00Z date_updated: 2019-01-24T13:07:32Z day: '22' department: - _id: VlKo extern: 0 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5655 month: '09' oa: 1 publication_status: published publisher: IST Austria publist_id: '4671' quality_controlled: 0 status: public title: Reweighted message passing revisited type: report year: '2013' ... --- _id: '2278' abstract: - lang: eng text: It is firmly established that interactions between neurons and glia are fundamental across species for the correct establishment of a functional brain. Here, we found that the glia of the Drosophila larval brain display an essential non-autonomous role during the development of the optic lobe. The optic lobe develops from neuroepithelial cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc) is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal transduction pathway at the leading edge of a proneural wave that sweeps from medial to lateral neuroepithelium, promoting this switch. This process is tightly regulated by the tissue-autonomous function within the neuroepithelium of multiple signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial cells. This complex is crucial for interactions between glia and neuroepithelial cells during optic lobe development. Ser is tissue-autonomously required in the glia where it activates Notch to regulate its proliferation, and non-autonomously in the neuroepithelium where Ser induces Notch signaling to avoid the premature activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different Notch activity reporters showed very different expression patterns in the glia and in the neuroepithelium, suggesting the existence of tissue-specific factors that promote the expression of particular Notch target genes or/and a reporter response dependent on different thresholds of Notch signaling. author: - first_name: Raquel full_name: Pérez Gómez, Raquel last_name: Pérez Gómez - first_name: Jana full_name: Slovakova, Jana id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87 last_name: Slovakova - first_name: Noemí full_name: Rives Quinto, Noemí last_name: Rives Quinto - first_name: Alena full_name: Krejčí, Alena last_name: Krejčí - first_name: Ana full_name: Carmena, Ana last_name: Carmena citation: ama: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 2013;126(21):4873-4884. doi:10.1242/jcs.125617 apa: Pérez Gómez, R., Slovakova, J., Rives Quinto, N., Krejčí, A., & Carmena, A. (2013). A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.125617 chicago: Pérez Gómez, Raquel, Jana Slovakova, Noemí Rives Quinto, Alena Krejčí, and Ana Carmena. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.125617. ieee: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, and A. Carmena, “A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development,” Journal of Cell Science, vol. 126, no. 21. Company of Biologists, pp. 4873–4884, 2013. ista: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. 2013. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 126(21), 4873–4884. mla: Pérez Gómez, Raquel, et al. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science, vol. 126, no. 21, Company of Biologists, 2013, pp. 4873–84, doi:10.1242/jcs.125617. short: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, A. Carmena, Journal of Cell Science 126 (2013) 4873–4884. date_created: 2018-12-11T11:56:43Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:56:29Z day: '01' department: - _id: CaHe doi: 10.1242/jcs.125617 intvolume: ' 126' issue: '21' language: - iso: eng month: '11' oa_version: None page: 4873 - 4884 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '4658' quality_controlled: '1' scopus_import: 1 status: public title: A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 126 year: '2013' ... --- _id: '2276' abstract: - lang: eng text: The problem of minimizing the Potts energy function frequently occurs in computer vision applications. One way to tackle this NP-hard problem was proposed by Kovtun [19, 20]. It identifies a part of an optimal solution by running k maxflow computations, where k is the number of labels. The number of “labeled” pixels can be significant in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce the runtime to O (log k) maxflow computations (or one parametric maxflow computation). Furthermore, the output of our algorithm allows to speed-up the subsequent alpha expansion for the unlabeled part, or can be used as it is for time-critical applications. To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7] for Tree Metrics . We also show a connection to k-submodular functions from combinatorial optimization, and discuss k-submodular relaxations for general energy functions. author: - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular functions. In: IEEE; 2013:2320-2327. doi:10.1109/ICCV.2013.288' apa: 'Gridchyn, I., & Kolmogorov, V. (2013). Potts model, parametric maxflow and k-submodular functions (pp. 2320–2327). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.288' chicago: Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow and k-Submodular Functions,” 2320–27. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.288. ieee: 'I. Gridchyn and V. Kolmogorov, “Potts model, parametric maxflow and k-submodular functions,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 2320–2327.' ista: 'Gridchyn I, Kolmogorov V. 2013. Potts model, parametric maxflow and k-submodular functions. ICCV: International Conference on Computer Vision, 2320–2327.' mla: Gridchyn, Igor, and Vladimir Kolmogorov. Potts Model, Parametric Maxflow and k-Submodular Functions. IEEE, 2013, pp. 2320–27, doi:10.1109/ICCV.2013.288. short: I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:43Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:28Z day: '01' department: - _id: JoCs - _id: VlKo doi: 10.1109/ICCV.2013.288 external_id: arxiv: - '1310.1771' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.1771 month: '12' oa: 1 oa_version: Preprint page: 2320 - 2327 publication_status: published publisher: IEEE publist_id: '4668' quality_controlled: '1' status: public title: Potts model, parametric maxflow and k-submodular functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2280' abstract: - lang: eng text: The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented. author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Stephen full_name: Wright, Stephen last_name: Wright citation: ama: Uhler C, Wright S. Packing ellipsoids with overlap. SIAM Review. 2013;55(4):671-706. doi:10.1137/120872309 apa: Uhler, C., & Wright, S. (2013). Packing ellipsoids with overlap. SIAM Review. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120872309 chicago: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120872309. ieee: C. Uhler and S. Wright, “Packing ellipsoids with overlap,” SIAM Review, vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706, 2013. ista: Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706. mla: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013, pp. 671–706, doi:10.1137/120872309. short: C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706. date_created: 2018-12-11T11:56:44Z date_published: 2013-11-07T00:00:00Z date_updated: 2021-01-12T06:56:30Z day: '07' department: - _id: CaUh doi: 10.1137/120872309 external_id: arxiv: - '1204.0235' intvolume: ' 55' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.0235 month: '11' oa: 1 oa_version: Preprint page: 671 - 706 publication: SIAM Review publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '4655' quality_controlled: '1' scopus_import: 1 status: public title: Packing ellipsoids with overlap type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2013' ... --- _id: '2287' abstract: - lang: eng text: Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465 apa: Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465 chicago: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465. ieee: M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013. ista: Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639. mla: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465. short: M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639. date_created: 2018-12-11T11:56:47Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:56:32Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1002/ece3.465 file: - access_level: open_access checksum: b5531bab4c0dec396bf5c8497fe178bf content_type: application/pdf creator: system date_created: 2018-12-12T10:17:35Z date_updated: 2020-07-14T12:45:37Z file_id: '5290' file_name: IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf file_size: 626949 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version page: 629 - 639 publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '4644' pubrep_id: '416' quality_controlled: '1' scopus_import: 1 status: public title: The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2282' abstract: - lang: eng text: Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: 'This work was supported by the IST Austria and MPI-CBG ' author: - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Jonas full_name: Ranft, Jonas last_name: Ranft - first_name: Thomas full_name: Risler, Thomas last_name: Risler - first_name: Nicolas full_name: Minc, Nicolas last_name: Minc - 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 citation: ama: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 2013;15:1405-1414. doi:10.1038/ncb2869 apa: Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., & Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2869 chicago: Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2869. ieee: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” Nature Cell Biology, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013. ista: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414. mla: Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:10.1038/ncb2869. short: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414. date_created: 2018-12-11T11:56:45Z date_published: 2013-11-10T00:00:00Z date_updated: 2023-02-21T17:02:44Z day: '10' department: - _id: CaHe doi: 10.1038/ncb2869 intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: http://hal.upmc.fr/hal-00983313/ month: '11' oa: 1 oa_version: Submitted Version page: 1405 - 1414 project: - _id: 252ABD0A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 930-B20 name: Control of Epithelial Cell Layer Spreading in Zebrafish publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '4652' quality_controlled: '1' related_material: record: - id: '1403' relation: dissertation_contains status: public scopus_import: 1 status: public title: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2283' abstract: - lang: eng text: Pathogens exert a strong selection pressure on organisms to evolve effective immune defences. In addition to individual immunity, social organisms can act cooperatively to produce collective defences. In many ant species, queens have the option to found a colony alone or in groups with other, often unrelated, conspecifics. These associations are transient, usually lasting only as long as each queen benefits from the presence of others. In fact, once the first workers emerge, queens fight to the death for dominance. One potential advantage of co-founding may be that queens benefit from collective disease defences, such as mutual grooming, that act against common soil pathogens. We test this hypothesis by exposing single and co-founding queens to a fungal parasite, in order to assess whether queens in co-founding associations have improved survival. Surprisingly, co-foundresses exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative disease defences, and consequently, we find no direct benefit of multiple queens on survival. However, an indirect benefit was observed, with parasite-exposed queens producing more brood when they co-founded, than when they were alone. We suggest this is due to a trade-off between reproduction and immunity. Additionally, we report an extraordinary ability of the queens to tolerate an infection for long periods after parasite exposure. Our study suggests that there are no social immunity benefits for co-founding ant queens, but that in parasite-rich environments, the presence of additional queens may nevertheless improve the chances of colony founding success. author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: William full_name: Hughes, William last_name: Hughes - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown citation: ama: 'Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 2013;100(12):1125-1136. doi:10.1007/s00114-013-1115-5' apa: 'Pull, C., Hughes, W., & Brown, M. (2013). Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-013-1115-5' chicago: 'Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften. Springer, 2013. https://doi.org/10.1007/s00114-013-1115-5.' ieee: 'C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ,” Naturwissenschaften, vol. 100, no. 12. Springer, pp. 1125–1136, 2013.' ista: 'Pull C, Hughes W, Brown M. 2013. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 100(12), 1125–1136.' mla: 'Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften, vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:10.1007/s00114-013-1115-5.' short: C. Pull, W. Hughes, M. Brown, Naturwissenschaften 100 (2013) 1125–1136. date_created: 2018-12-11T11:56:45Z date_published: 2013-11-14T00:00:00Z date_updated: 2021-01-12T06:56:31Z day: '14' department: - _id: SyCr doi: 10.1007/s00114-013-1115-5 intvolume: ' 100' issue: '12' language: - iso: eng month: '11' oa_version: None page: 1125 - 1136 publication: Naturwissenschaften publication_status: published publisher: Springer publist_id: '4649' quality_controlled: '1' scopus_import: 1 status: public title: 'Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2013' ... --- _id: '2286' abstract: - lang: eng text: The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation. author: - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 - 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 citation: ama: Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. EMBO Journal. 2013;32(21):2783-2784. doi:10.1038/emboj.2013.225 apa: Campinho, P., & Heisenberg, C.-P. J. (2013). The force and effect of cell proliferation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.225 chicago: Campinho, Pedro, and Carl-Philipp J Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.225. ieee: P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,” EMBO Journal, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013. ista: Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation. EMBO Journal. 32(21), 2783–2784. mla: Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal, vol. 32, no. 21, Wiley-Blackwell, 2013, pp. 2783–84, doi:10.1038/emboj.2013.225. short: P. Campinho, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 2783–2784. date_created: 2018-12-11T11:56:46Z date_published: 2013-10-04T00:00:00Z date_updated: 2021-01-12T06:56:32Z day: '04' department: - _id: CaHe doi: 10.1038/emboj.2013.225 external_id: pmid: - '24097062' intvolume: ' 32' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/ month: '10' oa: 1 oa_version: Submitted Version page: 2783 - 2784 pmid: 1 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '4645' quality_controlled: '1' scopus_import: 1 status: public title: The force and effect of cell proliferation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2289' abstract: - lang: eng text: Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness, which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments. author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Henzinger TA. Quantitative reactive modeling and verification. Computer Science Research and Development. 2013;28(4):331-344. doi:10.1007/s00450-013-0251-7 apa: Henzinger, T. A. (2013). Quantitative reactive modeling and verification. Computer Science Research and Development. Springer. https://doi.org/10.1007/s00450-013-0251-7 chicago: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development. Springer, 2013. https://doi.org/10.1007/s00450-013-0251-7. ieee: T. A. Henzinger, “Quantitative reactive modeling and verification,” Computer Science Research and Development, vol. 28, no. 4. Springer, pp. 331–344, 2013. ista: Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer Science Research and Development. 28(4), 331–344. mla: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development, vol. 28, no. 4, Springer, 2013, pp. 331–44, doi:10.1007/s00450-013-0251-7. short: T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344. date_created: 2018-12-11T11:56:47Z date_published: 2013-10-05T00:00:00Z date_updated: 2021-01-12T06:56:33Z day: '05' ddc: - '000' department: - _id: ToHe doi: 10.1007/s00450-013-0251-7 ec_funded: 1 file: - access_level: open_access checksum: f117a00f9f046165bfa95595681e08a0 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:51Z date_updated: 2020-07-14T12:45:37Z file_id: '5308' file_name: IST-2016-626-v1+1_s00450-013-0251-7.pdf file_size: 570361 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 28' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 331 - 344 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Computer Science Research and Development publication_status: published publisher: Springer publist_id: '4642' pubrep_id: '626' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative reactive modeling and verification tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2013' ... --- _id: '2290' abstract: - lang: eng text: The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development. author: - first_name: Yohann full_name: Boutté, Yohann last_name: Boutté - first_name: Kristoffer full_name: Jonsson, Kristoffer last_name: Jonsson - first_name: Heather full_name: Mcfarlane, Heather last_name: Mcfarlane - first_name: Errin full_name: Johnson, Errin last_name: Johnson - first_name: Delphine full_name: Gendre, Delphine last_name: Gendre - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lacey full_name: Samuels, Lacey last_name: Samuels - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Rishikesh full_name: Bhalerao, Rishikesh last_name: Bhalerao citation: ama: Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264. doi:10.1073/pnas.1309057110 apa: Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R., … Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110 chicago: Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110. ieee: Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National Academy of Sciences, pp. 16259–16264, 2013. ista: Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J, Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264. mla: Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110. short: Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J. Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264. date_created: 2018-12-11T11:56:48Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:56:33Z day: '01' department: - _id: JiFr doi: 10.1073/pnas.1309057110 external_id: pmid: - '24043780' intvolume: ' 110' issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/ month: '10' oa: 1 oa_version: Submitted Version page: 16259 - 16264 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4639' quality_controlled: '1' scopus_import: 1 status: public title: ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2294' abstract: - lang: eng text: "In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.\r\nWhile the system is designed to solve an actual problem in biological research, we believe that the principle underly-\r\ning it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.\r\nIn our biological setup, the information sources are the shape and the staining patterns of embryo images. We show\r\nexperimentally that while neither of the methods \ can be used by itself to achieve satisfactory results, their combina-\r\ntion achieves prediction quality comparable to human performance." author: - first_name: Tomas full_name: Kazmar, Tomas last_name: Kazmar - first_name: Evgeny full_name: Kvon, Evgeny last_name: Kvon - first_name: Alexander full_name: Stark, Alexander last_name: Stark - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139' apa: 'Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139' chicago: Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139. ieee: 'T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation using Label Propagation,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013.' ista: 'Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision.' mla: Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation. IEEE, 2013, doi:10.1109/ICCV.2013.139. short: T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:35Z day: '01' department: - _id: ChLa doi: 10.1109/ICCV.2013.139 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://www.cv-foundation.org/openaccess/ICCV2013.py month: '12' oa: 1 oa_version: Submitted Version project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: IEEE publist_id: '4634' quality_controlled: '1' scopus_import: 1 status: public title: Drosophila Embryo Stage Annotation using Label Propagation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2292' abstract: - lang: eng text: This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence. alternative_title: - LNCS citation: ama: Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science 2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2 apa: 'Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2' chicago: Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40313-2. ieee: K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer Science 2013, vol. 8087. Springer, 2013, p. VI-854. ista: Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p. mla: Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2. short: K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013. conference: end_date: 2013-08-30 location: Klosterneuburg, Austria name: 'MFCS: Mathematical Foundations of Computer Science' start_date: 2013-08-26 date_created: 2018-12-11T11:56:48Z date_published: 2013-08-08T00:00:00Z date_updated: 2020-08-11T10:09:45Z day: '08' department: - _id: KrCh doi: 10.1007/978-3-642-40313-2 editor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jiri full_name: Sgall, Jiri last_name: Sgall intvolume: ' 8087' language: - iso: eng month: '08' oa_version: None page: VI - 854 publication_identifier: isbn: - 978-3-642-40312-5 publication_status: published publisher: Springer publist_id: '4636' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Mathematical Foundations of Computer Science 2013 type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8087 year: '2013' ... --- _id: '2293' abstract: - lang: eng text: Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results. author: - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107' apa: 'Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107' chicago: Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107. ieee: 'V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged information,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 825–832.' ista: 'Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832.' mla: Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information. IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107. short: V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2023-02-23T10:36:41Z day: '01' department: - _id: ChLa doi: 10.1109/ICCV.2013.107 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf month: '12' oa: 1 oa_version: Submitted Version page: 825 - 832 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: IEEE publist_id: '4635' quality_controlled: '1' scopus_import: 1 status: public title: Learning to rank using privileged information type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2291' abstract: - lang: eng text: "Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. \r\n" author: - first_name: Anna full_name: Ferrara, Anna last_name: Ferrara - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Bogdan full_name: Warinschi, Bogdan last_name: Warinschi citation: ama: 'Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:10.1109/CSF.2013.15' apa: 'Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15' chicago: Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15. ieee: 'A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United States, 2013, pp. 115–129.' ista: 'Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.' mla: Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp. 115–29, doi:10.1109/CSF.2013.15. short: A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129. conference: end_date: 2013-09-28 location: New Orleans, LA, United States name: 'CSF: Computer Security Foundations' start_date: 2013-09-26 date_created: 2018-12-11T11:56:48Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:56:34Z day: '01' department: - _id: KrPi doi: 10.1109/CSF.2013.15 language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2013/492 month: '09' oa: 1 oa_version: Submitted Version page: 115 - 129 publication_status: published publisher: IEEE publist_id: '4637' quality_controlled: '1' scopus_import: 1 status: public title: Cryptographically enforced RBAC type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2288' abstract: - lang: eng text: This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms. alternative_title: - LNCS citation: ama: Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology. Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6 apa: 'Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6' chicago: Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6. ieee: A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology, vol. 8130. Springer, 2013. ista: Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p. mla: Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6. short: A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013. conference: end_date: 2013-09-24 location: Klosterneuburg, Austria name: 'CMSB: Computational Methods in Systems Biology' start_date: 2013-09-22 date_created: 2018-12-11T11:56:47Z date_published: 2013-07-01T00:00:00Z date_updated: 2019-08-02T12:37:44Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-642-40708-6 editor: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 intvolume: ' 8130' language: - iso: eng month: '07' oa_version: None publication_identifier: isbn: - 978-3-642-40707-9 publication_status: published publisher: Springer publist_id: '4643' quality_controlled: '1' status: public title: Computational Methods in Systems Biology type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8130 year: '2013' ... --- _id: '2298' abstract: - lang: eng text: "We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.\r\n" alternative_title: - LNCS author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Mihaela full_name: Sighireanu, Mihaela last_name: Sighireanu citation: ama: 'Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10' apa: 'Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10' chicago: Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10. ieee: 'C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.' ista: 'Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.' mla: Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures. Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10. short: C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171. conference: end_date: 2013-06-22 location: Seattle, WA, United States name: 'SAS: Static Analysis Symposium' start_date: 2013-06-20 date_created: 2018-12-11T11:56:50Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:36Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1007/978-3-642-38856-9_10 ec_funded: 1 file: - access_level: open_access checksum: 907edd33a5892e3af093365f1fd57ed7 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:36Z date_updated: 2020-07-14T12:45:37Z file_id: '4824' file_name: IST-2014-196-v1+1_sas13.pdf file_size: 299004 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 7935' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 150 - 171 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '4630' pubrep_id: '196' quality_controlled: '1' scopus_import: 1 status: public title: Local shape analysis for overlaid data structures type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7935 year: '2013' ... --- _id: '2299' abstract: - lang: eng text: 'The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.' author: - first_name: Yashdeep full_name: Godhal, Yashdeep id: 5B547124-EB61-11E9-8887-89D9C04DBDF5 last_name: Godhal - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 2013;15(5-6):585-601. doi:10.1007/s10009-011-0207-9' apa: 'Godhal, Y., Chatterjee, K., & Henzinger, T. A. (2013). Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-011-0207-9' chicago: 'Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer. Springer, 2013. https://doi.org/10.1007/s10009-011-0207-9.' ieee: 'Y. Godhal, K. Chatterjee, and T. A. Henzinger, “Synthesis of AMBA AHB from formal specification: A case study,” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6. Springer, pp. 585–601, 2013.' ista: 'Godhal Y, Chatterjee K, Henzinger TA. 2013. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 15(5–6), 585–601.' mla: 'Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:10.1007/s10009-011-0207-9.' short: Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 15 (2013) 585–601. date_created: 2018-12-11T11:56:51Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:56:37Z day: '01' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1007/s10009-011-0207-9 file: - access_level: open_access checksum: 57b06a732dd8d6349190dba6b5b0d33b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:53Z date_updated: 2020-07-14T12:45:37Z file_id: '4910' file_name: IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf file_size: 277372 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 15' issue: 5-6 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 585 - 601 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: International Journal on Software Tools for Technology Transfer publication_status: published publisher: Springer publist_id: '4629' pubrep_id: '87' quality_controlled: '1' scopus_import: 1 status: public title: 'Synthesis of AMBA AHB from formal specification: A case study' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2297' abstract: - lang: eng text: We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation. author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Seiringer R. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 2013;8(2):185-232. doi:10.1007/s11537-013-1264-5' apa: 'Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. Springer. https://doi.org/10.1007/s11537-013-1264-5' chicago: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics. Springer, 2013. https://doi.org/10.1007/s11537-013-1264-5.' ieee: 'R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,” Japanese Journal of Mathematics, vol. 8, no. 2. Springer, pp. 185–232, 2013.' ista: 'Seiringer R. 2013. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 8(2), 185–232.' mla: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics, vol. 8, no. 2, Springer, 2013, pp. 185–232, doi:10.1007/s11537-013-1264-5.' short: R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232. date_created: 2018-12-11T11:56:50Z date_published: 2013-09-24T00:00:00Z date_updated: 2021-01-12T06:56:36Z day: '24' department: - _id: RoSe doi: 10.1007/s11537-013-1264-5 external_id: arxiv: - '0908.3686' intvolume: ' 8' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0908.3686 month: '09' oa: 1 oa_version: Preprint page: 185 - 232 publication: Japanese Journal of Mathematics publication_status: published publisher: Springer publist_id: '4631' quality_controlled: '1' scopus_import: 1 status: public title: 'Hot topics in cold gases: A mathematical physics perspective' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2306' abstract: - lang: ger text: Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind. alternative_title: - Bibliotheks- und Informationspraxis article_processing_charge: No author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Adrian full_name: Pohl, Adrian last_name: Pohl citation: ama: Danowski P, Pohl A. (Open) Linked Data in Bibliotheken. Vol 50. De Gruyter; 2013. doi:10.1515/9783110278736 apa: Danowski, P., & Pohl, A. (2013). (Open) Linked Data in Bibliotheken (Vol. 50). De Gruyter. https://doi.org/10.1515/9783110278736 chicago: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50. De Gruyter, 2013. https://doi.org/10.1515/9783110278736. ieee: P. Danowski and A. Pohl, (Open) Linked Data in Bibliotheken, vol. 50. De Gruyter, 2013. ista: Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p. mla: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50, De Gruyter, 2013, doi:10.1515/9783110278736. short: P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013. date_created: 2018-12-11T11:56:53Z date_published: 2013-09-13T00:00:00Z date_updated: 2021-12-21T12:17:19Z day: '13' ddc: - '020' department: - _id: E-Lib doi: 10.1515/9783110278736 file: - access_level: open_access checksum: 807a408bbee519d792702828a32c6e85 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:49Z date_updated: 2020-07-14T12:45:38Z file_id: '4774' file_name: IST-2017-725-v1+1_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Frontmatter.pdf file_size: 67731 relation: main_file - access_level: open_access checksum: 587e95c2ba24307a5a5d5bd1579429d9 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:50Z date_updated: 2020-07-14T12:45:38Z file_id: '4775' file_name: IST-2017-725-v1+2_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Inhalt.pdf file_size: 43563 relation: main_file - access_level: open_access checksum: dbcada36bb32d725d9838615706e700f content_type: application/pdf creator: system date_created: 2018-12-12T10:09:51Z date_updated: 2020-07-14T12:45:38Z file_id: '4776' file_name: IST-2017-725-v1+3_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Linked_Open_Data_in_der_Bibliothekswelt__Grundlagen_und_Überblick.pdf file_size: 11318599 relation: main_file - access_level: open_access checksum: 5235712bf0a49ccc8c2cb4f6c2560d43 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:52Z date_updated: 2020-07-14T12:45:38Z file_id: '4777' file_name: IST-2017-725-v1+4_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Vokabulare_für_bibliographische_Daten.pdf file_size: 330210 relation: main_file - access_level: open_access checksum: d851cc91f705da80617ac7df33c1c0e1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:53Z date_updated: 2020-07-14T12:45:38Z file_id: '4778' file_name: IST-2017-725-v1+5_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_FRBR,_Serials_und_CIDOC_CRM_-_Modellierung_von_fortlaufenden_Sammelwerken_unter_Verwendung_von_FRBRoo.pdf file_size: 10652088 relation: main_file - access_level: open_access checksum: 4e77b182692c58e50fc5251bf23cc584 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:54Z date_updated: 2020-07-14T12:45:38Z file_id: '4779' file_name: IST-2017-725-v1+6_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Die_Provenienz_von_Linked_Data.pdf file_size: 6125273 relation: main_file - access_level: open_access checksum: 3debae38064d5099d22f855c353a57ec content_type: application/pdf creator: system date_created: 2018-12-12T10:09:55Z date_updated: 2020-07-14T12:45:38Z file_id: '4780' file_name: IST-2017-725-v1+7_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Forschungsdaten.pdf file_size: 1893872 relation: main_file - access_level: open_access checksum: e630b330dc0b7522d2cf204587030252 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:56Z date_updated: 2020-07-14T12:45:38Z file_id: '4781' file_name: IST-2017-725-v1+8_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Datenanreicherung_auf_LOD-Basis.pdf file_size: 1095929 relation: main_file - access_level: open_access checksum: 17edda91271bfcce8e1b6e77ca1c9d11 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:57Z date_updated: 2020-07-14T12:45:38Z file_id: '4782' file_name: IST-2017-725-v1+9_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Herausforderung_Wissensvernetzung.pdf file_size: 149699 relation: main_file - access_level: open_access checksum: aacef6734b1de58aeb58024fc47c2373 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:58Z date_updated: 2020-07-14T12:45:38Z file_id: '4783' file_name: IST-2017-725-v1+10_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Linked_Open_Data_geht_in_die_Fläche__Der_B3Kat_stellt_seine_Daten_frei.pdf file_size: 8828405 relation: main_file - access_level: open_access checksum: 0619451f7ff3ea641ce0b10c97831f47 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:59Z date_updated: 2020-07-14T12:45:38Z file_id: '4784' file_name: IST-2017-725-v1+11_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Open_Data_und_Linked_Data_in_einem_Informationssystem_für_die_Archäologie.pdf file_size: 3191208 relation: main_file - access_level: open_access checksum: 44dc8a9fc003f0edd912968958715a23 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:00Z date_updated: 2020-07-14T12:45:38Z file_id: '4785' file_name: IST-2017-725-v1+12_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Definition__Offenes_Wissen.pdf file_size: 78315 relation: main_file - access_level: open_access checksum: 48133cecebfd839b77f84f557d530c00 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:01Z date_updated: 2020-07-14T12:45:38Z file_id: '4786' file_name: IST-2017-725-v1+13_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Prinzipien_zu_offenen_bibliographischen_Daten.pdf file_size: 90532 relation: main_file - access_level: open_access checksum: a359224ddfdb178fed72b228dcfb699a content_type: application/pdf creator: system date_created: 2018-12-12T10:10:02Z date_updated: 2020-07-14T12:45:38Z file_id: '4787' file_name: IST-2017-725-v1+14_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Empfehlungen_zur_Öffnung_bibliothekarischer_Daten.pdf file_size: 90771 relation: main_file - access_level: open_access checksum: 0d2dd31d537c7a495999149d00eaffbf content_type: application/pdf creator: system date_created: 2018-12-12T10:10:03Z date_updated: 2020-07-14T12:45:38Z file_id: '4788' file_name: IST-2017-725-v1+15_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Glossar.pdf file_size: 1830232 relation: main_file file_date_updated: 2020-07-14T12:45:38Z has_accepted_license: '1' intvolume: ' 50' language: - iso: ger month: '09' oa: 1 oa_version: Published Version publication_identifier: eisbn: - 9-783-1102-7873-6 isbn: - ' 978-3-11-027634-3' issn: - 2191-3587 publication_status: published publisher: De Gruyter publist_id: '4621' pubrep_id: '725' quality_controlled: '1' status: public title: (Open) Linked Data in Bibliotheken tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 50 year: '2013' ... --- _id: '2301' abstract: - lang: eng text: We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P. author: - first_name: Ankush full_name: Desai, Ankush last_name: Desai - first_name: Vivek full_name: Gupta, Vivek last_name: Gupta - first_name: Ethan full_name: Jackson, Ethan last_name: Jackson - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer - first_name: Sriram full_name: Rajamani, Sriram last_name: Rajamani - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. ACM; 2013:321-331. doi:10.1145/2491956.2462184' apa: 'Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., & Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 321–331). Seattle, WA, United States: ACM. https://doi.org/10.1145/2491956.2462184' chicago: 'Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, 321–31. ACM, 2013. https://doi.org/10.1145/2491956.2462184.' ieee: 'A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, Seattle, WA, United States, 2013, pp. 321–331.' ista: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Languages Design and Implementation, 321–331.' mla: 'Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–31, doi:10.1145/2491956.2462184.' short: A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331. conference: end_date: 2013-06-19 location: Seattle, WA, United States name: 'PLDI: Programming Languages Design and Implementation' start_date: 2013-06-16 date_created: 2018-12-11T11:56:52Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '01' department: - _id: ToHe doi: 10.1145/2491956.2462184 ec_funded: 1 language: - iso: eng main_file_link: - url: http://research.microsoft.com/pubs/191069/pldi212_desai.pdf month: '06' oa_version: None page: 321 - 331 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation publication_status: published publisher: ACM publist_id: '4626' quality_controlled: '1' scopus_import: 1 status: public title: 'P: Safe asynchronous event-driven programming' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2300' abstract: - lang: eng text: We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability. article_number: '064401' author: - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401 apa: Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.88.064401 chicago: Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401. ieee: A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” Physical Review B, vol. 88, no. 6. American Physical Society, 2013. ista: Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401. mla: Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:10.1103/PhysRevB.88.064401. short: A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013). date_created: 2018-12-11T11:56:51Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '01' department: - _id: RoSe doi: 10.1103/PhysRevB.88.064401 external_id: arxiv: - '1305.5323' intvolume: ' 88' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.5323 month: '08' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '4627' quality_controlled: '1' scopus_import: 1 status: public title: Realization of stripes and slabs in two and three dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2013' ... --- _id: '2303' abstract: - lang: eng text: MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools. acknowledgement: This work was supported by IST Austria institutional funds. article_type: review author: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6 apa: Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6 chicago: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013. https://doi.org/10.1007/s11515-013-1279-6. ieee: S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer, pp. 557–568, 2013. ista: Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568. mla: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:10.1007/s11515-013-1279-6. short: S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568. date_created: 2018-12-11T11:56:52Z date_published: 2013-09-03T00:00:00Z date_updated: 2021-01-12T06:56:39Z day: '03' department: - _id: SiHi doi: 10.1007/s11515-013-1279-6 intvolume: ' 8' issue: '6' language: - iso: eng month: '09' oa_version: None page: 557 - 568 publication: Frontiers in Biology publication_status: published publisher: Springer publist_id: '4624' quality_controlled: '1' scopus_import: 1 status: public title: Dissection of gene function at clonal level using mosaic analysis with double markers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 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: '2315' abstract: - lang: eng text: ' We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. ' article_processing_charge: No author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason - first_name: Valentin full_name: Zagrebnov, Valentin last_name: Zagrebnov citation: ama: 'Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates with interaction. In: World Scientific Publishing; 2013:610-619. doi:10.1142/9789814449243_0063' apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Disordered Bose-Einstein condensates with interaction (pp. 610–619). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0063' chicago: Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered Bose-Einstein Condensates with Interaction,” 610–19. World Scientific Publishing, 2013. https://doi.org/10.1142/9789814449243_0063. ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates with interaction,” presented at the ICMP: International Congress on Mathematical Physics, 2013, pp. 610–619.' ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Disordered Bose-Einstein condensates with interaction. ICMP: International Congress on Mathematical Physics, 610–619.' mla: Seiringer, Robert, et al. Disordered Bose-Einstein Condensates with Interaction. World Scientific Publishing, 2013, pp. 610–19, doi:10.1142/9789814449243_0063. short: R. Seiringer, J. Yngvason, V. Zagrebnov, in:, World Scientific Publishing, 2013, pp. 610–619. conference: name: 'ICMP: International Congress on Mathematical Physics' date_created: 2018-12-11T11:56:57Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:43Z doi: 10.1142/9789814449243_0063 extern: '1' external_id: arxiv: - '1209.4046' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.4046 oa: 1 oa_version: None page: 610-619 publication_status: published publisher: World Scientific Publishing publist_id: '4612' status: public title: Disordered Bose-Einstein condensates with interaction type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2319' abstract: - lang: eng text: In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej citation: ama: 'Frank R, Hainzl C, Seiringer R, Solovej J. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. In: Springer; 2013:57-88. doi:10.1007/978-3-0348-0531-5_3' apa: 'Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2013). Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction (pp. 57–88). Presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, Springer. https://doi.org/10.1007/978-3-0348-0531-5_3' chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “ Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction,” 57–88. Springer, 2013. https://doi.org/10.1007/978-3-0348-0531-5_3. ieee: 'R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction,” presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2013, pp. 57–88.' ista: 'Frank R, Hainzl C, Seiringer R, Solovej J. 2013. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. OTAMP: Operator Theory, Analysis and Mathematical Physics, 57–88.' mla: Frank, Rupert, et al. Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction. Springer, 2013, pp. 57–88, doi:10.1007/978-3-0348-0531-5_3. short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, Springer, 2013, pp. 57–88. conference: name: 'OTAMP: Operator Theory, Analysis and Mathematical Physics' date_created: 2018-12-11T11:56:58Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:45Z day: '01' doi: 10.1007/978-3-0348-0531-5_3 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1103.1866 month: '01' oa: 1 page: 57 - 88 publication_status: published publisher: Springer publist_id: '4608' quality_controlled: 0 status: public title: ' Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction' type: conference year: '2013' ... --- _id: '2328' abstract: - lang: eng text: "Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof." alternative_title: - LNCS author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin - first_name: Viktor full_name: Vafeiadis, Viktor last_name: Vafeiadis citation: ama: Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:10.1007/978-3-642-40184-8_18 apa: 'Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-40184-8_18' chicago: Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.1007/978-3-642-40184-8_18. ieee: T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013. ista: Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256. mla: Henzinger, Thomas A., et al. Aspect-Oriented Linearizability Proofs. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:10.1007/978-3-642-40184-8_18. short: T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256. conference: end_date: 2013-08-30 location: Buenos Aires, Argentina name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:01Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T10:16:27Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1007/978-3-642-40184-8_18 ec_funded: 1 file: - access_level: open_access checksum: bdbb520de91751fe0136309ad4ef67e4 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:58Z date_updated: 2020-07-14T12:45:39Z file_id: '4721' file_name: IST-2014-197-v1+1_main-queue-verification.pdf file_size: 337059 relation: main_file file_date_updated: 2020-07-14T12:45:39Z has_accepted_license: '1' intvolume: ' 8052' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 242 - 256 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4598' pubrep_id: '197' quality_controlled: '1' related_material: record: - id: '1832' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Aspect-oriented linearizability proofs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '2404' abstract: - lang: eng text: The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials). author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 2013;162(3):435-495. doi:10.1215/00127094-2019477 apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2013). A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2019477 chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal. Duke University Press, 2013. https://doi.org/10.1215/00127094-2019477. ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue of the Lieb-Thirring inequality,” Duke Mathematical Journal, vol. 162, no. 3. Duke University Press, pp. 435–495, 2013. ista: Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495. mla: Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal, vol. 162, no. 3, Duke University Press, 2013, pp. 435–95, doi:10.1215/00127094-2019477. short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162 (2013) 435–495. date_created: 2018-12-11T11:57:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1215/00127094-2019477 extern: 1 intvolume: ' 162' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1108.4246 month: '02' oa: 1 page: 435 - 495 publication: Duke Mathematical Journal publication_status: published publisher: Duke University Press publist_id: '4521' quality_controlled: 0 status: public title: A positive density analogue of the Lieb-Thirring inequality type: journal_article volume: 162 year: '2013' ... --- _id: '2406' abstract: - lang: eng text: We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason - first_name: Valentin full_name: Zagrebnov, Valentin A last_name: Zagrebnov citation: ama: 'Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 2013;217(1):103-107. doi:10.1140/epjst/e2013-01759-5' apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. Springer. https://doi.org/10.1140/epjst/e2013-01759-5' chicago: 'Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics. Springer, 2013. https://doi.org/10.1140/epjst/e2013-01759-5.' ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting bosons in a random potential,” European Physical Journal: Special Topics, vol. 217, no. 1. Springer, pp. 103–107, 2013.' ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 217(1), 103–107.' mla: 'Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics, vol. 217, no. 1, Springer, 2013, pp. 103–07, doi:10.1140/epjst/e2013-01759-5.' short: 'R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special Topics 217 (2013) 103–107.' date_created: 2018-12-11T11:57:29Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1140/epjst/e2013-01759-5 extern: 1 intvolume: ' 217' issue: '1' month: '02' page: 103 - 107 publication: 'European Physical Journal: Special Topics' publication_status: published publisher: Springer publist_id: '4520' quality_controlled: 0 status: public title: Condensation of interacting bosons in a random potential type: journal_article volume: 217 year: '2013' ... --- _id: '2405' abstract: - lang: eng text: We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 2013;319(2):557-573. doi:10.1007/s00220-012-1604-y apa: Frank, R., Lieb, É., & Seiringer, R. (2013). Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1604-y chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-012-1604-y. ieee: R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for small Coulomb repulsion,” Communications in Mathematical Physics, vol. 319, no. 2. Springer, pp. 557–573, 2013. ista: Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573. mla: Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics, vol. 319, no. 2, Springer, 2013, pp. 557–73, doi:10.1007/s00220-012-1604-y. short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319 (2013) 557–573. date_created: 2018-12-11T11:57:28Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1007/s00220-012-1604-y extern: 1 intvolume: ' 319' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1201.3954 month: '04' oa: 1 page: 557 - 573 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4522' quality_controlled: 0 status: public title: Symmetry of bipolaron bound states for small Coulomb repulsion type: journal_article volume: 319 year: '2013' ... --- _id: '2408' abstract: - lang: eng text: We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation. author: - first_name: Philip full_name: Grech, Philip last_name: Grech - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 2013;322(2):559-591. doi:10.1007/s00220-013-1736-8 apa: Grech, P., & Seiringer, R. (2013). The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1736-8 chicago: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1736-8. ieee: P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting Bosons in a trap,” Communications in Mathematical Physics, vol. 322, no. 2. Springer, pp. 559–591, 2013. ista: Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591. mla: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics, vol. 322, no. 2, Springer, 2013, pp. 559–91, doi:10.1007/s00220-013-1736-8. short: P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013) 559–591. date_created: 2018-12-11T11:57:29Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:57:18Z day: '01' doi: 10.1007/s00220-013-1736-8 extern: 1 intvolume: ' 322' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1205.5259 month: '09' oa: 1 page: 559 - 591 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4518' quality_controlled: 0 status: public title: The excitation spectrum for weakly interacting Bosons in a trap type: journal_article volume: 322 year: '2013' ... --- _id: '2412' abstract: - lang: eng text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54 apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54 chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54. ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013. ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54. mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54. short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54. date_created: 2018-12-11T11:57:31Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '26' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-54 file: - access_level: open_access checksum: 029c7e0b198c19312b66ecce3cabb22f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:15Z date_updated: 2020-07-14T12:45:40Z file_id: '5268' file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf file_size: 518729 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 54 - 54 publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4514' pubrep_id: '397' quality_controlled: '1' scopus_import: 1 status: public title: 'Probabilistic models for CRISPR spacer content evolution ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '2413' abstract: - lang: eng text: 'Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.' alternative_title: - Reviews of Nonlinear Dynamics and Complexity author: - first_name: Mario full_name: Valderrama, Mario last_name: Valderrama - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Michel full_name: Le Van Quyen, Michel last_name: Le Van Quyen citation: ama: 'Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013. doi:10.1002/9783527671632.ch08' apa: 'Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer & Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08' chicago: 'Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.' ieee: 'M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013.' ista: 'Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .' mla: 'Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.' short: 'M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.' date_created: 2018-12-11T11:57:31Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '01' department: - _id: GaTk doi: 10.1002/9783527671632.ch08 editor: - first_name: Misha full_name: Meyer, Misha last_name: Meyer - first_name: Z. full_name: Pesenson, Z. last_name: Pesenson language: - iso: eng month: '08' oa_version: None publication: 'Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain' publication_identifier: eisbn: - '9783527671632' isbn: - '9783527411986 ' publication_status: published publisher: Wiley-VCH publist_id: '4513' quality_controlled: '1' scopus_import: 1 status: public title: 'Neuronal oscillations scale up and scale down the brain dynamics ' type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2410' abstract: - lang: eng text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ' author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Gertraud full_name: Stift, Gertraud id: 2DB195CA-F248-11E8-B48F-1D18A9856A87 last_name: Stift - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13 apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13 chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13. ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013. ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3). mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13. short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013). date_created: 2018-12-11T11:57:30Z date_published: 2013-06-13T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '13' ddc: - '576' department: - _id: JoBo - _id: LifeSc doi: 10.1128/genomeA.00216-13 file: - access_level: open_access checksum: 0751ec74b695567e0cdf02aaf9c26829 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:40Z file_id: '5291' file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf file_size: 130026 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genome Announcements publication_status: published publisher: American Society for Microbiology publist_id: '4516' pubrep_id: '398' quality_controlled: '1' scopus_import: 1 status: public title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '2447' abstract: - lang: eng text: "Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n" alternative_title: - LNCS article_processing_charge: No author: - first_name: Ruzica full_name: Piskac, Ruzica last_name: Piskac - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:10.1007/978-3-642-39799-8_54 apa: 'Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54' chicago: Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54. ieee: R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013. ista: Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789. mla: Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044, Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54. short: R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:43Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-642-39799-8_54 file: - access_level: open_access checksum: 2e866932ab688f47ecd504acb4d5c7d4 content_type: application/pdf creator: dernst date_created: 2020-05-15T11:13:01Z date_updated: 2020-07-14T12:45:41Z file_id: '7859' file_name: 2013_CAV_Piskac.pdf file_size: 309182 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8044' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 773 - 789 publication_status: published publisher: Springer publist_id: '4456' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Automating separation logic using SMT type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2443' abstract: - lang: eng text: The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery. acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.). article_processing_charge: No article_type: original author: - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Martin full_name: Kubeš, Martin last_name: Kubeš - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 2013;200(4):1034-1048. doi:10.1111/nph.12437' apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437' chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist. Wiley, 2013. https://doi.org/10.1111/nph.12437.' ieee: 'S. Simon et al., “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” New Phytologist, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.' ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.' mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.' short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048. date_created: 2018-12-11T11:57:41Z date_published: 2013-12-01T00:00:00Z date_updated: 2022-06-07T08:57:52Z day: '01' department: - _id: JiFr doi: 10.1111/nph.12437 ec_funded: 1 intvolume: ' 200' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.12437 month: '12' oa: 1 oa_version: Published Version page: 1034 - 1048 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: New Phytologist publication_status: published publisher: Wiley publist_id: '4460' quality_controlled: '1' scopus_import: '1' status: public title: 'Defining the selectivity of processes along the auxin response chain: A study using auxin analogues' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 200 year: '2013' ... --- _id: '2446' abstract: - lang: eng text: The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Gaiser, Andreas last_name: Gaiser - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37 apa: 'Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37' chicago: Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37. ieee: K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013. ista: Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575. mla: Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013, pp. 559–75, doi:10.1007/978-3-642-39799-8_37. short: K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:42Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-39799-8_37 ec_funded: 1 external_id: arxiv: - '1304.5281' intvolume: ' 8044' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.5281 month: '07' oa: 1 oa_version: Preprint page: 559 - 575 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4457' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2444' abstract: - lang: eng text: 'We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jakub full_name: Ła̧Cki, Jakub last_name: Ła̧Cki citation: ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36 apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36' chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_36. ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013. ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558. mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36. short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:42Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-39799-8_36 ec_funded: 1 external_id: arxiv: - '1304.0084' intvolume: ' 8044' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.0084 month: '07' oa: 1 oa_version: Preprint page: 543 - 558 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4459' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Faster algorithms for Markov decision processes with low treewidth type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2449' abstract: - lang: eng text: 'Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. ' author: - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Murguel full_name: Feraru, Murguel last_name: Feraru - first_name: Sibylle full_name: Hirsch, Sibylle last_name: Hirsch - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Claudiu full_name: Nicuales, Claudiu last_name: Nicuales - first_name: Jelle full_name: Van Leene, Jelle last_name: Van Leene - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 2013;6(6):1849-1862. doi:10.1093/mp/sst044 apa: Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press. https://doi.org/10.1093/mp/sst044 chicago: Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044. ieee: T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013. ista: Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862. mla: Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044. short: T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862. date_created: 2018-12-11T11:57:44Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:57:33Z day: '01' department: - _id: JiFr doi: 10.1093/mp/sst044 intvolume: ' 6' issue: '6' language: - iso: eng month: '11' oa_version: None page: 1849 - 1862 publication: Molecular Plant publication_status: published publisher: Cell Press publist_id: '4454' quality_controlled: '1' scopus_import: 1 status: public title: Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '2452' abstract: - lang: eng text: 'Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.' author: - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Martina full_name: Laňková, Martina last_name: Laňková - first_name: Markéta full_name: Pařezová, Markéta last_name: Pařezová - first_name: Alexis full_name: Maizel, Alexis last_name: Maizel - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn citation: ama: Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1). doi:10.1186/1471-2229-13-20 apa: Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20 chicago: Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20. ieee: E. Barbez et al., “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1). mla: Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central, 2013, doi:10.1186/1471-2229-13-20. short: E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013). date_created: 2018-12-11T11:57:45Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:34Z day: '01' doi: 10.1186/1471-2229-13-20 extern: 1 intvolume: ' 13' issue: '1' month: '02' publication: BMC Plant Biology publication_status: published publisher: BioMed Central publist_id: '4451' quality_controlled: 0 status: public title: Single-cell-based system to monitor carrier driven cellular auxin homeostasis type: journal_article volume: 13 year: '2013' ... --- _id: '2450' abstract: - lang: eng text: 'Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network' author: - first_name: Junli full_name: Liu, Junli last_name: Liu - first_name: Saher full_name: Menhi, Saher last_name: Menhi - first_name: Jennifer full_name: Topping, Jennifer last_name: Topping - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Keith full_name: Lindsey, Keith last_name: Lindsey citation: ama: Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 2013;4(75). doi:10.3389/fpls.2013.00075 apa: Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075 chicago: Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075. ieee: J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013. ista: Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75). mla: Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00075. short: J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:57:44Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:57:34Z day: '01' doi: 10.3389/fpls.2013.00075 extern: 1 intvolume: ' 4' issue: '75' month: '04' publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '4453' quality_controlled: 0 status: public title: Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development type: journal_article volume: 4 year: '2013' ... --- _id: '245' abstract: - lang: eng text: For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ. author: - first_name: Stephan full_name: Baier, Stephan last_name: Baier - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151. doi:10.1515/crelle.2012.039 apa: Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039 chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039. ieee: S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, no. 680. Walter de Gruyter, pp. 69–151, 2013. ista: Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151. mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039. short: S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151. date_created: 2018-12-11T11:45:24Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:57:33Z day: '01' doi: 10.1515/crelle.2012.039 extern: 1 issue: '680' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1011.3434 month: '07' oa: 1 page: 69 - 151 publication: Journal fur die Reine und Angewandte Mathematik publication_status: published publisher: Walter de Gruyter publist_id: '7659' quality_controlled: 0 status: public title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces type: journal_article year: '2013' ... --- _id: '2457' author: - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Stefan full_name: Rensing, Stefan last_name: Rensing - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10. doi:10.1016/j.tplants.2012.08.009 apa: Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009 chicago: Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009. ieee: T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” Trends in Plant Science, vol. 18, no. 1. Cell Press, pp. 5–10, 2013. ista: Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10. mla: Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:10.1016/j.tplants.2012.08.009. short: T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10. date_created: 2018-12-11T11:57:46Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:57:36Z day: '01' doi: 10.1016/j.tplants.2012.08.009 extern: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '01' oa_version: None page: 5 - 10 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '4446' quality_controlled: '1' status: public title: Origin and evolution of PIN auxin transporters in the green lineage type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2013' ... --- _id: '246' abstract: - lang: eng text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i). acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ritabrata full_name: Munshi, Ritabrata last_name: Munshi citation: ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics. Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185 apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185 chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica. Cambridge University Press, 2013. https://doi.org/10.1112/S0010437X13007185. ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013. ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494. mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185. short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494. date_created: 2018-12-11T11:45:25Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:57:37Z day: '01' doi: 10.1112/S0010437X13007185 extern: 1 intvolume: ' 149' issue: '9' month: '09' page: 1457 - 1494 publication: Compositio Mathematica publication_status: published publisher: Cambridge University Press publist_id: '7658' quality_controlled: 0 status: public title: Rational points on singular intersections of quadrics type: journal_article volume: 149 year: '2013' ... --- _id: '2471' abstract: - lang: eng text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation. article_number: e70013 author: - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Antonio full_name: Ariza, Antonio last_name: Ariza - first_name: Keith full_name: Wilson, Keith last_name: Wilson - first_name: Michael full_name: Skjøt, Michael last_name: Skjøt - first_name: Jesper full_name: Vind, Jesper last_name: Vind - first_name: Leonardo full_name: De Maria, Leonardo last_name: De Maria - first_name: Lars full_name: Skov, Lars last_name: Skov - first_name: Jose full_name: Sánchez Ruiz, Jose last_name: Sánchez Ruiz citation: ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013 apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013 chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013. ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013. mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:10.1371/journal.pone.0070013. short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013). date_created: 2018-12-11T11:57:51Z date_published: 2013-07-30T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '30' ddc: - '570' department: - _id: HaJa doi: 10.1371/journal.pone.0070013 file: - access_level: open_access checksum: c0c96cc76ed7ef0d036a31a7e33c9a37 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:07Z date_updated: 2020-07-14T12:45:41Z file_id: '5124' file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf file_size: 1323666 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4430' pubrep_id: '414' quality_controlled: '1' scopus_import: 1 status: public title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2472' abstract: - lang: eng text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development. article_number: e70069 author: - first_name: Christopher full_name: Cazzonelli, Christopher last_name: Cazzonelli - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kuide full_name: Yin, Kuide last_name: Yin - first_name: Ashley full_name: Carron Arthur, Ashley last_name: Carron Arthur - first_name: Nazia full_name: Nisar, Nazia last_name: Nisar - first_name: Gauri full_name: Tarle, Gauri last_name: Tarle - first_name: Abby full_name: Cuttriss, Abby last_name: Cuttriss - first_name: Iain full_name: Searle, Iain last_name: Searle - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ulrike full_name: Mathesius, Ulrike last_name: Mathesius - first_name: Josette full_name: Masle, Josette last_name: Masle - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Barry full_name: Pogson, Barry last_name: Pogson citation: ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070069 apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070069 chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069. ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069. mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069. short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013). date_created: 2018-12-11T11:57:52Z date_published: 2013-07-29T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '29' ddc: - '580' - '570' department: - _id: JiFr - _id: EvBe doi: 10.1371/journal.pone.0070069 ec_funded: 1 file: - access_level: open_access checksum: 3be71828b6c2ba9c90eb7056e3f7f57a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:34Z date_updated: 2020-07-14T12:45:41Z file_id: '5222' file_name: IST-2015-393-v1+1_journal.pone.0070069.pdf file_size: 9003465 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4431' pubrep_id: '393' quality_controlled: '1' scopus_import: 1 status: public title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2470' abstract: - lang: eng text: Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients. article_number: e70050 author: - first_name: Milada full_name: Čovanová, Milada last_name: Čovanová - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jan full_name: Rychtář, Jan last_name: Rychtář - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050 apa: Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070050 chicago: Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070050. ieee: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050. mla: Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050. short: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013). date_created: 2018-12-11T11:57:51Z date_published: 2013-07-23T00:00:00Z date_updated: 2021-01-12T06:57:40Z day: '23' ddc: - '570' department: - _id: JiFr doi: 10.1371/journal.pone.0070050 file: - access_level: open_access checksum: 2d47ef47616ef4de1d517d146548184e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:21Z date_updated: 2020-07-14T12:45:41Z file_id: '4681' file_name: IST-2016-413-v1+1_journal.pone.0070050.pdf file_size: 2294955 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4432' pubrep_id: '413' quality_controlled: '1' scopus_import: 1 status: public title: Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2466' abstract: - lang: eng text: 'We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.' article_number: '103' author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982 apa: Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982 chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461982. ieee: R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103. mla: Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982. short: R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:14Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2461982 file: - access_level: open_access checksum: aeea6b0ff2b27c695aeb8408c7d2fc50 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:25Z date_updated: 2020-07-14T12:45:41Z file_id: '5279' file_name: IST-2016-605-v1+1_tetflip_fixed.pdf file_size: 8601561 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4436' pubrep_id: '605' quality_controlled: '1' scopus_import: 1 status: public title: Highly adaptive liquid simulations on tetrahedral meshes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2467' abstract: - lang: eng text: This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors. article_number: '34' author: - first_name: Gilbert full_name: Bernstein, Gilbert last_name: Bernstein - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027' apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027' chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2462027.' ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.' ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.' mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32, no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.' short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:16Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2462027 file: - access_level: open_access checksum: 9c8425d62246996ca632c5a01870515b content_type: application/pdf creator: system date_created: 2018-12-12T10:09:43Z date_updated: 2020-07-14T12:45:41Z file_id: '4768' file_name: IST-2016-604-v1+1_toptop2013.pdf file_size: 3514674 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4435' pubrep_id: '604' quality_controlled: '1' scopus_import: 1 status: public title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2468' abstract: - lang: eng text: Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers. article_number: '68' author: - first_name: Morten full_name: Bojsen-Hansen, Morten id: 439F0C8C-F248-11E8-B48F-1D18A9856A87 last_name: Bojsen-Hansen orcid: 0000-0002-4417-3224 - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991 apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991 chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991. ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68. mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013, doi:10.1145/2461912.2461991. short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:18Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2461991 file: - access_level: open_access checksum: 53d905e0180e23ef3e813b969ffed4e1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:37Z date_updated: 2020-07-14T12:45:41Z file_id: '4761' file_name: IST-2016-603-v1+1_liquidError_web.pdf file_size: 5813685 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4434' pubrep_id: '603' quality_controlled: '1' scopus_import: 1 status: public title: Liquid surface tracking with error compensation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ...