--- _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' ... --- _id: '1823' abstract: - lang: eng text: Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. article_number: '807' author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098 apa: Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.15252/msb.20156098 chicago: Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing Group, 2015. https://doi.org/10.15252/msb.20156098. ieee: G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015. ista: Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807. mla: Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098. short: G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015). date_created: 2018-12-11T11:54:12Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:26Z day: '01' ddc: - '570' department: - _id: ToBo doi: 10.15252/msb.20156098 ec_funded: 1 file: - access_level: open_access checksum: 4289b518fbe2166682fb1a1ef9b405f3 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:34Z date_updated: 2020-07-14T12:45:17Z file_id: '5087' file_name: IST-2015-395-v1+1_807.full.pdf file_size: 1273573 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '5283' pubrep_id: '395' quality_controlled: '1' scopus_import: 1 status: public title: Systematic discovery of drug interaction mechanisms 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: 11 year: '2015' ... --- _id: '1824' abstract: - lang: eng text: Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates. article_number: '6977' author: - first_name: Johannes full_name: Knebel, Johannes last_name: Knebel - first_name: Markus full_name: Weber, Markus last_name: Weber - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Erwin full_name: Frey, Erwin last_name: Frey citation: ama: Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977 apa: Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7977 chicago: Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977. ieee: J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977. mla: Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group, 2015, doi:10.1038/ncomms7977. short: J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015). date_created: 2018-12-11T11:54:13Z date_published: 2015-04-24T00:00:00Z date_updated: 2021-01-12T06:53:26Z day: '24' ddc: - '530' department: - _id: LaEr doi: 10.1038/ncomms7977 file: - access_level: open_access checksum: c4cffb5c8b245e658a34eac71a03e7cc content_type: application/pdf creator: system date_created: 2018-12-12T10:16:54Z date_updated: 2020-07-14T12:45:17Z file_id: '5245' file_name: IST-2016-451-v1+1_ncomms7977.pdf file_size: 1151501 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5282' pubrep_id: '451' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary games of condensates in coupled birth-death processes 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: 6 year: '2015' ... --- _id: '1831' abstract: - lang: eng text: This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research. acknowledgement: We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue. article_number: '20140116' author: - first_name: Peter full_name: Kappeler, Peter last_name: Kappeler - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Charles full_name: Nunn, Charles last_name: Nunn citation: ama: 'Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0116' apa: 'Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116' chicago: 'Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116.' ieee: 'P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015.' ista: 'Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116.' mla: 'Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.' short: P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015). date_created: 2018-12-11T11:54:15Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:29Z day: '01' department: - _id: SyCr doi: 10.1098/rstb.2014.0116 external_id: pmid: - '25870402' intvolume: ' 370' issue: '1669' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '5272' quality_controlled: '1' scopus_import: 1 status: public title: 'Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 370 year: '2015' ... --- _id: '1828' abstract: - lang: eng text: We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Pirogov, Sergey last_name: Pirogov - first_name: Aleksandr full_name: Rybko, Aleksandr last_name: Rybko citation: ama: Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5 apa: Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5 chicago: Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics. Springer, 2015. https://doi.org/10.1007/s10955-015-1238-5. ieee: A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp. 163–167, 2015. ista: Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167. mla: Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:10.1007/s10955-015-1238-5. short: A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167. date_created: 2018-12-11T11:54:14Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:53:28Z day: '01' department: - _id: HeEd doi: 10.1007/s10955-015-1238-5 ec_funded: 1 intvolume: ' 160' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: arxiv.org/abs/1406.5313 month: '07' oa: 1 oa_version: Preprint page: 163 - 167 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '5276' quality_controlled: '1' scopus_import: 1 status: public title: Invariant measures of genetic recombination process type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2015' ... --- _id: '1836' abstract: - lang: eng text: In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - 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: Laura full_name: Kovács, Laura last_name: Kovács - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Jakob full_name: Zwirchmayr, Jakob last_name: Zwirchmayr citation: ama: Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5 apa: 'Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46669-8_5' chicago: Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5. ieee: P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015. ista: Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131. mla: Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis. Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5. short: P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'ESOP: European Symposium on Programming' start_date: 2015-04-11 date_created: 2018-12-11T11:54:16Z date_published: 2015-04-01T00:00:00Z date_updated: 2020-08-11T10:09:32Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-662-46669-8_5 ec_funded: 1 intvolume: ' 9032' language: - iso: eng month: '04' oa_version: None page: 105 - 131 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5266' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Segment abstraction for worst-case execution time analysis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9032 year: '2015' ... --- _id: '1838' abstract: - lang: eng text: Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples. acknowledgement: 'This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).' alternative_title: - LNCS author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Swen full_name: Jacobs, Swen last_name: Jacobs - first_name: Robert full_name: Könighofer, Robert last_name: Könighofer citation: ama: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50' apa: 'Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50' chicago: Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50. ieee: 'R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.' ista: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.' mla: Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50. short: R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:17Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:32Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_50 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1411.4604 month: '01' oa: 1 oa_version: Preprint page: 517 - 532 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5264' scopus_import: 1 status: public title: Assume-guarantee synthesis for concurrent reactive programs with partial information type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1839' abstract: - lang: eng text: We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12' apa: 'Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12' chicago: 'Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.' ieee: 'T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.' ista: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.' mla: 'Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12.' short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2020-01-21T13:18:52Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_12 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.03093 month: '01' oa: 1 oa_version: Preprint page: 181 - 187 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_status: published publisher: Springer publist_id: '5263' quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: 'Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1837' abstract: - lang: eng text: 'Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.' article_number: R3 article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: P full_name: Braunshier, P last_name: Braunshier - first_name: M full_name: Schwegel, M last_name: Schwegel - first_name: Hendrik full_name: Kuhlmann, Hendrik last_name: Kuhlmann - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184 apa: Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184 chicago: Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184. ieee: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015. ista: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3. mla: Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184. short: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015). date_created: 2018-12-11T11:54:17Z date_published: 2015-04-08T00:00:00Z date_updated: 2021-01-12T06:53:31Z day: '08' department: - _id: BjHo doi: 10.1017/jfm.2015.184 ec_funded: 1 external_id: arxiv: - '1508.06559' intvolume: ' 770' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.06559 month: '04' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '5265' quality_controlled: '1' scopus_import: 1 status: public title: Subcritical versus supercritical transition to turbulence in curved pipes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 770 year: '2015' ... --- _id: '1848' abstract: - lang: eng text: The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis. article_processing_charge: No article_type: original author: - first_name: Bettina full_name: Schwamb, Bettina last_name: Schwamb - first_name: Robert full_name: Pick, Robert last_name: Pick - first_name: Sara full_name: Fernández, Sara last_name: Fernández - first_name: Kirsten full_name: Völp, Kirsten last_name: Völp - first_name: Jan full_name: Heering, Jan last_name: Heering - first_name: Volker full_name: Dötsch, Volker last_name: Dötsch - first_name: Susanne full_name: Bösser, Susanne last_name: Bösser - first_name: Jennifer full_name: Jung, Jennifer last_name: Jung - first_name: Rasa full_name: Beinoravičiute Kellner, Rasa last_name: Beinoravičiute Kellner - first_name: Josephine full_name: Wesely, Josephine last_name: Wesely - first_name: Inka full_name: Zörnig, Inka last_name: Zörnig - first_name: Matthias full_name: Hammerschmidt, Matthias last_name: Hammerschmidt - first_name: Matthias full_name: Nowak, Matthias id: 30845DAA-F248-11E8-B48F-1D18A9856A87 last_name: Nowak - first_name: Roland full_name: Penzel, Roland last_name: Penzel - first_name: Kurt full_name: Zatloukal, Kurt last_name: Zatloukal - first_name: Stefan full_name: Joos, Stefan last_name: Joos - first_name: Ralf full_name: Rieker, Ralf last_name: Rieker - first_name: Abbas full_name: Agaimy, Abbas last_name: Agaimy - first_name: Stephan full_name: Söder, Stephan last_name: Söder - first_name: Kmarie full_name: Reid Lombardo, Kmarie last_name: Reid Lombardo - first_name: Michael full_name: Kendrick, Michael last_name: Kendrick - first_name: Michael full_name: Bardsley, Michael last_name: Bardsley - first_name: Yujiro full_name: Hayashi, Yujiro last_name: Hayashi - first_name: David full_name: Asuzu, David last_name: Asuzu - first_name: Sabriya full_name: Syed, Sabriya last_name: Syed - first_name: Tamás full_name: Ördög, Tamás last_name: Ördög - first_name: Martin full_name: Zörnig, Martin last_name: Zörnig citation: ama: Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498 apa: Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498 chicago: Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498. ieee: B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015. ista: Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329. mla: Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498. short: B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329. date_created: 2018-12-11T11:54:20Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' department: - _id: LifeSc doi: 10.1002/ijc.29498 external_id: pmid: - '25716227' intvolume: ' 137' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/ month: '09' oa: 1 oa_version: Submitted Version page: 1318 - 1329 pmid: 1 publication: International Journal of Cancer publication_status: published publisher: Wiley publist_id: '5253' quality_controlled: '1' scopus_import: 1 status: public title: FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2015' ... --- _id: '1846' abstract: - lang: eng text: Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS. article_processing_charge: No article_type: original author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Kim full_name: Larsen, Kim last_name: Larsen - first_name: Mikael full_name: Möller, Mikael last_name: Möller - first_name: Salomon full_name: Sickert, Salomon last_name: Sickert - first_name: Jiří full_name: Srba, Jiří last_name: Srba citation: ama: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4 apa: Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4 chicago: Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4. ieee: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015. ista: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297. mla: Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4. short: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297. date_created: 2018-12-11T11:54:20Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/s00236-015-0215-4 ec_funded: 1 file: - access_level: open_access checksum: fb4037ddc4fc05f33080dd3547ede350 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:57:44Z date_updated: 2020-07-14T12:45:19Z file_id: '7854' file_name: 2015_ActaInfo_Benes.pdf file_size: 488482 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 52' issue: 2-3 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 269 - 297 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Acta Informatica publication_status: published publisher: Springer publist_id: '5255' quality_controlled: '1' scopus_import: 1 status: public title: Refinement checking on parametric modal transition systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2015' ... --- _id: '1845' abstract: - lang: eng text: Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. article_processing_charge: No author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006 apa: Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006 chicago: Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006. ieee: D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015. ista: Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151. mla: Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006. short: D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151. date_created: 2018-12-11T11:54:19Z date_published: 2015-03-18T00:00:00Z date_updated: 2021-10-08T09:07:34Z day: '18' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2015.03.006 file: - access_level: open_access checksum: d1808550e376a0eca2a950fda017cfa6 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5192' file_name: IST-2017-822-v1+1_Perspective_Fig__Final.pdf file_size: 411832 relation: main_file - access_level: open_access checksum: a279f4ae61e6c8f33d68f69a0d02097d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5193' file_name: IST-2017-822-v1+2_Perspective_Final2.pdf file_size: 100769 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 85' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '03' oa: 1 oa_version: Published Version page: 1149 - 1151 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5256' pubrep_id: '822' quality_controlled: '1' scopus_import: '1' status: public title: Excitement about inhibitory presynaptic terminals tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 85 year: '2015' ... --- _id: '1840' abstract: - lang: eng text: In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions. acknowledgement: "This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n" author: - first_name: Bernhard full_name: Geiger, Bernhard last_name: Geiger - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Gernot full_name: Kubin, Gernot last_name: Kubin - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl citation: ama: Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971 apa: Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971 chicago: Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971. ieee: B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015. ista: Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022. mla: Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971. short: B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022. date_created: 2018-12-11T11:54:18Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: CaGu - _id: ToHe doi: 10.1109/TAC.2014.2364971 intvolume: ' 60' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.6603 month: '04' oa: 1 oa_version: Preprint page: 1010 - 1022 publication: IEEE Transactions on Automatic Control publication_identifier: issn: - 0018-9286 publication_status: published publisher: IEEE publist_id: '5262' quality_controlled: '1' scopus_import: 1 status: public title: Optimal Kullback-Leibler aggregation via information bottleneck type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2015' ... --- _id: '1841' 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 Diffusion (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. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465 apa: Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465 chicago: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465. ieee: V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015. ista: Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930. mla: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465. short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930. date_created: 2018-12-11T11:54:18Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2014.2363465 ec_funded: 1 intvolume: ' 37' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5655 month: '05' oa: 1 oa_version: Preprint page: 919 - 930 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '5261' quality_controlled: '1' scopus_import: 1 status: public title: A new look at reweighted message passing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2015' ... --- _id: '1849' abstract: - lang: eng text: 'Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.' acknowledgement: The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.). author: - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017 apa: Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017 chicago: Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017. ieee: E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015. ista: Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172. mla: Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017. short: E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172. date_created: 2018-12-11T11:54:21Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' department: - _id: JiFr doi: 10.1016/j.bbamcr.2015.02.017 intvolume: ' 1853' issue: '9' language: - iso: eng month: '09' oa_version: None page: 2168 - 2172 publication: Biochimica et Biophysica Acta - Molecular Cell Research publication_status: published publisher: Elsevier publist_id: '5252' quality_controlled: '1' scopus_import: 1 status: public title: Calcium is an organizer of cell polarity in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1853 year: '2015' ... --- _id: '1847' 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). author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013' apa: 'Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013' chicago: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.' ieee: 'P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.' ista: 'Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.' mla: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.' short: P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358. date_created: 2018-12-11T11:54:20Z date_published: 2015-03-02T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '02' department: - _id: JiFr doi: 10.1016/j.molp.2014.12.013 intvolume: ' 8' issue: '3' language: - iso: eng month: '03' oa_version: None page: 356 - 358 publication: Molecular Plant publication_status: published publisher: Elsevier publist_id: '5254' quality_controlled: '1' scopus_import: 1 status: public title: 'ABP1: Finally docking' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ...