--- _id: '1327' abstract: - lang: eng text: 'We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. ' 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: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Anchit full_name: Gupta, Anchit last_name: Gupta - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.' apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (pp. 1465–1466). Singapore: ACM.' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 1465–66. ACM, 2016. ieee: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, Singapore, 2016, pp. 1465–1466. ista: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents & Multiagent Systems, 1465–1466.' mla: Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–66. short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466. conference: end_date: 2016-05-13 location: Singapore name: 'AAMAS: Autonomous Agents & Multiagent Systems' start_date: 2016-05-09 date_created: 2018-12-11T11:51:23Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:49:54Z day: '01' department: - _id: KrCh ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.07565 month: '01' oa: 1 oa_version: Preprint page: 1465 - 1466 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: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems publication_status: published publisher: ACM publist_id: '5942' quality_controlled: '1' scopus_import: 1 status: public title: Stochastic shortest path with energy constraints in POMDPs type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1328' abstract: - lang: eng text: Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples. acknowledgement: 'The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. ' author: - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger - first_name: Christoph full_name: Kloeffel, Christoph last_name: Kloeffel - first_name: Lada full_name: Vukusic, Lada id: 31E9F056-F248-11E8-B48F-1D18A9856A87 last_name: Vukusic orcid: 0000-0003-2424-8636 - first_name: Marta full_name: Rossell, Marta last_name: Rossell - first_name: Violetta full_name: Sessi, Violetta last_name: Sessi - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Raimund full_name: Kirchschlager, Raimund last_name: Kirchschlager - first_name: Elisabeth full_name: Lausecker, Elisabeth id: 33662F76-F248-11E8-B48F-1D18A9856A87 last_name: Lausecker - first_name: Alisha full_name: Truhlar, Alisha id: 49CBC780-F248-11E8-B48F-1D18A9856A87 last_name: Truhlar - first_name: Martin full_name: Glaser, Martin last_name: Glaser - first_name: Armando full_name: Rastelli, Armando last_name: Rastelli - first_name: Andreas full_name: Fuhrer, Andreas last_name: Fuhrer - first_name: Daniel full_name: Loss, Daniel last_name: Loss - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. Nano Letters. 2016;16(11):6879-6885. doi:10.1021/acs.nanolett.6b02715 apa: Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.6b02715 chicago: Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.nanolett.6b02715. ieee: H. Watzinger et al., “Heavy-hole states in germanium hut wires,” Nano Letters, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016. ista: Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885. mla: Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano Letters, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:10.1021/acs.nanolett.6b02715. short: H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885. date_created: 2018-12-11T11:51:24Z date_published: 2016-09-22T00:00:00Z date_updated: 2023-09-07T13:15:02Z day: '22' ddc: - '539' department: - _id: GeKa doi: 10.1021/acs.nanolett.6b02715 ec_funded: 1 file: - access_level: open_access checksum: b63feece90d7b620ece49ca632e34ff3 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:04Z date_updated: 2020-07-14T12:44:44Z file_id: '5053' file_name: IST-2016-664-v1+1_acs.nanolett.6b02715.pdf file_size: 535121 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 16' issue: '11' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 6879 - 6885 project: - _id: 25517E86-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335497' name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires publication: Nano Letters publication_status: published publisher: American Chemical Society publist_id: '5941' pubrep_id: '664' quality_controlled: '1' related_material: record: - id: '7977' relation: popular_science status: for_moderation - id: '7996' relation: dissertation_contains status: public scopus_import: 1 status: public title: Heavy-hole states in germanium hut wires 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2016' ... --- _id: '1329' abstract: - lang: eng text: Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species. acknowledgement: This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium. author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Alberto full_name: López Ezquerra, Alberto last_name: López Ezquerra - first_name: John full_name: Parsch, John last_name: Parsch - first_name: Mathilde full_name: Cordellier, Mathilde last_name: Cordellier citation: ama: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221 apa: Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evw221 chicago: Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/gbe/evw221. ieee: A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016. ista: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139. mla: Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:10.1093/gbe/evw221. short: A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139. date_created: 2018-12-11T11:51:24Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:49:55Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.1093/gbe/evw221 file: - access_level: open_access checksum: 25c7adcb452d39d3b6343ff4b57a652d content_type: application/pdf creator: system date_created: 2018-12-12T10:12:06Z date_updated: 2020-07-14T12:44:44Z file_id: '4924' file_name: IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf file_size: 1406265 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 8' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '10' oa: 1 oa_version: Published Version page: 3120 - 3139 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5940' pubrep_id: '663' quality_controlled: '1' scopus_import: 1 status: public title: De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2016' ... --- _id: '1330' abstract: - lang: eng text: In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K. acknowledgement: Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation. author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexey full_name: Balitskiy, Alexey last_name: Balitskiy citation: ama: Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z apa: Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z chicago: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z. ieee: A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845, 2016. ista: Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845. mla: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:10.1007/s11856-016-1429-z. short: A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845. date_created: 2018-12-11T11:51:24Z date_published: 2016-10-15T00:00:00Z date_updated: 2021-01-12T06:49:56Z day: '15' department: - _id: HeEd doi: 10.1007/s11856-016-1429-z ec_funded: 1 intvolume: ' 216' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.06014 month: '10' oa: 1 oa_version: Preprint page: 833 - 845 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '5938' quality_controlled: '1' scopus_import: 1 status: public title: Billiards in convex bodies with acute angles type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 216 year: '2016' ... --- _id: '1331' abstract: - lang: eng text: 'Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.' acknowledgement: "This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W)." article_processing_charge: No article_type: original author: - first_name: Paul full_name: Zwack, Paul last_name: Zwack - first_name: Inge full_name: De Clercq, Inge last_name: De Clercq - first_name: Timothy full_name: Howton, Timothy last_name: Howton - first_name: H Tucker full_name: Hallmark, H Tucker last_name: Hallmark - first_name: Andrej full_name: Hurny, Andrej id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87 last_name: Hurny - first_name: Erika full_name: Keshishian, Erika last_name: Keshishian - first_name: Alyssa full_name: Parish, Alyssa last_name: Parish - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: M Shahid full_name: Mukhtar, M Shahid last_name: Mukhtar - first_name: Frank full_name: Van Breusegem, Frank last_name: Van Breusegem - first_name: Aaron full_name: Rashotte, Aaron last_name: Rashotte citation: ama: Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415 apa: Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415 chicago: Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415. ieee: P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016. ista: Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258. mla: Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415. short: P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258. date_created: 2018-12-11T11:51:25Z date_published: 2016-10-02T00:00:00Z date_updated: 2022-05-24T09:26:03Z day: '02' department: - _id: EvBe doi: 10.1104/pp.16.00415 intvolume: ' 172' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1104/pp.16.00415 month: '10' oa: 1 oa_version: Published Version page: 1249 - 1258 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists publist_id: '5937' quality_controlled: '1' scopus_import: '1' status: public title: Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 172 year: '2016' ... --- _id: '1332' abstract: - lang: eng text: Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance. acknowledgement: This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891. article_number: '10333' author: - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Adam full_name: Palmer, Adam last_name: Palmer - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333 apa: Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333 chicago: Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333. ieee: R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333. mla: Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333. short: R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:25Z date_published: 2016-01-20T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '20' ddc: - '570' - '579' department: - _id: CaGu - _id: GaTk doi: 10.1038/ncomms10333 file: - access_level: open_access checksum: ef147bcbb8bd37e9079cf3ce06f5815d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:52Z date_updated: 2020-07-14T12:44:44Z file_id: '5039' file_name: IST-2016-662-v1+1_ncomms10333.pdf file_size: 1844107 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5936' pubrep_id: '662' quality_controlled: '1' scopus_import: 1 status: public title: Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1333' abstract: - lang: eng text: Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most. acknowledgement: We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding. article_number: '10915' author: - first_name: Manfred full_name: Milinski, Manfred last_name: Milinski - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Dirk full_name: Semmann, Dirk last_name: Semmann - first_name: Ralf full_name: Sommerfeld, Ralf last_name: Sommerfeld - first_name: Jochem full_name: Marotzke, Jochem last_name: Marotzke citation: ama: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 2016;7. doi:10.1038/ncomms10915 apa: Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915 chicago: Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10915. ieee: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915. mla: Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915, Nature Publishing Group, 2016, doi:10.1038/ncomms10915. short: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:25Z date_published: 2016-03-07T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '07' ddc: - '519' - '530' - '599' department: - _id: KrCh doi: 10.1038/ncomms10915 file: - access_level: open_access checksum: 9ea0d7ce59a555a1cb8353d5559407cb content_type: application/pdf creator: system date_created: 2018-12-12T10:10:44Z date_updated: 2020-07-14T12:44:44Z file_id: '4834' file_name: IST-2016-661-v1+1_ncomms10915.pdf file_size: 1432577 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5935' pubrep_id: '661' quality_controlled: '1' scopus_import: 1 status: public title: Humans choose representatives who enforce cooperation in social dilemmas through extortion 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1334' abstract: - lang: eng text: Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping. article_number: '11824' author: - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824 apa: Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11824 chicago: Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824. ieee: P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824. mla: Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications, vol. 7, 11824, Nature Publishing Group, 2016, doi:10.1038/ncomms11824. short: P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:26Z date_published: 2016-06-10T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '10' ddc: - '570' department: - _id: JoCs doi: 10.1038/ncomms11824 ec_funded: 1 file: - access_level: open_access checksum: e43307754abe65b840a21939fe163618 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:10Z date_updated: 2020-07-14T12:44:44Z file_id: '5196' file_name: IST-2016-660-v1+1_ncomms11824.pdf file_size: 1793846 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 257D4372-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I2072-B27 name: Interneuron plasticity during spatial learning publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5934' pubrep_id: '660' quality_controlled: '1' scopus_import: 1 status: public title: Activity dependent plasticity of hippocampal place maps 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1335' abstract: - lang: eng text: In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2' apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2. ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38.' ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.' mla: Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837, Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38. conference: end_date: 2016-09-10 location: Edinburgh, United Kingdom name: 'SAS: Static Analysis Symposium' start_date: 2016-09-08 date_created: 2018-12-11T11:51:26Z date_published: 2016-08-31T00:00:00Z date_updated: 2021-01-12T06:49:58Z day: '31' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-53413-7_2 ec_funded: 1 intvolume: ' 9837' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.06764 month: '08' oa: 1 oa_version: Preprint page: 23 - 38 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: Springer publist_id: '5932' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative monitor automata type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9837 year: '2016' ... --- _id: '1339' abstract: - lang: eng text: "We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n" acknowledgement: We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140). article_number: '143507' author: - first_name: Gerard full_name: Verbiest, Gerard last_name: Verbiest - first_name: Duo full_name: Xu, Duo id: 3454D55E-F248-11E8-B48F-1D18A9856A87 last_name: Xu - first_name: Matthias full_name: Goldsche, Matthias last_name: Goldsche - first_name: Timofiy full_name: Khodkov, Timofiy last_name: Khodkov - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Nils full_name: Von Den Driesch, Nils last_name: Von Den Driesch - first_name: Dan full_name: Buca, Dan last_name: Buca - first_name: Christoph full_name: Stampfer, Christoph last_name: Stampfer citation: ama: Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. 2016;109. doi:10.1063/1.4964122 apa: Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122 chicago: Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied  Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122. ieee: G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied  Physics Letter, vol. 109. American Institute of Physics, 2016. ista: Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied  Physics Letter. 109, 143507. mla: Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied  Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122. short: G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied  Physics Letter 109 (2016). date_created: 2018-12-11T11:51:28Z date_published: 2016-10-04T00:00:00Z date_updated: 2023-02-21T10:35:06Z day: '04' department: - _id: JoFi doi: 10.1063/1.4964122 intvolume: ' 109' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.04406 month: '10' oa: 1 oa_version: Preprint publication: Applied Physics Letter publication_status: published publisher: American Institute of Physics publist_id: '5928' quality_controlled: '1' scopus_import: 1 status: public title: Tunable mechanical coupling between driven microelectromechanical resonators type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2016' ... --- _id: '1340' abstract: - lang: eng text: We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11]. alternative_title: - LNCS author: - first_name: Kristoffer full_name: Hansen, Kristoffer last_name: Hansen - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Michal full_name: Koucký, Michal last_name: Koucký citation: ama: 'Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6' apa: 'Hansen, K., Ibsen-Jensen, R., & Koucký, M. (2016). The big match in small space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_6' chicago: Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6. ieee: 'K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 64–76.' ista: 'Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76.' mla: Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928, Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6. short: K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76. conference: end_date: 2016-09-21 location: Liverpool, United Kingdom name: 'SAGT: Symposium on Algorithmic Game Theory' start_date: 2016-09-19 date_created: 2018-12-11T11:51:28Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T06:50:00Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-53354-3_6 ec_funded: 1 intvolume: ' 9928' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.07634 month: '09' oa: 1 oa_version: Preprint page: 64 - 76 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided 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: '5927' quality_controlled: '1' scopus_import: 1 status: public title: The big match in small space type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9928 year: '2016' ... --- _id: '1341' abstract: - lang: eng text: In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability. acknowledgement: This research was supported in part by the European Research Council (ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). alternative_title: - LNCS author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - 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: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: 'Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In: Vol 9928. Springer; 2016:153-166. doi:10.1007/978-3-662-53354-3_13' apa: 'Avni, G., Henzinger, T. A., & Kupferman, O. (2016). Dynamic resource allocation games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_13' chicago: Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games,” 9928:153–66. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_13. ieee: 'G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 153–166.' ista: 'Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.' mla: Avni, Guy, et al. Dynamic Resource Allocation Games. Vol. 9928, Springer, 2016, pp. 153–66, doi:10.1007/978-3-662-53354-3_13. short: G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166. conference: end_date: 2016-09-21 location: Liverpool, United Kingdom name: 'SAGT: Symposium on Algorithmic Game Theory' start_date: 2016-09-19 date_created: 2018-12-11T11:51:28Z date_published: 2016-09-01T00:00:00Z date_updated: 2023-08-17T13:52:49Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-53354-3_13 ec_funded: 1 file: - access_level: open_access checksum: 0825eefd4e22774f6f62cb7d7389b05a content_type: application/pdf creator: system date_created: 2018-12-12T10:14:22Z date_updated: 2020-07-14T12:44:45Z file_id: '5073' file_name: IST-2016-645-v1+1_sagt-cr.pdf file_size: 243458 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 9928' language: - iso: eng month: '09' oa: 1 oa_version: Preprint page: 153 - 166 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 - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '5926' pubrep_id: '645' quality_controlled: '1' related_material: record: - id: '6761' relation: later_version status: public scopus_import: 1 status: public title: Dynamic resource allocation games type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9928 year: '2016' ... --- _id: '1342' abstract: - lang: eng text: A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics. author: - first_name: Michael full_name: Baym, Michael last_name: Baym - first_name: Tami full_name: Lieberman, Tami last_name: Lieberman - first_name: Eric full_name: Kelsic, Eric last_name: Kelsic - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Rotem full_name: Gross, Rotem last_name: Gross - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822 apa: Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822 chicago: Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822. ieee: M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016. ista: Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151. mla: Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822. short: M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151. date_created: 2018-12-11T11:51:29Z date_published: 2016-09-09T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '09' department: - _id: CaGu - _id: GaTk doi: 10.1126/science.aag0822 intvolume: ' 353' issue: '6304' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/ month: '09' oa: 1 oa_version: Preprint page: 1147 - 1151 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5911' quality_controlled: '1' scopus_import: 1 status: public title: Spatiotemporal microbial evolution on antibiotic landscapes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 353 year: '2016' ... --- _id: '1343' abstract: - lang: eng text: "The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a\r\n\r\npotential for explaining the mystery of high-temperature superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat using the machinery of dissipative quantum state engineering, one can observe the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe driven-dissipative dynamics. The proposed controlled dissipation channels described in this work\r\n\r\nare straightforward to add to already existing experimental setups." acknowledgement: "We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco, Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza, and Martin Zwierlein. The work was supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within SFB 1227 (DQ-mat)." article_number: '093042' author: - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Hendrik full_name: Weimer, Hendrik last_name: Weimer - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042 apa: Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042 chicago: Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042. ieee: J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no. 9. IOP Publishing Ltd., 2016. ista: Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042. mla: Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042. short: J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016). date_created: 2018-12-11T11:51:29Z date_published: 2016-09-22T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '22' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/18/9/093042 ec_funded: 1 file: - access_level: open_access checksum: 2a43e235222755e31ffbd369882c61de content_type: application/pdf creator: system date_created: 2018-12-12T10:17:52Z date_updated: 2020-07-14T12:44:45Z file_id: '5309' file_name: IST-2016-655-v1+1_njp_18_9_093042.pdf file_size: 1076029 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 18' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5909' pubrep_id: '655' quality_controlled: '1' scopus_import: 1 status: public title: Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2016' ... --- _id: '1344' abstract: - lang: eng text: Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms. acknowledgement: "The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP)." article_number: e19048 author: - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jeffrey full_name: Leung, Jeffrey last_name: Leung - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048 apa: Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048 chicago: Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048. ieee: M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016. ista: Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048. mla: Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048. short: M. Fendrych, J. Leung, J. Friml, ELife 5 (2016). date_created: 2018-12-11T11:51:29Z date_published: 2016-09-14T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '14' ddc: - '581' department: - _id: JiFr doi: 10.7554/eLife.19048 ec_funded: 1 file: - access_level: open_access checksum: 9209541fbba00f24daad21a5d568540d content_type: application/pdf creator: system date_created: 2018-12-12T10:09:24Z date_updated: 2020-07-14T12:44:45Z file_id: '4748' file_name: IST-2016-693-v1+1_e19048-download.pdf file_size: 5666343 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5908' pubrep_id: '654' quality_controlled: '1' scopus_import: 1 status: public title: TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2016' ... --- _id: '1345' abstract: - lang: eng text: The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components. article_number: '16102' author: - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102' apa: 'Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102' chicago: 'Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.' ieee: 'G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.' ista: 'Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.' mla: 'Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.' short: G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016). date_created: 2018-12-11T11:51:30Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:02Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1038/nplants.2016.102 file: - access_level: open_access checksum: 9ba65f558563b287f875f48fa9f30fb2 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:36Z date_updated: 2020-07-14T12:44:45Z file_id: '4954' file_name: IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf file_size: 127781 relation: main_file - access_level: open_access checksum: 550d252be808d8ca2b43e83dddb4212f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:37Z date_updated: 2020-07-14T12:44:45Z file_id: '4955' file_name: IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf file_size: 430556 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '5907' pubrep_id: '1007' quality_controlled: '1' scopus_import: 1 status: public title: 'Plasma membrane: Negative attraction' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2016' ... --- _id: '1346' abstract: - lang: eng text: ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane. acknowledgement: "We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R." article_number: '11710' author: - first_name: Wim full_name: Dejonghe, Wim last_name: Dejonghe - first_name: Sabine full_name: Kuenen, Sabine last_name: Kuenen - first_name: Evelien full_name: Mylle, Evelien last_name: Mylle - first_name: Mina K full_name: Vasileva, Mina K id: 3407EB18-F248-11E8-B48F-1D18A9856A87 last_name: Vasileva - first_name: Olivier full_name: Keech, Olivier last_name: Keech - first_name: Corrado full_name: Viotti, Corrado last_name: Viotti - first_name: Jef full_name: Swerts, Jef last_name: Swerts - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Fausto full_name: Ortiz Morea, Fausto last_name: Ortiz Morea - first_name: Kiril full_name: Mishev, Kiril last_name: Mishev - first_name: Simon full_name: Delang, Simon last_name: Delang - first_name: Stefan full_name: Scholl, Stefan last_name: Scholl - first_name: Xavier full_name: Zarza, Xavier last_name: Zarza - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Jiorgos full_name: Kourelis, Jiorgos last_name: Kourelis - first_name: Jaroslaw full_name: Kasprowicz, Jaroslaw last_name: Kasprowicz - first_name: Le full_name: Nguyen, Le last_name: Nguyen - first_name: Andrzej full_name: Drozdzecki, Andrzej last_name: Drozdzecki - first_name: Isabelle full_name: Van Houtte, Isabelle last_name: Van Houtte - first_name: Anna full_name: Szatmári, Anna last_name: Szatmári - first_name: Mateusz full_name: Majda, Mateusz last_name: Majda - first_name: Gary full_name: Baisa, Gary last_name: Baisa - first_name: Sebastian full_name: Bednarek, Sebastian last_name: Bednarek - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Dominique full_name: Audenaert, Dominique last_name: Audenaert - first_name: Christa full_name: Testerink, Christa last_name: Testerink - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Karin full_name: Schumacher, Karin last_name: Schumacher - first_name: Johan full_name: Winne, Johan last_name: Winne - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Patrik full_name: Verstreken, Patrik last_name: Verstreken - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 2016;7. doi:10.1038/ncomms11710 apa: Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11710 chicago: Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710. ieee: W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710. mla: Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications, vol. 7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710. short: W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:30Z date_published: 2016-06-08T00:00:00Z date_updated: 2023-09-07T12:54:35Z day: '08' ddc: - '570' department: - _id: JiFr doi: 10.1038/ncomms11710 ec_funded: 1 file: - access_level: open_access checksum: e8dc81b3e44db5a7718d7f1501ce1aa7 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:47Z date_updated: 2020-07-14T12:44:45Z file_id: '5369' file_name: IST-2016-653-v1+1_ncomms11710_1_.pdf file_size: 3532505 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5906' pubrep_id: '653' quality_controlled: '1' related_material: record: - id: '7172' relation: dissertation_contains status: public scopus_import: 1 status: public title: Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1347' abstract: - lang: eng text: 'During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem''s constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.' acknowledgement: We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory. article_number: '011012' author: - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012 apa: Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.011012 chicago: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.011012. ieee: R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical Society, 2016. ista: Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012. mla: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012. short: R. Schmidt, M. Lemeshko, Physical Review X 6 (2016). date_created: 2018-12-11T11:51:30Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1103/PhysRevX.6.011012 file: - access_level: open_access checksum: 6757a164d3c38905e05b2b5a188cb8ff content_type: application/pdf creator: system date_created: 2018-12-12T10:15:59Z date_updated: 2020-07-14T12:44:45Z file_id: '5183' file_name: IST-2016-652-v1+1_PhysRevX.6.011012.pdf file_size: 1165869 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '5902' pubrep_id: '652' quality_controlled: '1' scopus_import: 1 status: public title: Deformation of a quantum many-particle system by a rotating impurity 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2016' ... --- _id: '1348' abstract: - lang: eng text: 'A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.' alternative_title: - LNCS author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 citation: ama: 'Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:10.1007/978-3-319-44543-4_3' apa: 'Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3' chicago: Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3. ieee: 'R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.' ista: 'Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.' mla: Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843, Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3. short: R. Fulek, in:, Springer, 2016, pp. 31–42. conference: end_date: 2018-08-19 location: Helsinki, Finland name: 'IWOCA: International Workshop on Combinatorial Algorithms' start_date: 2016-08-17 date_created: 2018-12-11T11:51:31Z date_published: 2016-08-09T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '09' department: - _id: UlWa doi: 10.1007/978-3-319-44543-4_3 ec_funded: 1 intvolume: ' 9843' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.07144 month: '08' oa: 1 oa_version: Preprint page: 31 - 42 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5901' quality_controlled: '1' scopus_import: 1 status: public title: Bounded embeddings of graphs in the plane type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9843 year: '2016' ... --- _id: '1349' abstract: - lang: eng text: Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys. author: - first_name: Pietro full_name: Oliveto, Pietro last_name: Oliveto - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909' apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909' chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909. ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170. ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.' mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909. short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170. conference: end_date: 2016-07-24 location: Denver, CO, USA name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2016-07-20 date_created: 2018-12-11T11:51:31Z date_published: 2016-07-20T00:00:00Z date_updated: 2021-01-12T06:50:03Z day: '20' ddc: - '576' department: - _id: NiBa - _id: CaGu doi: 10.1145/2908812.2908909 ec_funded: 1 file: - access_level: open_access checksum: a1896e39e4113f2711e46b435d5f3e69 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:27Z date_updated: 2020-07-14T12:44:45Z file_id: '5214' file_name: IST-2016-650-v1+1_p1163-oliveto.pdf file_size: 979026 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1163 - 1170 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 ' publication_status: published publisher: ACM publist_id: '5900' pubrep_id: '650' quality_controlled: '1' scopus_import: 1 status: public title: When non-elitism outperforms elitism for crossing fitness valleys 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ...