--- _id: '1817' abstract: - lang: eng text: 'Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D''Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ' author: - first_name: Sean full_name: Porazinski, Sean last_name: Porazinski - first_name: Huijia full_name: Wang, Huijia last_name: Wang - first_name: Yoichi full_name: Asaoka, Yoichi last_name: Asaoka - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Tatsuo full_name: Miyamoto, Tatsuo last_name: Miyamoto - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Shoji full_name: Hata, Shoji last_name: Hata - first_name: Takashi full_name: Sasaki, Takashi last_name: Sasaki - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Yumi full_name: Osada, Yumi last_name: Osada - first_name: Satoshi full_name: Asaka, Satoshi last_name: Asaka - first_name: Akihiro full_name: Momoi, Akihiro last_name: Momoi - first_name: Sarah full_name: Linton, Sarah last_name: Linton - first_name: Joel full_name: Miesfeld, Joel last_name: Miesfeld - first_name: Brian full_name: Link, Brian last_name: Link - first_name: Takeshi full_name: Senga, Takeshi last_name: Senga - first_name: Atahualpa full_name: Castillo Morales, Atahualpa last_name: Castillo Morales - first_name: Araxi full_name: Urrutia, Araxi last_name: Urrutia - first_name: Nobuyoshi full_name: Shimizu, Nobuyoshi last_name: Shimizu - first_name: Hideaki full_name: Nagase, Hideaki last_name: Nagase - first_name: Shinya full_name: Matsuura, Shinya last_name: Matsuura - first_name: Stefan full_name: Bagby, Stefan last_name: Bagby - first_name: Hisato full_name: Kondoh, Hisato last_name: Kondoh - first_name: Hiroshi full_name: Nishina, Hiroshi last_name: Nishina - 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 - first_name: Makoto full_name: Furutani Seiki, Makoto last_name: Furutani Seiki citation: ama: Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215 apa: Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215 chicago: Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215. ieee: S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015. ista: Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221. mla: Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215. short: S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221. date_created: 2018-12-11T11:54:10Z date_published: 2015-03-16T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '16' department: - _id: CaHe doi: 10.1038/nature14215 external_id: pmid: - '25778702' intvolume: ' 521' issue: '7551' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/ month: '03' oa: 1 oa_version: Submitted Version page: 217 - 221 pmid: 1 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5289' quality_controlled: '1' scopus_import: 1 status: public title: YAP is essential for tissue tension to ensure vertebrate 3D body shape type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 521 year: '2015' ... --- _id: '1820' abstract: - lang: eng text: 'We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.' acknowledgement: ' The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' alternative_title: - Artifical Intelligence author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: ama: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.' apa: 'Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.' chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015. ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502. ista: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.' mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502. short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502. conference: end_date: 2015-01-30 location: Austin, TX, USA name: 'IAAI: Innovative Applications of Artificial Intelligence' start_date: 2015-01-25 date_created: 2018-12-11T11:54:11Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:02:57Z day: '01' department: - _id: KrCh ec_funded: 1 external_id: arxiv: - '1411.3880' intvolume: ' 5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1411.3880 month: '06' oa: 1 oa_version: Preprint page: 3496-3502 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: 'Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ' publication_status: published publisher: AAAI Press publist_id: '5286' quality_controlled: '1' related_material: record: - id: '1529' relation: later_version status: public scopus_import: 1 status: public title: Optimal cost almost-sure reachability in POMDPs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2015' ... --- _id: '1814' abstract: - lang: eng text: 'We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.' article_number: '27' author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - 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: Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572 apa: Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572 chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572. ieee: S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015. ista: Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27. mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015). date_created: 2018-12-11T11:54:09Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T10:15:40Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2714572 ec_funded: 1 file: - access_level: open_access checksum: 67c9f4fa370def68cdf31299e48bc91f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:15Z date_updated: 2020-07-14T12:45:17Z file_id: '4933' file_name: IST-2016-575-v1+1_wavefront_preprint.pdf file_size: 23712153 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 34' issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '5292' pubrep_id: '575' quality_controlled: '1' scopus_import: 1 status: public title: Water wave animation via wavefront parameter interpolation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1818' abstract: - lang: eng text: 'Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species'' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species'' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.' author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112 apa: Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112 chicago: Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112. ieee: J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015. ista: Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406. mla: Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112. short: J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406. date_created: 2018-12-11T11:54:11Z date_published: 2015-05-19T00:00:00Z date_updated: 2021-01-12T06:53:24Z day: '19' department: - _id: NiBa doi: 10.1073/pnas.1421515112 ec_funded: 1 external_id: pmid: - '25941385' intvolume: ' 112' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/ month: '05' oa: 1 oa_version: Submitted Version page: 6401 - 6406 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5288' quality_controlled: '1' scopus_import: 1 status: public title: Limits to adaptation along environmental gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1819' abstract: - lang: eng text: 'The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.' acknowledgement: This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N.. author: - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007 apa: Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007 chicago: Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007. ieee: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015. ista: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187. mla: Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007. short: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187. date_created: 2018-12-11T11:54:11Z date_published: 2015-08-03T00:00:00Z date_updated: 2021-01-12T06:53:24Z day: '03' department: - _id: JiFr doi: 10.1016/j.molp.2015.03.007 ec_funded: 1 intvolume: ' 8' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1175 - 1187 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Molecular Plant publication_status: published publisher: Elsevier publist_id: '5287' quality_controlled: '1' scopus_import: 1 status: public title: Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ...