--- _id: '495' abstract: - lang: eng text: An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice. alternative_title: - EPTCS author: - first_name: Alex full_name: Kruckman, Alex last_name: Kruckman - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin - first_name: John full_name: Sheridan, John last_name: Sheridan - first_name: Ben full_name: Zax, Ben last_name: Zax citation: ama: 'Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata with advice. In: Proceedings GandALF 2012. Vol 96. Open Publishing Association; 2012:238-246. doi:10.4204/EPTCS.96.18' apa: 'Kruckman, A., Rubin, S., Sheridan, J., & Zax, B. (2012). A Myhill Nerode theorem for automata with advice. In Proceedings GandALF 2012 (Vol. 96, pp. 238–246). Napoli, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.96.18' chicago: Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode Theorem for Automata with Advice.” In Proceedings GandALF 2012, 96:238–46. Open Publishing Association, 2012. https://doi.org/10.4204/EPTCS.96.18. ieee: A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for automata with advice,” in Proceedings GandALF 2012, Napoli, Italy, 2012, vol. 96, pp. 238–246. ista: 'Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246.' mla: Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” Proceedings GandALF 2012, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:10.4204/EPTCS.96.18. short: A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246. conference: end_date: 2012-09-08 location: Napoli, Italy name: 'GandALF: Games, Automata, Logics and Formal Verification' start_date: 2012-09-06 date_created: 2018-12-11T11:46:47Z date_published: 2012-10-07T00:00:00Z date_updated: 2021-01-12T08:01:04Z day: '07' ddc: - '004' department: - _id: KrCh doi: 10.4204/EPTCS.96.18 ec_funded: 1 file: - access_level: open_access checksum: 56277f95edc9d531fa3bdc5f9579fda8 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:31Z date_updated: 2020-07-14T12:46:35Z file_id: '5152' file_name: IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf file_size: 97736 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 96' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 238 - 246 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings GandALF 2012 publication_status: published publisher: Open Publishing Association publist_id: '7325' pubrep_id: '944' quality_controlled: '1' scopus_import: 1 status: public title: A Myhill Nerode theorem for automata with advice 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 volume: 96 year: '2012' ... --- _id: '498' abstract: - lang: eng text: Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n" author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x' apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x' chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.' ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” Evolutionary Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.' ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.' mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.' short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924. date_created: 2018-12-11T11:46:48Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T08:01:06Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/j.1752-4571.2012.00284.x file: - access_level: open_access checksum: 233007138606aca5a2f75f7ae1742f43 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:33Z date_updated: 2020-07-14T12:46:35Z file_id: '4821' file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf file_size: 396136 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 5' issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: 913 - 924 publication: Evolutionary Applications publication_status: published publisher: Wiley-Blackwell publist_id: '7322' pubrep_id: '942' quality_controlled: '1' status: public title: 'Predicting local adaptation in fragmented plant populations: Implications for restoration genetics' 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: 5 year: '2012' ... --- _id: '496' abstract: - lang: eng text: 'We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by ''finitary'' set-interpretations.' alternative_title: - LICS article_number: '6280474' author: - first_name: Alexander full_name: Rabinovich, Alexander last_name: Rabinovich - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin citation: ama: 'Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:10.1109/LICS.2012.65' apa: 'Rabinovich, A., & Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.65' chicago: Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. https://doi.org/10.1109/LICS.2012.65. ieee: 'A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.' ista: 'Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.' mla: Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65. short: A. Rabinovich, S. Rubin, in:, IEEE, 2012. conference: end_date: 2012-06-28 location: Dubrovnik, Croatia name: 'LICS: Symposium on Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T11:46:47Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:01:05Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2012.65 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf month: '01' oa: 1 oa_version: Preprint project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: IEEE publist_id: '7324' quality_controlled: '1' scopus_import: 1 status: public title: Interpretations in trees with countably many branches type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '494' abstract: - lang: eng text: We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata. article_number: '29' author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: Boker U, Kupferman O. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 2012;13(4). doi:10.1145/2362355.2362357 apa: Boker, U., & Kupferman, O. (2012). Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2362355.2362357 chicago: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” ACM Transactions on Computational Logic (TOCL). ACM, 2012. https://doi.org/10.1145/2362355.2362357. ieee: U. Boker and O. Kupferman, “Translating to Co-Büchi made tight, unified, and useful,” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 4. ACM, 2012. ista: Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29. mla: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 4, 29, ACM, 2012, doi:10.1145/2362355.2362357. short: U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13 (2012). date_created: 2018-12-11T11:46:47Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:01:03Z day: '01' department: - _id: ToHe doi: 10.1145/2362355.2362357 intvolume: ' 13' issue: '4' language: - iso: eng month: '10' oa_version: None publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '7326' quality_controlled: '1' scopus_import: 1 status: public title: Translating to Co-Büchi made tight, unified, and useful type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '506' article_processing_charge: No article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 2012;197(3):347-349. doi:10.1083/jcb.201204039' apa: 'Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201204039' chicago: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” Journal of Cell Biology. Rockefeller University Press, 2012. https://doi.org/10.1083/jcb.201204039.' ieee: 'M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” Journal of Cell Biology, vol. 197, no. 3. Rockefeller University Press, pp. 347–349, 2012.' ista: 'Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.' mla: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” Journal of Cell Biology, vol. 197, no. 3, Rockefeller University Press, 2012, pp. 347–49, doi:10.1083/jcb.201204039.' short: M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349. date_created: 2018-12-11T11:46:51Z date_published: 2012-04-30T00:00:00Z date_updated: 2021-01-12T08:01:11Z day: '30' ddc: - '570' department: - _id: MiSi doi: 10.1083/jcb.201204039 file: - access_level: open_access checksum: 45c02be33ebd99fc3077d60b9c90bdfa content_type: application/pdf creator: kschuh date_created: 2019-02-12T09:03:09Z date_updated: 2020-07-14T12:46:36Z file_id: '5957' file_name: 2012_CellBiology_Sixt.pdf file_size: 986566 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 197' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '04' oa: 1 oa_version: Published Version page: 347 - 349 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '7314' quality_controlled: '1' scopus_import: 1 status: public title: 'Cell migration: Fibroblasts find a new way to get ahead' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 197 year: '2012' ... --- _id: '497' abstract: - lang: eng text: 'One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.' alternative_title: - LIPIcs author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Siddhesh full_name: Chaubal, Siddhesh last_name: Chaubal - first_name: Pritish full_name: Kamath, Pritish last_name: Kamath citation: ama: 'Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182. doi:10.4230/LIPIcs.CSL.2012.167' apa: 'Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2012.167' chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. https://doi.org/10.4230/LIPIcs.CSL.2012.167. ieee: 'K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.' ista: 'Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations. EACSL: European Association for Computer Science Logic, LIPIcs, vol. 16, 167–182.' mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–82, doi:10.4230/LIPIcs.CSL.2012.167. short: K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182. conference: end_date: 2012-09-06 location: Fontainebleau, France name: 'EACSL: European Association for Computer Science Logic' start_date: 2012-09-03 date_created: 2018-12-11T11:46:48Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-02-23T12:23:32Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.CSL.2012.167 ec_funded: 1 file: - access_level: open_access checksum: f1b0dd99240800db2d7dbf9b5131fe5e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:50Z date_updated: 2020-07-14T12:46:35Z file_id: '4712' file_name: IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf file_size: 471236 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 167 - 182 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7323' pubrep_id: '943' quality_controlled: '1' related_material: record: - id: '5378' relation: earlier_version status: public scopus_import: 1 status: public title: Faster algorithms for alternating refinement relations tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2012' ... --- _id: '3165' abstract: - lang: eng text: Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m > n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem. acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi games. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2012:1386-1399. doi:10.1137/1.9781611973099.109' apa: 'Chatterjee, K., & Henzinger, M. H. (2012). An O(n2) time algorithm for alternating Büchi games. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1386–1399). Kyoto, Japan: SIAM. https://doi.org/10.1137/1.9781611973099.109' chicago: Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 1386–99. SIAM, 2012. https://doi.org/10.1137/1.9781611973099.109. ieee: K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating Büchi games,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Kyoto, Japan, 2012, pp. 1386–1399. ista: 'Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1386–1399.' mla: Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–99, doi:10.1137/1.9781611973099.109. short: K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–1399. conference: end_date: 2012-01-19 location: Kyoto, Japan name: 'SODA: Symposium on Discrete Algorithms' start_date: 2012-01-17 date_created: 2018-12-11T12:01:46Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T12:23:35Z day: '01' department: - _id: KrCh doi: 10.1137/1.9781611973099.109 ec_funded: 1 external_id: arxiv: - '1109.5018' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1109.5018 month: '01' oa: 1 oa_version: None page: 1386 - 1399 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms publication_status: published publisher: SIAM publist_id: '3519' pubrep_id: '15' quality_controlled: '1' related_material: record: - id: '2141' relation: later_version status: public - id: '5379' relation: earlier_version status: public status: public title: An O(n2) time algorithm for alternating Büchi games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2956' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and parity objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two-player pushdown games. Finally we also show that all the problems have the same computational complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' acknowledgement: "The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the Israeli Centers of Research Excellence (ICORE) program, (Center No. 4/11), the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.\r\nA Technical Report of this paper is available via internal link." article_number: '6280438' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: 'Chatterjee K, Velner Y. Mean payoff pushdown games. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.30' apa: 'Chatterjee, K., & Velner, Y. (2012). Mean payoff pushdown games. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia : IEEE. https://doi.org/10.1109/LICS.2012.30' chicago: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.30. ieee: K. Chatterjee and Y. Velner, “Mean payoff pushdown games,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia , 2012. ista: 'Chatterjee K, Velner Y. 2012. Mean payoff pushdown games. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280438.' mla: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280438, IEEE, 2012, doi:10.1109/LICS.2012.30. short: K. Chatterjee, Y. Velner, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: 'Dubrovnik, Croatia ' name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:32Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:30Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.30 ec_funded: 1 language: - iso: eng month: '08' oa_version: None project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3770' quality_controlled: '1' related_material: record: - id: '5377' relation: earlier_version status: public scopus_import: 1 status: public title: Mean payoff pushdown games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5377' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Mean-Payoff Pushdown Games. IST Austria; 2012. doi:10.15479/AT:IST-2012-0002 apa: Chatterjee, K., & Velner, Y. (2012). Mean-payoff pushdown games. IST Austria. https://doi.org/10.15479/AT:IST-2012-0002 chicago: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0002. ieee: K. Chatterjee and Y. Velner, Mean-payoff pushdown games. IST Austria, 2012. ista: Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p. mla: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012, doi:10.15479/AT:IST-2012-0002. short: K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012. date_created: 2018-12-12T11:38:59Z date_published: 2012-07-02T00:00:00Z date_updated: 2023-02-23T11:05:50Z day: '02' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2012-0002 file: - access_level: open_access checksum: a03c08c1589dbb0c96183a8bcf3ab240 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:00Z date_updated: 2020-07-14T12:46:38Z file_id: '5522' file_name: IST-2012-002_IST-2012-0002.pdf file_size: 592098 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '10' related_material: record: - id: '2956' relation: later_version status: public status: public title: Mean-payoff pushdown games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5378' abstract: - lang: eng text: 'One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Siddhesh full_name: Chaubal, Siddhesh last_name: Chaubal - first_name: Pritish full_name: Kamath, Pritish last_name: Kamath citation: ama: Chatterjee K, Chaubal S, Kamath P. Faster Algorithms for Alternating Refinement Relations. IST Austria; 2012. doi:10.15479/AT:IST-2012-0001 apa: Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for alternating refinement relations. IST Austria. https://doi.org/10.15479/AT:IST-2012-0001 chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0001. ieee: K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating refinement relations. IST Austria, 2012. ista: Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p. mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001. short: K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012. date_created: 2018-12-12T11:38:59Z date_published: 2012-07-04T00:00:00Z date_updated: 2023-02-23T12:21:38Z day: '04' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2012-0001 file: - access_level: open_access checksum: ec8d1857cc7095d3de5107a0162ced37 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:28Z date_updated: 2020-07-14T12:46:39Z file_id: '5489' file_name: IST-2012-0001_IST-2012-0001.pdf file_size: 394256 relation: main_file file_date_updated: 2020-07-14T12:46:39Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '14' related_material: record: - id: '497' relation: later_version status: public status: public title: Faster algorithms for alternating refinement relations type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2955' abstract: - lang: eng text: 'We consider two-player stochastic games played on finite graphs with reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1), or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, the players (a) may not be allowed to use randomization (pure strategies), or (b) may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) may use full randomization. Our main results for pure strategies are as follows. (1) For one-sided games with player 1 having partial observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almostsure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete. (2) For one-sided games with player 2 having partial observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibits serious flaws in previous results of the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.' acknowledgement: 'This work was partially supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' article_number: '6280436' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.28' apa: 'Chatterjee, K., & Doyen, L. (2012). Partial-observation stochastic games: How to win when belief fails. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.28' chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.28.' ieee: 'K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.' ista: 'Chatterjee K, Doyen L. 2012. Partial-observation stochastic games: How to win when belief fails. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280436.' mla: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280436, IEEE, 2012, doi:10.1109/LICS.2012.28.' short: K. Chatterjee, L. Doyen, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: Dubrovnik, Croatia name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:32Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:43Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.28 ec_funded: 1 external_id: arxiv: - '1107.2141' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.2141 month: '08' oa: 1 oa_version: Preprint project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3771' quality_controlled: '1' related_material: record: - id: '2211' relation: later_version status: public - id: '5381' relation: earlier_version status: public scopus_import: 1 status: public title: 'Partial-observation stochastic games: How to win when belief fails' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3341' abstract: - lang: eng text: 'We consider two-player stochastic games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with \omega-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity gameswith respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition function is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).' 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 citation: ama: 'Chatterjee K. Robustness of structurally equivalent concurrent parity games. In: Vol 7213. Springer; 2012:270-285. doi:10.1007/978-3-642-28729-9_18' apa: 'Chatterjee, K. (2012). Robustness of structurally equivalent concurrent parity games (Vol. 7213, pp. 270–285). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia: Springer. https://doi.org/10.1007/978-3-642-28729-9_18' chicago: Chatterjee, Krishnendu. “Robustness of Structurally Equivalent Concurrent Parity Games,” 7213:270–85. Springer, 2012. https://doi.org/10.1007/978-3-642-28729-9_18. ieee: 'K. Chatterjee, “Robustness of structurally equivalent concurrent parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia, 2012, vol. 7213, pp. 270–285.' ista: 'Chatterjee K. 2012. Robustness of structurally equivalent concurrent parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 7213, 270–285.' mla: Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent Parity Games. Vol. 7213, Springer, 2012, pp. 270–85, doi:10.1007/978-3-642-28729-9_18. short: K. Chatterjee, in:, Springer, 2012, pp. 270–285. conference: end_date: 2012-04-01 location: Tallinn, Estonia name: 'FoSSaCS: Foundations of Software Science and Computation Structures' start_date: 2012-03-24 date_created: 2018-12-11T12:02:46Z date_published: 2012-03-22T00:00:00Z date_updated: 2023-02-23T12:23:46Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-642-28729-9_18 ec_funded: 1 external_id: arxiv: - '1107.2009' intvolume: ' 7213' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.2009 month: '03' oa: 1 oa_version: Preprint page: 270 - 285 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3284' quality_controlled: '1' related_material: record: - id: '5382' relation: earlier_version status: public scopus_import: 1 status: public title: Robustness of structurally equivalent concurrent parity games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7213 year: '2012' ... --- _id: '2957' abstract: - lang: eng text: 'We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether words are accepted with probability arbitrarily close to 1. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape (regular) words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions. For most decidable problems we show an optimal PSPACE-complete complexity bound.' article_number: '6280437' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: 'Chatterjee K, Tracol M. Decidable problems for probabilistic automata on infinite words. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.29' apa: 'Chatterjee, K., & Tracol, M. (2012). Decidable problems for probabilistic automata on infinite words. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia : IEEE. https://doi.org/10.1109/LICS.2012.29' chicago: Chatterjee, Krishnendu, and Mathieu Tracol. “Decidable Problems for Probabilistic Automata on Infinite Words.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.29. ieee: K. Chatterjee and M. Tracol, “Decidable problems for probabilistic automata on infinite words,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia , 2012. ista: 'Chatterjee K, Tracol M. 2012. Decidable problems for probabilistic automata on infinite words. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280437.' mla: Chatterjee, Krishnendu, and Mathieu Tracol. “Decidable Problems for Probabilistic Automata on Infinite Words.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280437, IEEE, 2012, doi:10.1109/LICS.2012.29. short: K. Chatterjee, M. Tracol, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: 'Dubrovnik, Croatia ' name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:33Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:51Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.29 ec_funded: 1 external_id: arxiv: - '1107.2091' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1107.2091 month: '08' oa: 1 oa_version: Preprint project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3769' quality_controlled: '1' related_material: record: - id: '5384' relation: earlier_version status: public scopus_import: 1 status: public title: Decidable problems for probabilistic automata on infinite words type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3249' abstract: - lang: eng text: Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of "fit" or "desirability". We extend the simulation preorder to the quantitative setting by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes. acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), the European Union project COMBEST and the European Network of Excellence Artist Design. author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. Theoretical Computer Science. 2012;413(1):21-35. doi:10.1016/j.tcs.2011.08.002 apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2012). Simulation distances. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.08.002 chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.08.002. ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” Theoretical Computer Science, vol. 413, no. 1. Elsevier, pp. 21–35, 2012. ista: Cerny P, Henzinger TA, Radhakrishna A. 2012. Simulation distances. Theoretical Computer Science. 413(1), 21–35. mla: Cerny, Pavol, et al. “Simulation Distances.” Theoretical Computer Science, vol. 413, no. 1, Elsevier, 2012, pp. 21–35, doi:10.1016/j.tcs.2011.08.002. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 413 (2012) 21–35. date_created: 2018-12-11T12:02:15Z date_published: 2012-01-06T00:00:00Z date_updated: 2023-02-23T12:24:04Z day: '06' department: - _id: ToHe doi: 10.1016/j.tcs.2011.08.002 ec_funded: 1 intvolume: ' 413' issue: '1' language: - iso: eng month: '01' oa_version: None page: 21 - 35 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: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '3408' pubrep_id: '42' quality_controlled: '1' related_material: record: - id: '4393' relation: earlier_version status: public - id: '5389' relation: earlier_version status: public scopus_import: 1 status: public title: Simulation distances type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 413 year: '2012' ... --- _id: '3124' abstract: - lang: eng text: "We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n" alternative_title: - Inferning 2012 author: - first_name: Filip full_name: Korc, Filip id: 476A2FD6-F248-11E8-B48F-1D18A9856A87 last_name: Korc - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.' apa: 'Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.' chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012. ieee: 'F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012.' ista: 'Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .' mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. ICML, 2012. short: F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012. conference: end_date: 2012-07-01 location: Edinburgh, Scotland name: 'ICML: International Conference on Machine Learning' start_date: 2012-06-26 date_created: 2018-12-11T12:01:31Z date_published: 2012-06-30T00:00:00Z date_updated: 2023-02-23T12:24:24Z day: '30' ddc: - '000' department: - _id: ChLa - _id: VlKo file: - access_level: open_access checksum: 3d0d4246548c736857302aadb2ff5d15 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:34Z date_updated: 2020-07-14T12:46:00Z file_id: '4889' file_name: IST-2016-565-v1+1_DM-inferning2012.pdf file_size: 305836 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version publication_status: published publisher: ICML publist_id: '3575' pubrep_id: '565' quality_controlled: '1' related_material: record: - id: '5396' relation: later_version status: public status: public title: Approximating marginals using discrete energy minimization type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5396' abstract: - lang: eng text: We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can out-perform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions. alternative_title: - IST Austria Technical Report author: - first_name: Filip full_name: Korc, Filip id: 476A2FD6-F248-11E8-B48F-1D18A9856A87 last_name: Korc - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Korc F, Kolmogorov V, Lampert C. Approximating Marginals Using Discrete Energy Minimization. IST Austria; 2012. doi:10.15479/AT:IST-2012-0003 apa: Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. IST Austria. https://doi.org/10.15479/AT:IST-2012-0003 chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0003. ieee: F. Korc, V. Kolmogorov, and C. Lampert, Approximating marginals using discrete energy minimization. IST Austria, 2012. ista: Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p. mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012, doi:10.15479/AT:IST-2012-0003. short: F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012. date_created: 2018-12-12T11:39:06Z date_published: 2012-07-23T00:00:00Z date_updated: 2023-02-23T11:13:22Z day: '23' ddc: - '000' department: - _id: VlKo - _id: ChLa doi: 10.15479/AT:IST-2012-0003 file: - access_level: open_access checksum: 7e0ba85ad123b13223aaf6cdde2d288c content_type: application/pdf creator: system date_created: 2018-12-12T11:53:29Z date_updated: 2020-07-14T12:46:44Z file_id: '5490' file_name: IST-2012-0003_IST-2012-0003.pdf file_size: 618744 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '13' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '36' related_material: record: - id: '3124' relation: earlier_version status: public status: public title: Approximating marginals using discrete energy minimization type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5398' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Actual State of Research Data @ ISTAustria. IST Austria; 2012. apa: Porsche, J. (2012). Actual state of research data @ ISTAustria. IST Austria. chicago: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012. ieee: J. Porsche, Actual state of research data @ ISTAustria. IST Austria, 2012. ista: Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p. mla: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012. short: J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012. date_created: 2018-12-12T11:39:06Z date_published: 2012-11-12T00:00:00Z date_updated: 2020-07-14T23:04:49Z day: '12' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: e0a7c041eea1ca4b70ab6f9ec5177f4e content_type: application/pdf creator: system date_created: 2018-12-12T11:53:11Z date_updated: 2020-07-14T12:46:44Z file_id: '5472' file_name: IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf file_size: 238544 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '103' status: public title: Actual state of research data @ ISTAustria type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5839' abstract: - lang: eng text: "Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two \r\nsignificant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe \ gradient image. Due to poor illumination, the region boundaries in \ an image may become vague, creating \r\nuncertainties in the gradient \ image. In this paper, we have proposed an algorithm based on the \ concept of type-2 fuzzy sets to handle uncertainties that automatically \ selects the threshold values needed to segment the gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). " author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Jaya full_name: Sil, Jaya last_name: Sil citation: ama: Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 2012;4:820-824. doi:10.1016/j.protcy.2012.05.134 apa: Biswas, R., & Sil, J. (2012). An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. Elsevier. https://doi.org/10.1016/j.protcy.2012.05.134 chicago: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology. Elsevier, 2012. https://doi.org/10.1016/j.protcy.2012.05.134. ieee: R. Biswas and J. Sil, “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets,” Procedia Technology, vol. 4. Elsevier, pp. 820–824, 2012. ista: Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824. mla: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology, vol. 4, Elsevier, 2012, pp. 820–24, doi:10.1016/j.protcy.2012.05.134. short: R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824. date_created: 2019-01-17T11:54:21Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T08:03:43Z day: '01' ddc: - '000' doi: 10.1016/j.protcy.2012.05.134 extern: '1' file: - access_level: open_access checksum: ba0185986b151d8c11201f48cd505ceb content_type: application/pdf creator: dernst date_created: 2019-01-21T07:28:06Z date_updated: 2020-07-14T12:47:12Z file_id: '5863' file_name: 2012_Procedia_Biswas.pdf file_size: 305426 relation: main_file file_date_updated: 2020-07-14T12:47:12Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 820-824 publication: Procedia Technology publication_identifier: issn: - 2212-0173 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2012' ... --- _id: '596' abstract: - lang: eng text: The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation. article_processing_charge: No author: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Dylan full_name: Taatjes, Dylan last_name: Taatjes citation: ama: Bernecky C, Taatjes D. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 2012;417(5):387-394. doi:10.1016/j.jmb.2012.02.014 apa: Bernecky, C., & Taatjes, D. (2012). Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2012.02.014 chicago: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology. Elsevier, 2012. https://doi.org/10.1016/j.jmb.2012.02.014. ieee: C. Bernecky and D. Taatjes, “Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly,” Journal of Molecular Biology, vol. 417, no. 5. Elsevier, pp. 387–394, 2012. ista: Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 417(5), 387–394. mla: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology, vol. 417, no. 5, Elsevier, 2012, pp. 387–94, doi:10.1016/j.jmb.2012.02.014. short: C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394. date_created: 2018-12-11T11:47:24Z date_published: 2012-04-13T00:00:00Z date_updated: 2021-01-12T08:05:21Z day: '13' doi: 10.1016/j.jmb.2012.02.014 extern: '1' intvolume: ' 417' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/ month: '04' oa: 1 oa_version: None page: 387 - 394 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '7208' status: public title: Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 417 year: '2012' ... --- _id: '6136' abstract: - lang: eng text: Tonic receptors convey stimulus duration and intensity and are implicated in homeostatic control. However, how tonic homeostatic signals are generated and how they reconfigure neural circuits and modify animal behavior is poorly understood. Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors that continuously signal ambient [O2] to set the animal's behavioral state. Sustained signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels, the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked continuous neuropeptide release, which helps elicit the enduring behavioral state associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream neural circuits, including the hub interneuron RMG. O2 receptors evoked similar locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt. However, a phasic component of the URX receptors' response to high d[O2]/dt, as well as tonic-to-phasic transformations in downstream interneurons, enabled transient reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic signals can generate both transient and enduring behavioral change. author: - first_name: Karl Emanuel full_name: Busch, Karl Emanuel last_name: Busch - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: Zoltan full_name: Soltesz, Zoltan last_name: Soltesz - first_name: Robin Joseph full_name: Murphy, Robin Joseph last_name: Murphy - first_name: Olivier full_name: Faivre, Olivier last_name: Faivre - first_name: Berthold full_name: Hedwig, Berthold last_name: Hedwig - first_name: Martin full_name: Thomas, Martin last_name: Thomas - first_name: Heather L full_name: Smith, Heather L last_name: Smith - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Busch KE, Laurent P, Soltesz Z, et al. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 2012;15(4):581-591. doi:10.1038/nn.3061 apa: Busch, K. E., Laurent, P., Soltesz, Z., Murphy, R. J., Faivre, O., Hedwig, B., … de Bono, M. (2012). Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn.3061 chicago: Busch, Karl Emanuel, Patrick Laurent, Zoltan Soltesz, Robin Joseph Murphy, Olivier Faivre, Berthold Hedwig, Martin Thomas, Heather L Smith, and Mario de Bono. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience. Springer Nature, 2012. https://doi.org/10.1038/nn.3061. ieee: K. E. Busch et al., “Tonic signaling from O2 sensors sets neural circuit activity and behavioral state,” Nature Neuroscience, vol. 15, no. 4. Springer Nature, pp. 581–591, 2012. ista: Busch KE, Laurent P, Soltesz Z, Murphy RJ, Faivre O, Hedwig B, Thomas M, Smith HL, de Bono M. 2012. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 15(4), 581–591. mla: Busch, Karl Emanuel, et al. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience, vol. 15, no. 4, Springer Nature, 2012, pp. 581–91, doi:10.1038/nn.3061. short: K.E. Busch, P. Laurent, Z. Soltesz, R.J. Murphy, O. Faivre, B. Hedwig, M. Thomas, H.L. Smith, M. de Bono, Nature Neuroscience 15 (2012) 581–591. date_created: 2019-03-20T14:23:30Z date_published: 2012-03-04T00:00:00Z date_updated: 2021-01-12T08:06:17Z day: '04' doi: 10.1038/nn.3061 extern: '1' external_id: pmid: - '22388961' intvolume: ' 15' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/ month: '03' oa: 1 oa_version: Submitted Version page: 581-591 pmid: 1 publication: Nature Neuroscience publication_identifier: issn: - 1097-6256 - 1546-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Tonic signaling from O2 sensors sets neural circuit activity and behavioral state type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '6746' abstract: - lang: eng text: This paper proposes a novel cooperative approach for two-hop amplify-and-forward (A&F) relaying that exploits both the signal forwarded by the relay and the one directly transmitted by the source in impulse-radio ultra-wideband (IR-UWB) systems. Specifically, we focus on a non-coherent setup employing a double-differential encoding scheme at the source node and a single differential demodulation at the relay and destination. The log-likelihood ratio based decision rule is derived at the destination node. A semi-analytical power allocation strategy is presented by evaluating a closed-form expression for the effective signal to noise ratio (SNR) at the destination, which is maximized by exhaustive search. Numerical simulations show that the proposed system outperforms both the direct transmission with single differential encoding and the non-cooperative multi-hop approach in different scenarios. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Qi full_name: Zhou, Qi last_name: Zhou - first_name: Xiaoli full_name: Ma, Xiaoli last_name: Ma - first_name: Vincenzo full_name: Lottici, Vincenzo last_name: Lottici citation: ama: 'Mondelli M, Zhou Q, Ma X, Lottici V. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE; 2012:2905-2908. doi:10.1109/icassp.2012.6288524' apa: 'Mondelli, M., Zhou, Q., Ma, X., & Lottici, V. (2012). A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 2905–2908). Kyoto, Japan: IEEE. https://doi.org/10.1109/icassp.2012.6288524' chicago: Mondelli, Marco, Qi Zhou, Xiaoli Ma, and Vincenzo Lottici. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2905–8. IEEE, 2012. https://doi.org/10.1109/icassp.2012.6288524. ieee: M. Mondelli, Q. Zhou, X. Ma, and V. Lottici, “A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems,” in 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Kyoto, Japan, 2012, pp. 2905–2908. ista: 'Mondelli M, Zhou Q, Ma X, Lottici V. 2012. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). ICASSP: International Conference on Acoustics, Speech and Signal Processing, 2905–2908.' mla: Mondelli, Marco, et al. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–08, doi:10.1109/icassp.2012.6288524. short: M. Mondelli, Q. Zhou, X. Ma, V. Lottici, in:, 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–2908. conference: end_date: 2012-03-30 location: Kyoto, Japan name: 'ICASSP: International Conference on Acoustics, Speech and Signal Processing' start_date: 2012-03-25 date_created: 2019-07-31T09:14:48Z date_published: 2012-07-31T00:00:00Z date_updated: 2021-01-12T08:08:49Z day: '31' doi: 10.1109/icassp.2012.6288524 extern: '1' language: - iso: eng month: '07' oa_version: None page: 2905-2908 publication: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) publication_identifier: issn: - 1520-6149 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '7074' abstract: - lang: eng text: The Seebeck coefficients, electrical resistivities, total thermal conductivities, and magnetization are reported for temperatures between 5 and 350 K for n-type Bi0.88Sb0.12 nano-composite alloys made by Ho-doping at the 0, 1, and 3 % atomic levels. The alloys were prepared using a dc hot-pressing method, and are shown to be single phase for both Ho contents with grain sizes on the average of 900 nm. We find the parent compound has a maximum of ZT = 0.28 at 231 K, while doping 1 % Ho increases the maximum ZT to 0.31 at 221 K and the 3 % doped sample suppresses the maximum ZT = 0.24 at a temperature of 260 K. article_processing_charge: No article_type: original author: - first_name: K. C. full_name: Lukas, K. C. last_name: Lukas - first_name: G. full_name: Joshi, G. last_name: Joshi - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Z. F. full_name: Ren, Z. F. last_name: Ren - first_name: C. P. full_name: Opeil, C. P. last_name: Opeil citation: ama: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 2012;47(15):5729-5734. doi:10.1007/s10853-012-6463-6 apa: Lukas, K. C., Joshi, G., Modic, K. A., Ren, Z. F., & Opeil, C. P. (2012). Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. Springer Nature. https://doi.org/10.1007/s10853-012-6463-6 chicago: Lukas, K. C., G. Joshi, Kimberly A Modic, Z. F. Ren, and C. P. Opeil. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science. Springer Nature, 2012. https://doi.org/10.1007/s10853-012-6463-6. ieee: K. C. Lukas, G. Joshi, K. A. Modic, Z. F. Ren, and C. P. Opeil, “Thermoelectric properties of Ho-doped Bi0.88Sb0.12,” Journal of Materials Science, vol. 47, no. 15. Springer Nature, pp. 5729–5734, 2012. ista: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. 2012. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 47(15), 5729–5734. mla: Lukas, K. C., et al. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science, vol. 47, no. 15, Springer Nature, 2012, pp. 5729–34, doi:10.1007/s10853-012-6463-6. short: K.C. Lukas, G. Joshi, K.A. Modic, Z.F. Ren, C.P. Opeil, Journal of Materials Science 47 (2012) 5729–5734. date_created: 2019-11-19T13:36:54Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T08:11:43Z day: '01' doi: 10.1007/s10853-012-6463-6 extern: '1' intvolume: ' 47' issue: '15' language: - iso: eng month: '08' oa_version: None page: 5729-5734 publication: Journal of Materials Science publication_identifier: eissn: - 1573-4803 issn: - 0022-2461 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Thermoelectric properties of Ho-doped Bi0.88Sb0.12 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '7308' abstract: - lang: eng text: 'Carbon has been used widely as the basis of porous cathodes for nonaqueous Li–O2 cells. However, the stability of carbon and the effect of carbon on electrolyte decomposition in such cells are complex and depend on the hydrophobicity/hydrophilicity of the carbon surface. Analyzing carbon cathodes, cycled in Li–O2 cells between 2 and 4 V, using acid treatment and Fenton’s reagent, and combined with differential electrochemical mass spectrometry and FTIR, demonstrates the following: Carbon is relatively stable below 3.5 V (vs Li/Li+) on discharge or charge, especially so for hydrophobic carbon, but is unstable on charging above 3.5 V (in the presence of Li2O2), oxidatively decomposing to form Li2CO3. Direct chemical reaction with Li2O2 accounts for only a small proportion of the total carbon decomposition on cycling. Carbon promotes electrolyte decomposition during discharge and charge in a Li–O2 cell, giving rise to Li2CO3 and Li carboxylates (DMSO and tetraglyme electrolytes). The Li2CO3 and Li carboxylates present at the end of discharge and those that form on charge result in polarization on the subsequent charge. Li2CO3 (derived from carbon and from the electrolyte) as well as the Li carboxylates (derived from the electrolyte) decompose and form on charging. Oxidation of Li2CO3 on charging to ∼4 V is incomplete; Li2CO3 accumulates on cycling resulting in electrode passivation and capacity fading. Hydrophilic carbon is less stable and more catalytically active toward electrolyte decomposition than carbon with a hydrophobic surface. If the Li–O2 cell could be charged at or below 3.5 V, then carbon may be relatively stable, however, its ability to promote electrolyte decomposition, presenting problems for its use in a practical Li–O2 battery. The results emphasize that stable cycling of Li2O2 at the cathode in a Li–O2 cell depends on the synergy between electrolyte and electrode; the stability of the electrode and the electrolyte cannot be considered in isolation.' article_processing_charge: No article_type: original author: - first_name: Muhammed M. full_name: Ottakam Thotiyl, Muhammed M. last_name: Ottakam Thotiyl - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 2012;135(1):494-500. doi:10.1021/ja310258x apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., & Bruce, P. G. (2012). The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja310258x chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, and Peter G. Bruce. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja310258x. ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, and P. G. Bruce, “The carbon electrode in nonaqueous Li–O2 cells,” Journal of the American Chemical Society, vol. 135, no. 1. ACS, pp. 494–500, 2012. ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. 2012. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 135(1), 494–500. mla: Ottakam Thotiyl, Muhammed M., et al. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society, vol. 135, no. 1, ACS, 2012, pp. 494–500, doi:10.1021/ja310258x. short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, P.G. Bruce, Journal of the American Chemical Society 135 (2012) 494–500. date_created: 2020-01-15T12:18:57Z date_published: 2012-11-28T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '28' doi: 10.1021/ja310258x extern: '1' intvolume: ' 135' issue: '1' language: - iso: eng month: '11' oa_version: None page: 494-500 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: ACS quality_controlled: '1' status: public title: The carbon electrode in nonaqueous Li–O2 cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2012' ... --- _id: '7309' abstract: - lang: eng text: Energy‐storage technologies, including electrical double‐layer capacitors and rechargeable batteries, have attracted significant attention for applications in portable electronic devices, electric vehicles, bulk electricity storage at power stations, and “load leveling” of renewable sources, such as solar energy and wind power. Transforming lithium batteries and electric double‐layer capacitors requires a step change in the science underpinning these devices, including the discovery of new materials, new electrochemistry, and an increased understanding of the processes on which the devices depend. The Review will consider some of the current scientific issues underpinning lithium batteries and electric double‐layer capacitors. article_processing_charge: No article_type: original author: - first_name: Nam-Soon full_name: Choi, Nam-Soon last_name: Choi - first_name: Zonghai full_name: Chen, Zonghai last_name: Chen - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Xiulei full_name: Ji, Xiulei last_name: Ji - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun - first_name: Khalil full_name: Amine, Khalil last_name: Amine - first_name: Gleb full_name: Yushin, Gleb last_name: Yushin - first_name: Linda F. full_name: Nazar, Linda F. last_name: Nazar - first_name: Jaephil full_name: Cho, Jaephil last_name: Cho - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Choi N-S, Chen Z, Freunberger SA, et al. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 2012;51(40):9994-10024. doi:10.1002/anie.201201429 apa: Choi, N.-S., Chen, Z., Freunberger, S. A., Ji, X., Sun, Y.-K., Amine, K., … Bruce, P. G. (2012). Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201201429 chicago: Choi, Nam-Soon, Zonghai Chen, Stefan Alexander Freunberger, Xiulei Ji, Yang-Kook Sun, Khalil Amine, Gleb Yushin, Linda F. Nazar, Jaephil Cho, and Peter G. Bruce. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition. Wiley, 2012. https://doi.org/10.1002/anie.201201429. ieee: N.-S. Choi et al., “Challenges facing Lithium batteries and electrical double-layer capacitors,” Angewandte Chemie International Edition, vol. 51, no. 40. Wiley, pp. 9994–10024, 2012. ista: Choi N-S, Chen Z, Freunberger SA, Ji X, Sun Y-K, Amine K, Yushin G, Nazar LF, Cho J, Bruce PG. 2012. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 51(40), 9994–10024. mla: Choi, Nam-Soon, et al. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition, vol. 51, no. 40, Wiley, 2012, pp. 9994–10024, doi:10.1002/anie.201201429. short: N.-S. Choi, Z. Chen, S.A. Freunberger, X. Ji, Y.-K. Sun, K. Amine, G. Yushin, L.F. Nazar, J. Cho, P.G. Bruce, Angewandte Chemie International Edition 51 (2012) 9994–10024. date_created: 2020-01-15T12:19:11Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '01' doi: 10.1002/anie.201201429 extern: '1' intvolume: ' 51' issue: '40' language: - iso: eng month: '10' oa_version: None page: 9994-10024 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Challenges facing Lithium batteries and electrical double-layer capacitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2012' ... --- _id: '7310' abstract: - lang: eng text: The rechargeable nonaqueous lithium-air (Li-O2) battery is receiving a great deal of interest because, theoretically, its specific energy far exceeds the best that can be achieved with lithium-ion cells. Operation of the rechargeable Li-O2 battery depends critically on repeated and highly reversible formation/decomposition of lithium peroxide (Li2O2) at the cathode upon cycling. Here, we show that this process is possible with the use of a dimethyl sulfoxide electrolyte and a porous gold electrode (95% capacity retention from cycles 1 to 100), whereas previously only partial Li2O2 formation/decomposition and limited cycling could occur. Furthermore, we present data indicating that the kinetics of Li2O2 oxidation on charge is approximately 10 times faster than on carbon electrodes. article_processing_charge: No article_type: original author: - first_name: Z. full_name: Peng, Z. last_name: Peng - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Y. full_name: Chen, Y. last_name: Chen - first_name: P. G. full_name: Bruce, P. G. last_name: Bruce citation: ama: Peng Z, Freunberger SA, Chen Y, Bruce PG. A reversible and higher-rate Li-O2 battery. Science. 2012;337(6094):563-566. doi:10.1126/science.1223985 apa: Peng, Z., Freunberger, S. A., Chen, Y., & Bruce, P. G. (2012). A reversible and higher-rate Li-O2 battery. Science. AAAS. https://doi.org/10.1126/science.1223985 chicago: Peng, Z., Stefan Alexander Freunberger, Y. Chen, and P. G. Bruce. “A Reversible and Higher-Rate Li-O2 Battery.” Science. AAAS, 2012. https://doi.org/10.1126/science.1223985. ieee: Z. Peng, S. A. Freunberger, Y. Chen, and P. G. Bruce, “A reversible and higher-rate Li-O2 battery,” Science, vol. 337, no. 6094. AAAS, pp. 563–566, 2012. ista: Peng Z, Freunberger SA, Chen Y, Bruce PG. 2012. A reversible and higher-rate Li-O2 battery. Science. 337(6094), 563–566. mla: Peng, Z., et al. “A Reversible and Higher-Rate Li-O2 Battery.” Science, vol. 337, no. 6094, AAAS, 2012, pp. 563–66, doi:10.1126/science.1223985. short: Z. Peng, S.A. Freunberger, Y. Chen, P.G. Bruce, Science 337 (2012) 563–566. date_created: 2020-01-15T12:19:23Z date_published: 2012-08-03T00:00:00Z date_updated: 2021-01-12T08:12:57Z day: '03' doi: 10.1126/science.1223985 extern: '1' intvolume: ' 337' issue: '6094' language: - iso: eng month: '08' oa_version: None page: 563-566 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: A reversible and higher-rate Li-O2 battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 337 year: '2012' ... --- _id: '7311' abstract: - lang: eng text: Stability of the electrolyte toward reduced oxygen species generated at the cathode is a crucial challenge for the rechargeable nonaqueous Li–O2 battery. Here, we investigate dimethylformamide as the basis of an electrolyte. Although reactions at the O2 cathode on the first discharge–charge cycle are dominated by reversible Li2O2 formation/decomposition, there is also electrolyte decomposition, which increases on cycling. The products of decomposition at the cathode on discharge are Li2O2, Li2CO3, HCO2Li, CH3CO2Li, NO, H2O, and CO2. Li2CO3 accumulates in the electrode with cycling. The stability of dimethylformamide toward reduced oxygen species is insufficient for its use in the rechargeable nonaqueous Li–O2 battery. article_processing_charge: No article_type: original author: - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Fanny full_name: Bardé, Fanny last_name: Bardé - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 2012;134(18):7952-7957. doi:10.1021/ja302178w apa: Chen, Y., Freunberger, S. A., Peng, Z., Bardé, F., & Bruce, P. G. (2012). Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja302178w chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Fanny Bardé, and Peter G. Bruce. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja302178w. ieee: Y. Chen, S. A. Freunberger, Z. Peng, F. Bardé, and P. G. Bruce, “Li–O2 battery with a dimethylformamide electrolyte,” Journal of the American Chemical Society, vol. 134, no. 18. ACS, pp. 7952–7957, 2012. ista: Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. 2012. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 134(18), 7952–7957. mla: Chen, Yuhui, et al. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society, vol. 134, no. 18, ACS, 2012, pp. 7952–57, doi:10.1021/ja302178w. short: Y. Chen, S.A. Freunberger, Z. Peng, F. Bardé, P.G. Bruce, Journal of the American Chemical Society 134 (2012) 7952–7957. date_created: 2020-01-15T12:19:36Z date_published: 2012-04-19T00:00:00Z date_updated: 2021-01-12T08:12:58Z day: '19' doi: 10.1021/ja302178w extern: '1' intvolume: ' 134' issue: '18' language: - iso: eng month: '04' oa_version: None page: 7952-7957 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Li–O2 battery with a dimethylformamide electrolyte type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '762' abstract: - lang: eng text: Decades of research in distributed computing have led to a variety of perspectives on what it means for a concurrent algorithm to be efficient, depending on model assumptions, progress guarantees, and complexity metrics. It is therefore natural to ask whether one could compose algorithms that perform efficiently under different conditions, so that the composition preserves the performance of the original components when their conditions are met. In this paper, we evaluate the cost of composing shared-memory algorithms. First, we formally define the notion of safely composable algorithms and we show that every sequential type has a safely composable implementation, as long as enough state is transferred between modules. Since such generic implementations are inherently expensive, we present a more general light-weight specification that allows the designer to transfer very little state between modules, by taking advantage of the semantics of the implemented object. Using this framework, we implement a composed longlived test-and-set object, with the property that each of its modules is asymptotically optimal with respect to the progress condition it ensures, while the entire implementation only uses objects with consensus number at most two. Thus, we show that the overhead of composition can be negligible in the case of some important shared-memory abstractions. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Petr full_name: Kuznetsov, Petr last_name: Kuznetsov - first_name: Giuliano full_name: Losa, Giuliano last_name: Losa citation: ama: 'Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. On the cost of composing shared-memory algorithms. In: ACM; 2012:298-307. doi:10.1145/2312005.2312057' apa: 'Alistarh, D.-A., Guerraoui, R., Kuznetsov, P., & Losa, G. (2012). On the cost of composing shared-memory algorithms (pp. 298–307). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2312005.2312057' chicago: Alistarh, Dan-Adrian, Rachid Guerraoui, Petr Kuznetsov, and Giuliano Losa. “On the Cost of Composing Shared-Memory Algorithms,” 298–307. ACM, 2012. https://doi.org/10.1145/2312005.2312057. ieee: 'D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, and G. Losa, “On the cost of composing shared-memory algorithms,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2012, pp. 298–307.' ista: 'Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. 2012. On the cost of composing shared-memory algorithms. SPAA: Symposium on Parallelism in Algorithms and Architectures, 298–307.' mla: Alistarh, Dan-Adrian, et al. On the Cost of Composing Shared-Memory Algorithms. ACM, 2012, pp. 298–307, doi:10.1145/2312005.2312057. short: D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, G. Losa, in:, ACM, 2012, pp. 298–307. conference: name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' date_created: 2018-12-11T11:48:22Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:12:27Z day: '01' doi: 10.1145/2312005.2312057 extern: '1' language: - iso: eng month: '01' oa_version: None page: 298 - 307 publication_status: published publisher: ACM publist_id: '6892' status: public title: On the cost of composing shared-memory algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '763' abstract: - lang: eng text: Renaming is a fundamental problem in distributed computing, in which a set of n processes need to pick unique names from a namespace of limited size. In this paper, we present the first early-deciding upper bounds for synchronous renaming, in which the running time adapts to the actual number of failures f in the execution. We show that, surprisingly, renaming can be solved in constant time if the number of failures f is limited to O(√n), while for general f ≤ n - 1 renaming can always be solved in O(log f) communication rounds. In the wait-free case, i.e. for f = n - 1, our upper bounds match the Ω(log n) lower bound of Chaudhuri et al. [13]. acknowledgement: "Hagit Attiya - Supported in party by Israel Science Foundation (grant number 1227/10).\r\nCorentin Travers - Additional supports from the ANR projects ALADDIN and DISPLEXITY\r\n" alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Hagit full_name: Attiya, Hagit last_name: Attiya - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Attiya H, Guerraoui R, Travers C. Early deciding synchronous renaming in O(log f) rounds or less. In: Vol 7355 LNCS. Springer; 2012:195-206. doi:10.1007/978-3-642-31104-8_17' apa: 'Alistarh, D.-A., Attiya, H., Guerraoui, R., & Travers, C. (2012). Early deciding synchronous renaming in O(log f) rounds or less (Vol. 7355 LNCS, pp. 195–206). Presented at the SIROCCO: Structural Information and Communication Complexity, Springer. https://doi.org/10.1007/978-3-642-31104-8_17' chicago: Alistarh, Dan-Adrian, Hagit Attiya, Rachid Guerraoui, and Corentin Travers. “Early Deciding Synchronous Renaming in O(Log f) Rounds or Less,” 7355 LNCS:195–206. Springer, 2012. https://doi.org/10.1007/978-3-642-31104-8_17. ieee: 'D.-A. Alistarh, H. Attiya, R. Guerraoui, and C. Travers, “Early deciding synchronous renaming in O(log f) rounds or less,” presented at the SIROCCO: Structural Information and Communication Complexity, 2012, vol. 7355 LNCS, pp. 195–206.' ista: 'Alistarh D-A, Attiya H, Guerraoui R, Travers C. 2012. Early deciding synchronous renaming in O(log f) rounds or less. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 7355 LNCS, 195–206.' mla: Alistarh, Dan-Adrian, et al. Early Deciding Synchronous Renaming in O(Log f) Rounds or Less. Vol. 7355 LNCS, Springer, 2012, pp. 195–206, doi:10.1007/978-3-642-31104-8_17. short: D.-A. Alistarh, H. Attiya, R. Guerraoui, C. Travers, in:, Springer, 2012, pp. 195–206. conference: name: 'SIROCCO: Structural Information and Communication Complexity' date_created: 2018-12-11T11:48:22Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:12:41Z day: '01' doi: 10.1007/978-3-642-31104-8_17 extern: '1' language: - iso: eng month: '01' oa_version: None page: 195 - 206 publication_status: published publisher: Springer publist_id: '6893' status: public title: Early deciding synchronous renaming in O(log f) rounds or less type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7355 LNCS year: '2012' ... --- _id: '764' abstract: - lang: eng text: Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. In synchronous networks, too, the complexity of set agreement has been a significant research challenge that has now been resolved. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. Nothing specific is known about the complexity of set agreement in such a "partially synchronous" setting. In this paper, we address this challenge, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in a fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone message-passing system in which some fragments appear synchronous to some processes. We use this simulation technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. Specifically, we show that every set agreement protocol requires at least $\lfloor\frac t k \rfloor + 2$ synchronous rounds to decide. We present an (asymptotically) matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. From these two results, we derive the size of the minimal window of synchrony needed to solve set agreement. By relating synchronous, asynchronous and partially synchronous environments, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of Gafni et al. (in SIAM J. Comput. 40(1):63-78, 2011), and to re-derive the combinatorial topology lower bound of Guerraoui et al. (in Theor. Comput. Sci. 410(6-7):570-580, 2009) in an algorithmic way. acknowledgement: "We would like to thank Hagit Attiya, Keren Censor-Hillel, and the anonymous\r\nreviewers for their feedback on drafts of this paper.\r\nPart of the work was performed as C. Travers was a Post-Doctoral Fellow at the Technion, Haifa,\r\nsupported by the “Sam & Cecilia Neaman” Fellowship. Part of the work was performed as S. Gilbert was\r\na Post-Doctoral Fellow at the Swiss Federal Institute of Technology, Lausanne, Switzerland." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 2012;62(1-2):595-629. doi:10.1007/s00453-011-9581-7' apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). Springer. https://doi.org/10.1007/s00453-011-9581-7' chicago: 'Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York). Springer, 2012. https://doi.org/10.1007/s00453-011-9581-7.' ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” Algorithmica (New York), vol. 62, no. 1–2. Springer, pp. 595–629, 2012.' ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 62(1–2), 595–629.' mla: 'Alistarh, Dan-Adrian, et al. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York), vol. 62, no. 1–2, Springer, 2012, pp. 595–629, doi:10.1007/s00453-011-9581-7.' short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Algorithmica (New York) 62 (2012) 595–629. date_created: 2018-12-11T11:48:23Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-02-23T13:13:02Z day: '01' doi: 10.1007/s00453-011-9581-7 extern: '1' intvolume: ' 62' issue: 1-2 language: - iso: eng month: '02' oa_version: None page: 595 - 629 publication: Algorithmica (New York) publication_status: published publisher: Springer publist_id: '6894' status: public title: 'Of choices, failures and asynchrony: the many faces of set agreement' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2012' ... --- _id: '766' abstract: - lang: eng text: 'Asynchronous task allocation is a fundamental problem in distributed computing in which p asynchronous processes must execute a set of m tasks. Also known as write-all or do-all, this problem been studied extensively, both independently and as a key building block for various distributed algorithms. In this paper, we break new ground on this classic problem: we introduce the To-Do Tree concurrent data structure, which improves on the best known randomized and deterministic upper bounds. In the presence of an adaptive adversary, the randomized To-Do Tree algorithm has O(m + p log p log2 m) work complexity. We then show that there exists a deterministic variant of the To-Do Tree algorithm with work complexity O(m + p log5 m log2 max(m, p)). For all values of m and p, our algorithms are within log factors of the Ω(m + p log p) lower bound for this problem. The key technical ingredient in our results is a new approach for analyzing concurrent executions against a strong adaptive scheduler. This technique allows us to handle the complex dependencies between the processes'' coin flips and their scheduling, and to tightly bound the work needed to perform subsets of the tasks.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Michael full_name: Bender, Michael last_name: Bender - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui citation: ama: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously. In: IEEE; 2012:331-340. doi:10.1109/FOCS.2012.41' apa: 'Alistarh, D.-A., Bender, M., Gilbert, S., & Guerraoui, R. (2012). How to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2012.41' chicago: Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui. “How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. https://doi.org/10.1109/FOCS.2012.41. ieee: 'D.-A. Alistarh, M. Bender, S. Gilbert, and R. Guerraoui, “How to allocate tasks asynchronously,” presented at the FOCS: Foundations of Computer Science, 2012, pp. 331–340.' ista: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks asynchronously. FOCS: Foundations of Computer Science, 331–340.' mla: Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE, 2012, pp. 331–40, doi:10.1109/FOCS.2012.41. short: D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340. conference: name: 'FOCS: Foundations of Computer Science' date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:27Z day: '01' doi: 10.1109/FOCS.2012.41 extern: '1' language: - iso: eng month: '01' oa_version: None page: 331 - 340 publication_status: published publisher: IEEE publist_id: '6890' status: public title: How to allocate tasks asynchronously type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '767' abstract: - lang: eng text: Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronous timing into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms (Guerraoui, in PODC, pp. 289-297, 2000), which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for the class of colorless distributed tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm. acknowledgement: "Dan Alistarh was supported by the NCCR MICS Project. Corentin Travers had additional support from INRIA team REGAL and ANR project SPREADS.\r\nThe authors would like to thank Hagit Attiya and Nikola Kneževi\r\n ́\r\nc for their feed-\r\nback on previous drafts of this paper, and the anonymous reviewers for their useful comments." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 2012;51(4):404-424. doi:10.1007/s00224-012-9407-2 apa: Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Generating Fast Indulgent Algorithms. Theory of Computing Systems. Elsevier. https://doi.org/10.1007/s00224-012-9407-2 chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems. Elsevier, 2012. https://doi.org/10.1007/s00224-012-9407-2. ieee: D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast Indulgent Algorithms,” Theory of Computing Systems, vol. 51, no. 4. Elsevier, pp. 404–424, 2012. ista: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424. mla: Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:10.1007/s00224-012-9407-2. short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424. date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:40Z day: '01' doi: 10.1007/s00224-012-9407-2 extern: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '01' oa_version: None page: 404 - 424 publication: Theory of Computing Systems publication_status: published publisher: Elsevier publist_id: '6891' status: public title: Generating Fast Indulgent Algorithms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2012' ... --- _id: '7749' abstract: - lang: eng text: Although studies on laboratory species and natural populations of vertebrates have shown reproduction to impair later performance, little is known of the age‐specific associations between reproduction and survival, and how such findings apply to the ageing of large, long‐lived species. Herein we develop a framework to examine population‐level patterns of reproduction and survival across lifespan in long‐lived organisms, and decompose those changes into individual‐level effects, and the effects of age‐specific trade‐offs between fitness components. We apply this to an extensive longitudinal dataset on female semi‐captive Asian timber elephants (Elephas maximus) and report the first evidence of age‐specific fitness declines that are driven by age‐specific associations between fitness components in a long‐lived mammal. Associations between reproduction and survival are positive in early life, but negative in later life with up to 71% of later‐life survival declines associated with investing in the production of offspring within this population of this critically endangered species. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Khyne U full_name: Mar, Khyne U last_name: Mar - first_name: Virpi full_name: Lummaa, Virpi last_name: Lummaa citation: ama: Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 2012;15(3):260-266. doi:10.1111/j.1461-0248.2011.01735.x apa: Robinson, M. R., Mar, K. U., & Lummaa, V. (2012). Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2011.01735.x chicago: Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2011.01735.x. ieee: M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants,” Ecology Letters, vol. 15, no. 3. Wiley, pp. 260–266, 2012. ista: Robinson MR, Mar KU, Lummaa V. 2012. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 15(3), 260–266. mla: Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters, vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:10.1111/j.1461-0248.2011.01735.x. short: M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266. date_created: 2020-04-30T11:01:26Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T08:15:16Z day: '01' doi: 10.1111/j.1461-0248.2011.01735.x extern: '1' intvolume: ' 15' issue: '3' language: - iso: eng month: '03' oa_version: None page: 260-266 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7748' abstract: - lang: eng text: Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals. article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: G. full_name: Sander van Doorn, G. last_name: Sander van Doorn - first_name: Lars full_name: Gustafsson, Lars last_name: Gustafsson - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 2012;15(6):611-618. doi:10.1111/j.1461-0248.2012.01780.x apa: Robinson, M. R., Sander van Doorn, G., Gustafsson, L., & Qvarnström, A. (2012). Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2012.01780.x chicago: Robinson, Matthew Richard, G. Sander van Doorn, Lars Gustafsson, and Anna Qvarnström. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2012.01780.x. ieee: M. R. Robinson, G. Sander van Doorn, L. Gustafsson, and A. Qvarnström, “Environment-dependent selection on mate choice in a natural population of birds,” Ecology Letters, vol. 15, no. 6. Wiley, pp. 611–618, 2012. ista: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. 2012. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 15(6), 611–618. mla: Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters, vol. 15, no. 6, Wiley, 2012, pp. 611–18, doi:10.1111/j.1461-0248.2012.01780.x. short: M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618. date_created: 2020-04-30T11:01:07Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/j.1461-0248.2012.01780.x extern: '1' intvolume: ' 15' issue: '6' language: - iso: eng month: '06' oa_version: None page: 611-618 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Environment-dependent selection on mate choice in a natural population of birds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7776' abstract: - lang: eng text: We present an analysis of finite-size effects in jammed packings of N soft, frictionless spheres at zero temperature. There is a 1/N correction to the discrete jump in the contact number at the transition so that jammed packings exist only above isostaticity. As a result, the canonical power-law scalings of the contact number and elastic moduli break down at low pressure. These quantities exhibit scaling collapse with a nontrivial scaling function, demonstrating that the jamming transition can be considered a phase transition. Scaling is achieved as a function of N in both two and three dimensions, indicating an upper critical dimension of 2. article_number: '095704' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition. Physical Review Letters. 2012;109(9). doi:10.1103/physrevlett.109.095704 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2012). Finite-size scaling at the jamming transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.095704 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.095704. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming transition,” Physical Review Letters, vol. 109, no. 9. American Physical Society, 2012. ista: Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704. mla: Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters, vol. 109, no. 9, 095704, American Physical Society, 2012, doi:10.1103/physrevlett.109.095704. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012). date_created: 2020-04-30T11:44:12Z date_published: 2012-08-27T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '27' doi: 10.1103/physrevlett.109.095704 extern: '1' intvolume: ' 109' issue: '9' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Finite-size scaling at the jamming transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '801' abstract: - lang: eng text: Fungal cell walls frequently contain a polymer of mannose and galactose called galactomannan. In the pathogenic filamentous fungus Aspergillus fumigatus, this polysaccharide is made of a linear mannan backbone with side chains of galactofuran and is anchored to the plasma membrane via a glycosylphosphatidylinositol or is covalently linked to the cell wall. To date, the biosynthesis and significance of this polysaccharide are unknown. The present data demonstrate that deletion of the Golgi UDP-galactofuranose transporter GlfB or the GDP-mannose transporter GmtA leads to the absence of galactofuran or galactomannan, respectively. This indicates that the biosynthesis of galactomannan probably occurs in the lumen of the Golgi apparatus and thus contrasts with the biosynthesis of other fungal cell wall polysaccharides studied to date that takes place at the plasma membrane. Transglycosylation of galactomannan from the membrane to the cell wall is hypothesized because both the cell wall-bound and membrane-bound polysaccharide forms are affected in the generated mutants. Considering the severe growth defect of the A. fumigatus GmtA-deficient mutant, proving this paradigm might provide new targets for antifungal therapy. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft. article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Engel, Jakob last_name: Engel - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Françoise full_name: Routier, Françoise last_name: Routier citation: ama: Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 2012;287(53):44418-44424. doi:10.1074/jbc.M112.398321 apa: Engel, J., Schmalhorst, P. S., & Routier, F. (2012). Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M112.398321 chicago: Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2012. https://doi.org/10.1074/jbc.M112.398321. ieee: J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose,” Journal of Biological Chemistry, vol. 287, no. 53. American Society for Biochemistry and Molecular Biology, pp. 44418–44424, 2012. ista: Engel J, Schmalhorst PS, Routier F. 2012. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 287(53), 44418–44424. mla: Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry, vol. 287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp. 44418–24, doi:10.1074/jbc.M112.398321. short: J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424. date_created: 2018-12-11T11:48:34Z date_published: 2012-12-28T00:00:00Z date_updated: 2022-03-21T07:57:14Z day: '28' doi: 10.1074/jbc.M112.398321 extern: '1' external_id: pmid: - '23139423' intvolume: ' 287' issue: '53' language: - iso: eng month: '12' oa_version: None page: 44418 - 44424 pmid: 1 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '6852' quality_controlled: '1' scopus_import: '1' status: public title: Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 287 year: '2012' ... --- _id: '8024' abstract: - lang: eng text: In dynamical models of cortical networks, the recurrent connectivity can amplify the input given to the network in two distinct ways. One is induced by the presence of near-critical eigenvalues in the connectivity matrix W, producing large but slow activity fluctuations along the corresponding eigenvectors (dynamical slowing). The other relies on W not being normal, which allows the network activity to make large but fast excursions along specific directions. Here we investigate the trade-off between non-normal amplification and dynamical slowing in the spontaneous activity of large random neuronal networks composed of excitatory and inhibitory neurons. We use a Schur decomposition of W to separate the two amplification mechanisms. Assuming linear stochastic dynamics, we derive an exact expression for the expected amount of purely non-normal amplification. We find that amplification is very limited if dynamical slowing must be kept weak. We conclude that, to achieve strong transient amplification with little slowing, the connectivity must be structured. We show that unidirectional connections between neurons of the same type together with reciprocal connections between neurons of different types, allow for amplification already in the fast dynamical regime. Finally, our results also shed light on the differences between balanced networks in which inhibition exactly cancels excitation and those where inhibition dominates. article_number: '011909' article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced neuronal networks. Physical Review E. 2012;86(1). doi:10.1103/physreve.86.011909 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2012). Non-normal amplification in random balanced neuronal networks. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.86.011909 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E. American Physical Society, 2012. https://doi.org/10.1103/physreve.86.011909. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in random balanced neuronal networks,” Physical Review E, vol. 86, no. 1. American Physical Society, 2012. ista: Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 011909. mla: Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E, vol. 86, no. 1, 011909, American Physical Society, 2012, doi:10.1103/physreve.86.011909. short: G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012). date_created: 2020-06-25T13:09:06Z date_published: 2012-06-11T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '11' doi: 10.1103/physreve.86.011909 extern: '1' external_id: pmid: - '23005454' intvolume: ' 86' issue: '1' language: - iso: eng month: '06' oa_version: None pmid: 1 publication: Physical Review E publication_identifier: eisbn: - 1550-2376 issn: - 1539-3755 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Non-normal amplification in random balanced neuronal networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 86 year: '2012' ... --- _id: '808' abstract: - lang: eng text: Using correlated live-cell imaging and electron tomography we found that actin branch junctions in protruding and treadmilling lamellipodia are not concentrated at the front as previously supposed, but link actin filament subsets in which there is a continuum of distances from a junction to the filament plus ends, for up to at least 1 mm. When branch sites were observed closely spaced on the same filament their separation was commonly a multiple of the actin helical repeat of 36 nm. Image averaging of branch junctions in the tomograms yielded a model for the in vivo branch at 2.9 nm resolution, which was comparable with that derived for the in vitro actin- Arp2/3 complex. Lamellipodium initiation was monitored in an intracellular wound-healing model and was found to involve branching from the sides of actin filaments oriented parallel to the plasmalemma. Many filament plus ends, presumably capped, terminated behind the lamellipodium tip and localized on the dorsal and ventral surfaces of the actin network. These findings reveal how branching events initiate and maintain a network of actin filaments of variable length, and provide the first structural model of the branch junction in vivo. A possible role of filament capping in generating the lamellipodium leaflet is discussed and a mathematical model of protrusion is also presented. acknowledgement: This work was supported by the Austrian Science Fund [projects FWF I516-B09 and FWF P21292-B09 to J.V.S.]; the Vienna Science and Technology Fund [WWTF-grant numbers MA 09-004 to J.V.S. and C.S], ZIT - The Technology Agency of the City of Vienna [VSOE, CMCN to J.V.S. and G.P.R.]; the Deutsche Forschungsgemeinschaft [grant number RO 2414/1-2 to K.R.]; the Daiko research foundation [grant number 9134 to A.N.]; and a Grant-in-Aid for Scientific Research [S, grant number 20227008 to Y.M.] and a Grant-in-Aid for Young Scientists [B, grant number 22770145 to A.N.] (B) from The Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. Deposited in PMC for immediate release. We thank Tibor Kulcsar for assistance with graphics. author: - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Jan full_name: Mueller, Jan last_name: Mueller - first_name: Akihiro full_name: Narita, Akihiro last_name: Narita - first_name: Edit full_name: Urban, Edit last_name: Urban - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Stefan full_name: Koestler, Stefan last_name: Koestler - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Guenter full_name: Resch, Guenter last_name: Resch - first_name: Yuichiro full_name: Maéda, Yuichiro last_name: Maéda - first_name: John full_name: Small, John last_name: Small citation: ama: Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 2012;125(11):2775-2785. doi:10.1242/jcs.107623 apa: Vinzenz, M., Nemethova, M., Schur, F. K., Mueller, J., Narita, A., Urban, E., … Small, J. (2012). Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.107623 chicago: Vinzenz, Marlene, Maria Nemethova, Florian KM Schur, Jan Mueller, Akihiro Narita, Edit Urban, Christoph Winkler, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science. Company of Biologists, 2012. https://doi.org/10.1242/jcs.107623. ieee: M. Vinzenz et al., “Actin branching in the initiation and maintenance of lamellipodia,” Journal of Cell Science, vol. 125, no. 11. Company of Biologists, pp. 2775–2785, 2012. ista: Vinzenz M, Nemethova M, Schur FK, Mueller J, Narita A, Urban E, Winkler C, Schmeiser C, Koestler S, Rottner K, Resch G, Maéda Y, Small J. 2012. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 125(11), 2775–2785. mla: Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science, vol. 125, no. 11, Company of Biologists, 2012, pp. 2775–85, doi:10.1242/jcs.107623. short: M. Vinzenz, M. Nemethova, F.K. Schur, J. Mueller, A. Narita, E. Urban, C. Winkler, C. Schmeiser, S. Koestler, K. Rottner, G. Resch, Y. Maéda, J. Small, Journal of Cell Science 125 (2012) 2775–2785. date_created: 2018-12-11T11:48:37Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:16:47Z day: '01' ddc: - '570' doi: 10.1242/jcs.107623 extern: '1' file: - access_level: open_access checksum: 2f59e15cc3a85bb500a9887cef2aab67 content_type: application/pdf creator: kschuh date_created: 2019-02-12T08:54:51Z date_updated: 2020-07-14T12:48:09Z file_id: '5956' file_name: 2012_Biologists_Vinzenz.pdf file_size: 3326073 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 125' issue: '11' language: - iso: eng month: '06' oa: 1 oa_version: None page: 2775 - 2785 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6842' quality_controlled: '1' status: public title: Actin branching in the initiation and maintenance of lamellipodia tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2012' ... --- _id: '8246' abstract: - lang: eng text: The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins, MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent CWSS expression was up to 250-fold higher in single, double and triple LCP mutants than in wild type S. aureus in the absence of external stress. The LCP triple mutant was virtually depleted of wall teichoic acids (WTA), which could be restored to different degrees by any of the single LCP proteins. Subinhibitory concentrations of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could partially complement the severe growth defect of the LCP triple mutant. Both of the latter findings support a role for S. aureus LCP proteins in late WTA synthesis, as in Bacillus subtilis where LCP proteins were recently proposed to transfer WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading of the cell wall, highlight their important role(s) in S. aureus cell envelope biogenesis. article_processing_charge: No article_type: original author: - first_name: Vanina full_name: Dengler, Vanina last_name: Dengler - first_name: Patricia Stutzmann full_name: Meier, Patricia Stutzmann last_name: Meier - first_name: Ronald full_name: Heusser, Ronald last_name: Heusser - first_name: Peter full_name: Kupferschmied, Peter last_name: Kupferschmied - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Sarah full_name: Friebe, Sarah last_name: Friebe - first_name: Sibylle Burger full_name: Staufer, Sibylle Burger last_name: Staufer - first_name: Paul A. full_name: Majcherczyk, Paul A. last_name: Majcherczyk - first_name: Philippe full_name: Moreillon, Philippe last_name: Moreillon - first_name: Brigitte full_name: Berger-Bächi, Brigitte last_name: Berger-Bächi - first_name: Nadine full_name: McCallum, Nadine last_name: McCallum citation: ama: Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x apa: Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe, S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x chicago: Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied, Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x. ieee: V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012. ista: Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120. mla: Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x. short: V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe, S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS Microbiology Letters 333 (2012) 109–120. date_created: 2020-08-10T11:54:47Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T08:17:43Z day: '01' doi: 10.1111/j.1574-6968.2012.02603.x extern: '1' external_id: pmid: - '22640011' intvolume: ' 333' issue: '2' language: - iso: eng month: '08' oa_version: None page: 109-120 pmid: 1 publication: FEMS Microbiology Letters publication_identifier: issn: - 0378-1097 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 333 year: '2012' ... --- _id: '826' abstract: - lang: eng text: Plants exhibit a unique developmental flexibility to ever-changing environmental conditions. To achieve their profound adaptability, plants are able to maintain permanent stem cell populations and form new organs during the entire plant life cycle. Signaling substances, called plant hormones, such as auxin, cytokinin, abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone, govern and coordinate these developmental processes. Physiological and genetic studies have dissected the molecular components of signal perception and transduction of the individual hormonal pathways. However, over recent years it has become evident that hormones do not act only in a linear pathway. Hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions. This raises questions about the molecular mechanisms underlying hormonal cross talk and about how these hormonal networks are established, maintained, and modulated throughout plant development. acknowledgement: We would like to thank Annick Bleys for help in preparing the manuscript. This work was supported by the European Research Council with a Starting Independent Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 (to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral fellow of the Research Foundation Flanders. We apologize that, because of space restrictions, the scientific contributions of only a limited number of original articles could be cited and discussed. author: - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 2012;28:463-487. doi:10.1146/annurev-cellbio-101011-155741 apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741 chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741. ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of plant development,” Annual Review of Cell and Developmental Biology, vol. 28. Annual Reviews, pp. 463–487, 2012. ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487. mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology, vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741. short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487. date_created: 2018-12-11T11:48:43Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:17:46Z day: '01' doi: 10.1146/annurev-cellbio-101011-155741 extern: 1 intvolume: ' 28' month: '11' page: 463 - 487 publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '6822' quality_controlled: 0 status: public title: Hormonal interactions in the regulation of plant development type: journal_article volume: 28 year: '2012' ... --- _id: '829' abstract: - lang: eng text: The architecture of a plant's root system, established postembryonically, results from both coordinated root growth and lateral root branching. The plant hormones auxin and cytokinin are central endogenous signaling molecules that regulate lateral root organogenesis positively and negatively, respectively. Tight control and mutual balance of their antagonistic activities are particularly important during the early phases of lateral root organogenesis to ensure continuous lateral root initiation (LRI) and proper development of lateral root primordia (LRP). Here, we show that the early phases of lateral root organogenesis, including priming and initiation, take place in root zones with a repressed cytokinin response. Accordingly, ectopic overproduction of cytokinin in the root basal meristem most efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between existing LRP might restrict LRI near existing LRP and, when compromised, ectopic LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive to perturbations in the cytokinin activity than are developmentally more advanced primordia. We hypothesize that the effect of cytokinin on the development of primordia possibly depends on the robustness and stability of the auxin gradient. acknowledgement: We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt, and Laurent Laplaze for sharing published material, Jiri Friml for discussions, and Martine De Cock and Annick Bleys for help in preparing the manuscript. This work was supported by a Starting Independent Research grant from the European Research Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the Central European Institute of Technology to E.B. and grants from the Ministry of Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01) to P.T. author: - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Katerina full_name: Podlesakova, Katerina last_name: Podlesakova - first_name: Peter full_name: Peter Marhavy id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Candela full_name: Candela Cuesta id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Bruno full_name: Muller, Bruno last_name: Muller - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Petr full_name: Tarkowski, Petr last_name: Tarkowski - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981. doi:10.1105/tpc.112.103044 apa: Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller, B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.103044 chicago: Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq, Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044. ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American Society of Plant Biologists, pp. 3967–3981, 2012. ista: Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981. mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044. short: A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller, W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981. date_created: 2018-12-11T11:48:43Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:17:55Z day: '01' doi: 10.1105/tpc.112.103044 extern: 1 intvolume: ' 24' issue: '10' month: '10' page: 3967 - 3981 publication: The Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '6819' quality_controlled: 0 status: public title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin type: journal_article volume: 24 year: '2012' ... --- _id: '846' abstract: - lang: eng text: Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function. acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096 apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evs096 chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/gbe/evs096. ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012. ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222. mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096. short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222. date_created: 2018-12-11T11:48:49Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/gbe/evs096 extern: 1 intvolume: ' 4' issue: '12' month: '01' page: 1213 - 1222 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6802' quality_controlled: 0 status: public title: Estimating the rate of irreversibility in protein evolution 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 volume: 4 year: '2012' ... --- _id: '8463' abstract: - lang: eng text: The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein, the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external field of 19.96 T (850 MHz), we find that using a proton concentration between 15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity and resolution, with an achievable average 1H linewidth on the order of 40–50 Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C correlation experiments. In total, we find that spectra recorded with a 1.3 mm rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The improved sensitivity is attributed to 1H line narrowing due to fast MAS and to the increased efficiency of the 1.3 mm coil. article_processing_charge: No article_type: original author: - first_name: Sam full_name: Asami, Sam last_name: Asami - first_name: Kathrin full_name: Szekely, Kathrin last_name: Szekely - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Bernd full_name: Reif, Bernd last_name: Reif citation: ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168. doi:10.1007/s10858-012-9659-9 apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-012-9659-9 chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9. ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency,” Journal of Biomolecular NMR, vol. 54, no. 2. Springer Nature, pp. 155–168, 2012. ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168. mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9. short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168. date_created: 2020-09-18T10:09:18Z date_published: 2012-08-23T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '23' doi: 10.1007/s10858-012-9659-9 extern: '1' intvolume: ' 54' issue: '2' language: - iso: eng month: '08' oa_version: None page: 155-168 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2012' ... --- _id: '8465' abstract: - lang: eng text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers. article_processing_charge: No article_type: original author: - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 2012;134(36):14800-14807. doi:10.1021/ja303591y apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P. (2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst, and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y. ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy,” Journal of the American Chemical Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012. ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 134(36), 14800–14807. mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society, vol. 134, no. 36, American Chemical Society, 2012, pp. 14800–07, doi:10.1021/ja303591y. short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807. date_created: 2020-09-18T10:10:20Z date_published: 2012-08-21T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '21' doi: 10.1021/ja303591y extern: '1' intvolume: ' 134' issue: '36' language: - iso: eng month: '08' oa_version: None page: 14800-14807 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8466' abstract: - lang: eng text: Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min. article_processing_charge: No article_type: original author: - first_name: Enrico full_name: Rennella, Enrico last_name: Rennella - first_name: Thomas full_name: Cutuil, Thomas last_name: Cutuil - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Vincent full_name: Forge, Vincent last_name: Forge - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069. doi:10.1021/ja302598j apa: Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher, B. (2012). Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja302598j chicago: Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j. ieee: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher, “Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate,” Journal of the American Chemical Society, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012. ista: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069. mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:10.1021/ja302598j. short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069. date_created: 2020-09-18T10:10:28Z date_published: 2012-05-03T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '03' doi: 10.1021/ja302598j extern: '1' intvolume: ' 134' issue: '19' language: - iso: eng month: '05' oa_version: None page: 8066-8069 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8467' abstract: - lang: eng text: Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups. article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Huber, Matthias last_name: Huber - first_name: Oliver full_name: With, Oliver last_name: With - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: René full_name: Verel, René last_name: Verel - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier citation: ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 2012;214:76-80. doi:10.1016/j.jmr.2011.10.010 apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010 chicago: Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst, and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010. ieee: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic Resonance, vol. 214. Elsevier, pp. 76–80, 2012. ista: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 214, 76–80. mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012, pp. 76–80, doi:10.1016/j.jmr.2011.10.010. short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80. date_created: 2020-09-18T10:10:36Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '01' doi: 10.1016/j.jmr.2011.10.010 extern: '1' intvolume: ' 214' language: - iso: eng month: '01' oa_version: None page: 76-80 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: A supplementary coil for 2H decoupling with commercial HCN MAS probes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 214 year: '2012' ... --- _id: '8502' abstract: - lang: eng text: 'The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface.' article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x apa: Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x chicago: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x. ieee: V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012. ista: Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 315(3), 643–697. mla: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:10.1007/s00220-012-1532-x. short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697. date_created: 2020-09-18T10:47:16Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.1007/s00220-012-1532-x extern: '1' intvolume: ' 315' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '11' oa_version: None page: 643-697 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 315 year: '2012' ... --- _id: '858' abstract: - lang: eng text: 'ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers'' Comments section.' acknowledgement: | We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards. author: - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alice full_name: Ledda, Alice last_name: Ledda - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov citation: ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30 apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30 chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30. ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012. ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7. mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30. short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012). date_created: 2018-12-11T11:48:52Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T08:20:08Z day: '01' doi: 10.1186/1745-6150-7-30 extern: 1 intvolume: ' 7' month: '09' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6792' quality_controlled: 0 status: public title: Stop codons in bacteria are not selectively equivalent 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 volume: 7 year: '2012' ... --- _id: '900' abstract: - lang: eng text: 'The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution.' acknowledgement: | The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538. mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538. date_created: 2018-12-11T11:49:06Z date_published: 2012-10-25T00:00:00Z date_updated: 2021-01-12T08:21:45Z day: '25' doi: 10.1038/nature11510 extern: 1 intvolume: ' 490' issue: '7421' month: '10' page: 535 - 538 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6748' quality_controlled: 0 status: public title: Epistasis as the primary factor in molecular evolution type: journal_article volume: 490 year: '2012' ... --- _id: '9014' abstract: - lang: eng text: In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers. article_number: '268303' article_processing_charge: No article_type: letter_note author: - first_name: I. full_name: Theurkauff, I. last_name: Theurkauff - first_name: C. full_name: Cottin-Bizonne, C. last_name: Cottin-Bizonne - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: C. full_name: Ybert, C. last_name: Ybert - first_name: L. full_name: Bocquet, L. last_name: Bocquet citation: ama: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 2012;108(26). doi:10.1103/physrevlett.108.268303 apa: Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303 chicago: Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303. ieee: I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” Physical Review Letters, vol. 108, no. 26. American Physical Society , 2012. ista: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303. mla: Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:10.1103/physrevlett.108.268303. short: I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012). date_created: 2021-01-19T10:26:59Z date_published: 2012-06-29T00:00:00Z date_updated: 2023-02-23T13:46:45Z day: '29' doi: 10.1103/physrevlett.108.268303 extern: '1' external_id: arxiv: - '1202.6264' pmid: - '23005020' intvolume: ' 108' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1202.6264 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: 'American Physical Society ' quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering in active colloidal suspensions with chemical signaling type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 108 year: '2012' ... --- _id: '91' abstract: - lang: eng text: 'We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ' acknowledgement: This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.). article_number: '033512' author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Jacqueline full_name: Cole, Jacqueline last_name: Cole - first_name: Martin full_name: Blood Forsythe, Martin last_name: Blood Forsythe - first_name: Daniel full_name: Hickstein, Daniel last_name: Hickstein citation: ama: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 2012;111(3). doi:10.1063/1.3678593 apa: Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593 chicago: Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3678593. ieee: A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” Journal of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012. ista: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512. mla: Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593. short: A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012). date_created: 2018-12-11T11:44:35Z date_published: 2012-02-07T00:00:00Z date_updated: 2021-01-12T08:21:50Z day: '07' doi: 10.1063/1.3678593 extern: '1' intvolume: ' 111' issue: '3' language: - iso: eng month: '02' oa_version: None publication: Journal of Applied Physics publication_status: published publisher: American Institute of Physics publist_id: '7963' quality_controlled: '1' status: public title: Identifying and evaluating organic nonlinear optical materials via molecular moments type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2012' ... --- _id: '9142' abstract: - lang: eng text: "In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback." article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Isaac M. full_name: Held, Isaac M. last_name: Held citation: ama: Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565. doi:10.1175/jas-d-11-0257.1 apa: Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1 chicago: Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences. American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1. ieee: C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012. ista: Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565. mla: Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1. short: C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565. date_created: 2021-02-15T14:39:03Z date_published: 2012-08-01T00:00:00Z date_updated: 2022-01-24T13:49:41Z day: '01' doi: 10.1175/jas-d-11-0257.1 extern: '1' intvolume: ' 69' issue: '8' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JAS-D-11-0257.1 month: '08' oa: 1 oa_version: Published Version page: 2551-2565 publication: Journal of the Atmospheric Sciences publication_identifier: issn: - 0022-4928 - 1520-0469 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Detailed investigation of the self-aggregation of convection in cloud-resolving simulations type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 69 year: '2012' ... --- _id: '9451' abstract: - lang: eng text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. article_processing_charge: No article_type: original author: - first_name: Christian A. full_name: Ibarra, Christian A. last_name: Ibarra - first_name: Xiaoqi full_name: Feng, Xiaoqi last_name: Feng - first_name: Vera K. full_name: Schoft, Vera K. last_name: Schoft - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Nina full_name: Chumak, Nina last_name: Chumak - first_name: Adriana full_name: Machlicova, Adriana last_name: Machlicova - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Denisse full_name: Rojas, Denisse last_name: Rojas - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Hisashi full_name: Tamaru, Hisashi last_name: Tamaru - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839 apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839 chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839. ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012. ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364. mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839. short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364. date_created: 2021-06-04T07:51:31Z date_published: 2012-09-14T00:00:00Z date_updated: 2021-12-14T08:28:51Z day: '14' ddc: - '580' department: - _id: DaZi doi: 10.1126/science.1224839 extern: '1' external_id: pmid: - '22984074' has_accepted_license: '1' intvolume: ' 337' issue: '6100' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/ month: '09' oa: 1 oa_version: Published Version page: 1360-1364 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 337 year: '2012' ... --- _id: '9535' abstract: - lang: eng text: The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies. article_processing_charge: No article_type: review author: - first_name: D. full_name: Coleman-Derr, D. last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944 apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944 chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944. ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012. ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154. mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944. short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154. date_created: 2021-06-08T13:01:23Z date_published: 2012-12-18T00:00:00Z date_updated: 2021-12-14T08:33:09Z day: '18' department: - _id: DaZi doi: 10.1101/sqb.2012.77.014944 extern: '1' external_id: pmid: - '23250988' intvolume: ' 77' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/sqb.2012.77.014944 month: '12' oa: 1 oa_version: Published Version page: 147-154 pmid: 1 publication: Cold Spring Harbor Symposia on Quantitative Biology publication_identifier: eissn: - 1943-4456 issn: - 0091-7451 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation, H2A.Z, and the regulation of constitutive expression type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 77 year: '2012' ... --- _id: '3242' abstract: - lang: eng text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). acknowledgement: Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/i​ndex.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_number: e1001300 author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Meghan full_name: Vyleta, Meghan id: 418901AA-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Fabian full_name: Theis, Fabian last_name: Theis - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Martina full_name: Klatt, Martina id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38 last_name: Klatt - first_name: Verena full_name: Drescher, Verena last_name: Drescher - first_name: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001300 apa: Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001300 chicago: Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001300. ieee: M. Konrad et al., “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012. ista: Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300. mla: Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001300. short: M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012). date_created: 2018-12-11T12:02:13Z date_published: 2012-04-03T00:00:00Z date_updated: 2023-02-23T14:07:11Z day: '03' ddc: - '570' - '579' department: - _id: SyCr doi: 10.1371/journal.pbio.1001300 ec_funded: 1 file: - access_level: open_access checksum: 4ebacefd9fbab5c68adf829124115fd1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:28Z date_updated: 2020-07-14T12:46:04Z file_id: '4689' file_name: IST-2012-96-v1+1_journal.pbio.1001300.pdf file_size: 674228 relation: main_file file_date_updated: 2020-07-14T12:46:04Z has_accepted_license: '1' intvolume: ' 10' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25E0E184-B435-11E9-9278-68D0E5697425 name: Antnet publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '3434' pubrep_id: '96' quality_controlled: '1' related_material: record: - id: '9755' relation: research_data status: public scopus_import: 1 status: public title: Social transfer of pathogenic fungus promotes active immunisation in ant colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2012' ... --- _id: '9755' abstract: - lang: eng text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). article_processing_charge: No author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Meghan full_name: Vyleta, Meghan id: 418901AA-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Fabian full_name: Theis, Fabian last_name: Theis - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Martina full_name: Klatt, Martina id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38 last_name: Klatt - first_name: Verena full_name: Drescher, Verena last_name: Drescher - first_name: Carsten full_name: Marr, Carsten last_name: Marr - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s' apa: 'Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s' chicago: 'Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.' ieee: 'M. Konrad et al., “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.' ista: 'Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s.' mla: 'Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.' short: M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012). date_created: 2021-07-30T08:39:13Z date_published: 2012-09-27T00:00:00Z date_updated: 2023-02-23T11:18:41Z day: '27' department: - _id: SyCr doi: 10.5061/dryad.sv37s main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.sv37s month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '3242' relation: used_in_publication status: public status: public title: 'Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '9758' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' article_processing_charge: No author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.' mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1.' short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012). date_created: 2021-07-30T12:36:39Z date_published: 2012-11-14T00:00:00Z date_updated: 2023-02-23T11:05:19Z day: '14' department: - _id: NiBa doi: 10.5061/dryad.274b1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.274b1 month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2944' relation: used_in_publication status: public status: public title: 'Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '9757' abstract: - lang: eng text: To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies. article_processing_charge: No author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Barbara full_name: Mitteregger, Barbara id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1 last_name: Mitteregger - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:10.5061/dryad.61649' apa: 'Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649' chicago: 'Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649.' ieee: 'S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.' ista: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, 10.5061/dryad.61649.' mla: 'Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.' short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012). date_created: 2021-07-30T12:31:31Z date_published: 2012-12-14T00:00:00Z date_updated: 2023-02-23T11:04:28Z day: '14' department: - _id: SyCr doi: 10.5061/dryad.61649 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.61649 month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2926' relation: used_in_publication status: public status: public title: 'Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2012' ... --- _id: '8504' abstract: - lang: eng text: In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: O. S. full_name: KOZLOVSKI, O. S. last_name: KOZLOVSKI citation: ama: Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165. doi:10.1017/s0143385710000817 apa: Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817 chicago: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817. ieee: V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast growth of the number of periodic points,” Ergodic Theory and Dynamical Systems, vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012. ista: Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1), 159–165. mla: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817. short: V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012) 159–165. date_created: 2020-09-18T10:47:33Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.1017/s0143385710000817 extern: '1' intvolume: ' 32' issue: '1' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '02' oa_version: None page: 159-165 publication: Ergodic Theory and Dynamical Systems publication_identifier: issn: - 0143-3857 - 1469-4417 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: A Cr unimodal map with an arbitrary fast growth of the number of periodic points type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2012' ... --- _id: '8503' abstract: - lang: eng text: We prove there are finitely many isometry classes of planar central configurations (also called relative equilibria) in the Newtonian 5-body problem, except perhaps if the 5-tuple of positive masses belongs to a given codimension 2 subvariety of the mass space. article_processing_charge: No article_type: original author: - first_name: Alain full_name: Albouy, Alain last_name: Albouy - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10 apa: Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.176.1.10 chicago: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10. ieee: A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University Press, pp. 535–588, 2012. ista: Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 176(1), 535–588. mla: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10. short: A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588. date_created: 2020-09-18T10:47:24Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.4007/annals.2012.176.1.10 extern: '1' intvolume: ' 176' issue: '1' language: - iso: eng month: '07' oa_version: None page: 535-588 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Princeton University Press quality_controlled: '1' status: public title: Finiteness of central configurations of five bodies in the plane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 176 year: '2012' ... --- _id: '887' abstract: - lang: eng text: A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications. acknowledgement: The work was supported by a Plan Nacional grant no. BFU2009-09271 from the Spanish Ministry of Science and Innovation. The author is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108 apa: Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108 chicago: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108. ieee: F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057, 2012. ista: Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057. mla: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108. short: F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057. date_created: 2018-12-11T11:49:01Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1098/rspb.2012.1108 extern: 1 intvolume: ' 279' issue: '1749' month: '01' page: 5048 - 5057 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6765' quality_controlled: 0 status: public title: Gene duplication as a mechanism of genomic adaptation to a changing environment 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 volume: 279 year: '2012' ... --- _id: '9049' abstract: - lang: eng text: 'Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.' article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Cécile full_name: Cottin-Bizonne, Cécile last_name: Cottin-Bizonne - first_name: Christophe full_name: Ybert, Christophe last_name: Ybert - first_name: Lydéric full_name: Bocquet, Lydéric last_name: Bocquet citation: ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b. ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012. ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994. mla: Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b. short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994. date_created: 2021-02-01T13:43:10Z date_published: 2012-01-28T00:00:00Z date_updated: 2023-02-23T13:47:31Z day: '28' doi: 10.1039/c1sm06395b extern: '1' intvolume: ' 8' issue: '4' language: - iso: eng month: '01' oa_version: None page: 980-994 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 8 year: '2012' ... --- _id: '922' abstract: - lang: eng text: 'We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young''s modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.' article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities of biological tubes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.018101 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.018101. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society, 2012. ista: Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1). mla: Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.018101. short: E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:49:13Z date_published: 2012-07-03T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '03' doi: 10.1103/PhysRevLett.109.018101 extern: '1' external_id: arxiv: - '1207.1516' intvolume: ' 109' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1207.1516 month: '07' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6519' status: public title: Mechanical instabilities of biological tubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '9499' abstract: - lang: eng text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism. article_number: e1002512 article_processing_charge: No article_type: original author: - first_name: Sang Yeol full_name: Kim, Sang Yeol last_name: Kim - first_name: Jungeun full_name: Lee, Jungeun last_name: Lee - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Z. Renee full_name: Sung, Z. Renee last_name: Sung citation: ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512 apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512 chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512. ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012. ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512. mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512. short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012). date_created: 2021-06-07T11:07:56Z date_published: 2012-03-22T00:00:00Z date_updated: 2021-12-14T08:31:14Z day: '22' department: - _id: DaZi doi: 10.1371/journal.pgen.1002512 extern: '1' external_id: pmid: - '22457632' intvolume: ' 8' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002512 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9497' abstract: - lang: eng text: The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. article_number: e1002988 article_processing_charge: No article_type: original author: - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988 apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988 chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988. ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012. ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988. mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988. short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012). date_created: 2021-06-07T10:55:27Z date_published: 2012-10-11T00:00:00Z date_updated: 2021-12-14T08:29:57Z day: '11' department: - _id: DaZi doi: 10.1371/journal.pgen.1002988 extern: '1' external_id: pmid: - '23071449' intvolume: ' 8' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002988 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Deposition of histone variant H2A.Z within gene bodies regulates responsive genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9528' abstract: - lang: eng text: Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory. article_processing_charge: No article_type: review author: - first_name: Jason T. full_name: Huff, Jason T. last_name: Huff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007 apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007 chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007. ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012. ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138. mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007. short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138. date_created: 2021-06-08T08:58:52Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-12-14T08:32:38Z department: - _id: DaZi doi: 10.1016/j.gde.2012.01.007 extern: '1' external_id: pmid: - '22336527' intvolume: ' 22' issue: '2' language: - iso: eng month: '04' oa_version: None page: 132-138 pmid: 1 publication: Current Opinion in Genetics and Development publication_identifier: issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Regulation of biological accuracy, precision, and memory by plant chromatin organization type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 22 year: '2012' ... --- _id: '966' abstract: - lang: eng text: Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario. acknowledgement: We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF). author: - first_name: Samuel full_name: Bieri, Samuel last_name: Bieri - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409 apa: Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409 chicago: Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409. ieee: S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012. ista: Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22). mla: Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409. short: S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012). date_created: 2018-12-11T11:49:27Z date_published: 2012-12-13T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '13' doi: 10.1103/PhysRevB.86.224409 extern: 1 intvolume: ' 86' issue: '22' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1208.3231 month: '12' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6431' quality_controlled: 0 status: public title: Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice type: journal_article volume: 86 year: '2012' ... --- _id: '2968' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. acknowledgement: "This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. " author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: George full_name: Melika, George last_name: Melika - first_name: Graham full_name: Stone, Graham last_name: Stone citation: ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x. ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012. ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617. mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x. short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617. date_created: 2018-12-11T12:00:36Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-05-30T13:07:47Z day: '01' ddc: - '570' - '579' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05700.x ec_funded: 1 file: - access_level: open_access checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb content_type: application/pdf creator: system date_created: 2018-12-12T10:17:47Z date_updated: 2020-07-14T12:45:57Z file_id: '5304' file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf file_size: 235820 relation: main_file - access_level: open_access checksum: f00afc5b887c8222014b57375b8caece content_type: application/pdf creator: system date_created: 2018-12-12T10:17:48Z date_updated: 2020-07-14T12:45:57Z file_id: '5305' file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf file_size: 41975 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 21' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 4605 - 4617 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3746' pubrep_id: '296' quality_controlled: '1' related_material: record: - id: '13075' relation: research_data status: public scopus_import: 1 status: public title: A likelihood based comparison of population histories in a parasitoid guild type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '13075' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. article_processing_charge: No author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: George full_name: Melika, George last_name: Melika citation: ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS' apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS' chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.' ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.' ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.' mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.' short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012). date_created: 2023-05-23T17:01:02Z date_published: 2012-06-08T00:00:00Z date_updated: 2023-05-30T13:07:48Z day: '08' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.0G0FS main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.0g0fs month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2968' relation: used_in_publication status: public status: public title: 'Data from: A likelihood-based comparison of population histories in a parasitoid guild' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '13407' abstract: - lang: eng text: We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light. article_processing_charge: No article_type: original author: - first_name: Olga full_name: Chovnik, Olga last_name: Chovnik - first_name: Renata full_name: Balgley, Renata last_name: Balgley - first_name: Joel R. full_name: Goldman, Joel R. last_name: Goldman - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 2012;134(48):19564-19567. doi:10.1021/ja309633v apa: Chovnik, O., Balgley, R., Goldman, J. R., & Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja309633v chicago: Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja309633v. ieee: O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” Journal of the American Chemical Society, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012. ista: Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567. mla: Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:10.1021/ja309633v. short: O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567. date_created: 2023-08-01T09:47:42Z date_published: 2012-11-26T00:00:00Z date_updated: 2023-08-08T07:51:10Z day: '26' doi: 10.1021/ja309633v extern: '1' external_id: pmid: - '23181449' intvolume: ' 134' issue: '48' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '11' oa_version: Published Version page: 19564-19567 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '13408' abstract: - lang: eng text: Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls. article_processing_charge: No article_type: original author: - first_name: Yonatan full_name: Ridelman, Yonatan last_name: Ridelman - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Ronit full_name: Popovitz-Biro, Ronit last_name: Popovitz-Biro - first_name: Sharon G. full_name: Wolf, Sharon G. last_name: Wolf - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882 apa: Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882 chicago: Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882. ieee: Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012. ista: Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660. mla: Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882. short: Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660. date_created: 2023-08-01T09:47:55Z date_published: 2012-03-12T00:00:00Z date_updated: 2023-08-08T07:55:10Z day: '12' doi: 10.1002/smll.201101882 extern: '1' external_id: pmid: - '22392681' intvolume: ' 8' issue: '5' keyword: - Biomaterials - Biotechnology - General Materials Science - General Chemistry language: - iso: eng month: '03' oa_version: None page: 654-660 pmid: 1 publication: Small publication_identifier: eissn: - 1613-6829 issn: - 1613-6810 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '10903' abstract: - lang: eng text: We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas. acknowledgement: This work has been partially supported by the French ANR project Veridyc alternative_title: - LNCS article_processing_charge: No author: - first_name: Ahmed full_name: Bouajjani, Ahmed last_name: Bouajjani - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Mihaela full_name: Sighireanu, Mihaela last_name: Sighireanu citation: ama: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:10.1007/978-3-642-33386-6_14' apa: 'Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-33386-6_14' chicago: 'Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In Automated Technology for Verification and Analysis, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_14.' ieee: A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182. ista: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.' mla: Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” Automated Technology for Verification and Analysis, vol. 7561, Springer, 2012, pp. 167–82, doi:10.1007/978-3-642-33386-6_14. short: A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182. conference: end_date: 2012-10-06 location: Thiruvananthapuram, India name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2012-10-03 date_created: 2022-03-21T07:58:39Z date_published: 2012-10-15T00:00:00Z date_updated: 2023-09-05T14:07:24Z day: '15' department: - _id: ToHe doi: 10.1007/978-3-642-33386-6_14 intvolume: ' 7561' language: - iso: eng month: '10' oa_version: None page: 167-182 place: Berlin, Heidelberg publication: Automated Technology for Verification and Analysis publication_identifier: eisbn: - '9783642333866' eissn: - 1611-3349 isbn: - '9783642333859' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Accurate invariant checking for programs manipulating lists and arrays with infinite data type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7561 year: '2012' ... --- _id: '10905' abstract: - lang: eng text: "Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help." acknowledgement: 'Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: Algorithms – ESA 2012. Vol 7501. Springer; 2012:301-312. doi:10.1007/978-3-642-33090-2_27' apa: 'Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In Algorithms – ESA 2012 (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. https://doi.org/10.1007/978-3-642-33090-2_27' chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In Algorithms – ESA 2012, 7501:301–12. Springer, 2012. https://doi.org/10.1007/978-3-642-33090-2_27. ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in Algorithms – ESA 2012, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312. ista: 'Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.' mla: Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithms – ESA 2012, vol. 7501, Springer, 2012, pp. 301–12, doi:10.1007/978-3-642-33090-2_27. short: K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312. conference: end_date: 2012-09-12 location: Ljubljana, Slovenia name: 'ESA: European Symposium on Algorithms' start_date: 2012-09-10 date_created: 2022-03-21T08:01:45Z date_published: 2012-10-01T00:00:00Z date_updated: 2023-09-05T14:09:30Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-33090-2_27 ec_funded: 1 external_id: arxiv: - '1604.08234' intvolume: ' 7501' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.08234 month: '10' oa: 1 oa_version: Preprint page: 301-312 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Algorithms – ESA 2012 publication_identifier: eisbn: - '9783642330902' eissn: - 1611-3349 isbn: - '9783642330896' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' related_material: record: - id: '535' relation: later_version status: public scopus_import: '1' status: public title: Polynomial-time algorithms for energy games with special weight structures type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7501 year: '2012' ... --- _id: '10906' abstract: - lang: eng text: HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool. alternative_title: - LNCS article_processing_charge: No author: - first_name: Sergey full_name: Grebenshchikov, Sergey last_name: Grebenshchikov - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Nuno P. full_name: Lopes, Nuno P. last_name: Lopes - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46' apa: 'Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan & B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46' chicago: 'Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-28756-5_46.' ieee: 'S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.' ista: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.' mla: 'Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:10.1007/978-3-642-28756-5_46.' short: S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551. conference: end_date: 2012-04-01 location: Tallinn, Estonia name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2012-03-24 date_created: 2022-03-21T08:03:30Z date_published: 2012-04-01T00:00:00Z date_updated: 2023-09-05T14:09:54Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-642-28756-5_46 editor: - first_name: Cormac full_name: Flanagan, Cormac last_name: Flanagan - first_name: Barbara full_name: König, Barbara last_name: König intvolume: ' 7214' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-642-28756-5_46 month: '04' oa: 1 oa_version: Published Version page: 549-551 place: Berlin, Heidelberg publication: Tools and Algorithms for the Construction and Analysis of Systems publication_identifier: eisbn: - '9783642287565' eissn: - 1611-3349 isbn: - '9783642287558' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: 'HSF(C): A software verifier based on Horn clauses' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7214 year: '2012' ... --- _id: '5745' article_processing_charge: No author: - first_name: Ashutosh full_name: Gupta, Ashutosh last_name: Gupta citation: ama: 'Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:10.1007/978-3-642-33386-6_10' apa: 'Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33386-6_10' chicago: 'Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In Automated Technology for Verification and Analysis, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.' ieee: 'A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in Automated Technology for Verification and Analysis, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.' ista: 'Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.' mla: Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” Automated Technology for Verification and Analysis, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10. short: A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121. conference: end_date: 2012-10-06 location: Thiruvananthapuram, Kerala, India name: ATVA 2012 start_date: 2012-10-03 date_created: 2018-12-18T13:01:46Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-09-05T14:15:29Z ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-642-33386-6_10 ec_funded: 1 file: - access_level: open_access checksum: 68415837a315de3cc4d120f6019d752c content_type: application/pdf creator: dernst date_created: 2018-12-18T13:07:35Z date_updated: 2020-07-14T12:47:10Z file_id: '5746' file_name: 2012_ATVA_Gupta.pdf file_size: 465502 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 7561' language: - iso: eng oa: 1 oa_version: None page: 107-121 place: Berlin, Heidelberg project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Automated Technology for Verification and Analysis publication_identifier: eissn: - 1611-3349 isbn: - '9783642333859' - '9783642333866' issn: - 0302-9743 publication_status: published publisher: Springer Berlin Heidelberg pubrep_id: '180' quality_controlled: '1' series_title: LNCS status: public title: Improved Single Pass Algorithms for Resolution Proof Reduction type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7561 year: '2012' ... --- _id: '3251' abstract: - lang: eng text: Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system. acknowledgement: This research was supported in part by the European Research Council (ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF) project S11402-N23. alternative_title: - LNCS author: - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition systems. In: Vol 7148. Springer; 2012:445-460. doi:10.1007/978-3-642-27940-9_29' apa: 'Zufferey, D., Wies, T., & Henzinger, T. A. (2012). Ideal abstractions for well structured transition systems (Vol. 7148, pp. 445–460). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_29' chicago: Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_29. ieee: 'D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured transition systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.' ista: 'Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 445–460.' mla: Zufferey, Damien, et al. Ideal Abstractions for Well Structured Transition Systems. Vol. 7148, Springer, 2012, pp. 445–60, doi:10.1007/978-3-642-27940-9_29. short: D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460. conference: end_date: 2012-01-24 location: Philadelphia, PA, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2012-01-22 date_created: 2018-12-11T12:02:16Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-09-07T11:36:36Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-642-27940-9_29 ec_funded: 1 file: - access_level: open_access checksum: f2f0d55efa32309ad1fe65a5fcaad90c content_type: application/pdf creator: system date_created: 2018-12-12T10:09:35Z date_updated: 2020-07-14T12:46:05Z file_id: '4759' file_name: IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf file_size: 217104 relation: main_file file_date_updated: 2020-07-14T12:46:05Z has_accepted_license: '1' intvolume: ' 7148' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 445 - 460 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '3406' pubrep_id: '100' quality_controlled: '1' related_material: record: - id: '1405' relation: dissertation_contains status: public status: public title: Ideal abstractions for well structured transition systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7148 year: '2012' ... --- _id: '3157' abstract: - lang: eng text: Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion. author: - first_name: Luis full_name: Diaz Jr, Luis last_name: Diaz Jr - first_name: Richard full_name: Williams, Richard last_name: Williams - first_name: Jian full_name: Wu, Jian last_name: Wu - first_name: Isaac full_name: Kinde, Isaac last_name: Kinde - first_name: Joel full_name: Hecht, Joel last_name: Hecht - first_name: Jordan full_name: Berlin, Jordan last_name: Berlin - first_name: Benjamin full_name: Allen, Benjamin last_name: Allen - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Kenneth full_name: Kinzler, Kenneth last_name: Kinzler - first_name: Kelly full_name: Oliner, Kelly last_name: Oliner - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein citation: ama: Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537-540. doi:10.1038/nature11219 apa: Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11219 chicago: Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11219. ieee: L. Diaz Jr et al., “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” Nature, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012. ista: Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540. mla: Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:10.1038/nature11219. short: L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540. date_created: 2018-12-11T12:01:43Z date_published: 2012-06-28T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '28' department: - _id: KrCh doi: 10.1038/nature11219 ec_funded: 1 external_id: pmid: - '22722843' intvolume: ' 486' issue: '7404' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/ month: '06' oa: 1 oa_version: Submitted Version page: 537 - 540 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3537' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 486 year: '2012' ... --- _id: '3260' abstract: - lang: eng text: "Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.\r\n" author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Chatterjee K, Reiter J, Nowak M. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 2012;81(1):69-80. doi:10.1016/j.tpb.2011.11.003 apa: Chatterjee, K., Reiter, J., & Nowak, M. (2012). Evolutionary dynamics of biological auctions. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2011.11.003 chicago: Chatterjee, Krishnendu, Johannes Reiter, and Martin Nowak. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology. Academic Press, 2012. https://doi.org/10.1016/j.tpb.2011.11.003. ieee: K. Chatterjee, J. Reiter, and M. Nowak, “Evolutionary dynamics of biological auctions,” Theoretical Population Biology, vol. 81, no. 1. Academic Press, pp. 69–80, 2012. ista: Chatterjee K, Reiter J, Nowak M. 2012. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 81(1), 69–80. mla: Chatterjee, Krishnendu, et al. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology, vol. 81, no. 1, Academic Press, 2012, pp. 69–80, doi:10.1016/j.tpb.2011.11.003. short: K. Chatterjee, J. Reiter, M. Nowak, Theoretical Population Biology 81 (2012) 69–80. date_created: 2018-12-11T12:02:19Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '01' department: - _id: KrCh doi: 10.1016/j.tpb.2011.11.003 ec_funded: 1 external_id: pmid: - '22120126' intvolume: ' 81' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279759/ ' month: '02' oa: 1 oa_version: Submitted Version page: 69 - 80 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '3388' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: Evolutionary dynamics of biological auctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2012' ... --- _id: '3258' abstract: - lang: eng text: CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. It is generally thought that proximal synapses from the mossy fibers activate these neurons most efficiently, whereas distal inputs from the perforant path have a weaker modulatory influence. We used confocally targeted patch-clamp recording from dendrites and axons to map the activation of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two distinct dendritic domains. In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed a high Na+-to-K+ conductance density ratio, providing ideal conditions for active backpropagation and dendritic spike initiation. Dendritic spikes may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (TR 3/B10) and the European Union (European Research Council Advanced grant to P.J.). article_processing_charge: No article_type: original author: - first_name: Sooyun full_name: Kim, Sooyun id: 394AB1C8-F248-11E8-B48F-1D18A9856A87 last_name: Kim - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Kim S, Guzmán J, Hu H, Jonas PM. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 2012;15(4):600-606. doi:10.1038/nn.3060 apa: Kim, S., Guzmán, J., Hu, H., & Jonas, P. M. (2012). Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3060 chicago: Kim, Sooyun, José Guzmán, Hua Hu, and Peter M Jonas. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3060. ieee: S. Kim, J. Guzmán, H. Hu, and P. M. Jonas, “Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons,” Nature Neuroscience, vol. 15, no. 4. Nature Publishing Group, pp. 600–606, 2012. ista: Kim S, Guzmán J, Hu H, Jonas PM. 2012. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 15(4), 600–606. mla: Kim, Sooyun, et al. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience, vol. 15, no. 4, Nature Publishing Group, 2012, pp. 600–06, doi:10.1038/nn.3060. short: S. Kim, J. Guzmán, H. Hu, P.M. Jonas, Nature Neuroscience 15 (2012) 600–606. date_created: 2018-12-11T12:02:18Z date_published: 2012-04-01T00:00:00Z date_updated: 2023-09-07T11:43:52Z day: '01' department: - _id: PeJo doi: 10.1038/nn.3060 external_id: pmid: - '22388958' intvolume: ' 15' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617474/ month: '04' oa: 1 oa_version: Published Version page: 600 - 606 pmid: 1 project: - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Nature Neuroscience publication_identifier: issn: - 1546-1726 publication_status: published publisher: Nature Publishing Group publist_id: '3390' quality_controlled: '1' related_material: record: - id: '2964' relation: dissertation_contains status: public scopus_import: '1' status: public title: Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 15 year: '2012' ... --- _id: '2964' abstract: - lang: eng text: 'CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. These neurons receive multiple excitatory inputs from numerous sources. Therefore, the rules of spatiotemporal integration of multiple synaptic inputs and propagation of action potentials are important to understand how CA3 neurons contribute to higher brain functions at cellular level. By using confocally targeted patch-clamp recording techniques, we investigated the biophysical properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic domains critical for action potential initiation and propagation: In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking synaptic events. These findings can be explained by a high Na+-to-K+ conductance density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently than distal perforant inputs by showing that the distal synapses trigger a different form of activity represented by dendritic spikes. The high probability of dendritic spike initiation in the distal area may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sooyun full_name: Kim, Sooyun id: 394AB1C8-F248-11E8-B48F-1D18A9856A87 last_name: Kim citation: ama: Kim S. Active properties of hippocampal CA3 pyramidal neuron dendrites. 2012. apa: Kim, S. (2012). Active properties of hippocampal CA3 pyramidal neuron dendrites. Institute of Science and Technology Austria. chicago: Kim, Sooyun. “Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites.” Institute of Science and Technology Austria, 2012. ieee: S. Kim, “Active properties of hippocampal CA3 pyramidal neuron dendrites,” Institute of Science and Technology Austria, 2012. ista: Kim S. 2012. Active properties of hippocampal CA3 pyramidal neuron dendrites. Institute of Science and Technology Austria. mla: Kim, Sooyun. Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites. Institute of Science and Technology Austria, 2012. short: S. Kim, Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites, Institute of Science and Technology Austria, 2012. date_created: 2018-12-11T12:00:35Z date_published: 2012-06-01T00:00:00Z date_updated: 2023-09-07T11:43:51Z day: '01' degree_awarded: PhD department: - _id: PeJo - _id: GradSch language: - iso: eng month: '06' oa_version: None page: '65' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '3755' related_material: record: - id: '3258' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Active properties of hippocampal CA3 pyramidal neuron dendrites type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2012' ... --- _id: '3246' abstract: - lang: eng text: Visualizing and analyzing shape changes at various scales, ranging from single molecules to whole organisms, are essential for understanding complex morphogenetic processes, such as early embryonic development. Embryo morphogenesis relies on the interplay between different tissues, the properties of which are again determined by the interaction between their constituent cells. Cell interactions, on the other hand, are controlled by various molecules, such as signaling and adhesion molecules, which in order to exert their functions need to be spatiotemporally organized within and between the interacting cells. In this review, we will focus on the role of cell adhesion functioning at different scales to organize cell, tissue and embryo morphogenesis. We will specifically ask how the subcellular distribution of adhesion molecules controls the formation of cell-cell contacts, how cell-cell contacts determine tissue shape, and how tissue interactions regulate embryo morphogenesis. acknowledgement: This review comes from a themed issue on Cell structure and dynamics Edited by Jason Swedlow and Gaudenz Danuser author: - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Barone V, Heisenberg C-PJ. Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. 2012;24(1):148-153. doi:10.1016/j.ceb.2011.11.006 apa: Barone, V., & Heisenberg, C.-P. J. (2012). Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.11.006 chicago: Barone, Vanessa, and Carl-Philipp J Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2011.11.006. ieee: V. Barone and C.-P. J. Heisenberg, “Cell adhesion in embryo morphogenesis,” Current Opinion in Cell Biology, vol. 24, no. 1. Elsevier, pp. 148–153, 2012. ista: Barone V, Heisenberg C-PJ. 2012. Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. 24(1), 148–153. mla: Barone, Vanessa, and Carl-Philipp J. Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” Current Opinion in Cell Biology, vol. 24, no. 1, Elsevier, 2012, pp. 148–53, doi:10.1016/j.ceb.2011.11.006. short: V. Barone, C.-P.J. Heisenberg, Current Opinion in Cell Biology 24 (2012) 148–153. date_created: 2018-12-11T12:02:14Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-09-07T12:05:08Z day: '01' department: - _id: CaHe doi: 10.1016/j.ceb.2011.11.006 intvolume: ' 24' issue: '1' language: - iso: eng month: '02' oa_version: None page: 148 - 153 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '3423' quality_controlled: '1' related_material: record: - id: '961' relation: dissertation_contains status: public scopus_import: 1 status: public title: Cell adhesion in embryo morphogenesis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '12198' abstract: - lang: eng text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications, the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415) to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935). article_processing_charge: No article_type: original author: - first_name: Christian A. full_name: Ibarra, Christian A. last_name: Ibarra - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Vera K. full_name: Schoft, Vera K. last_name: Schoft - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Nina full_name: Chumak, Nina last_name: Chumak - first_name: Adriana full_name: Machlicova, Adriana last_name: Machlicova - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Denisse full_name: Rojas, Denisse last_name: Rojas - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Hisashi full_name: Tamaru, Hisashi last_name: Tamaru - first_name: Daniel full_name: Zilberman, Daniel last_name: Zilberman citation: ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839 apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839 chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839. ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012. ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364. mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839. short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364. date_created: 2023-01-16T09:21:24Z date_published: 2012-09-14T00:00:00Z date_updated: 2023-10-16T09:27:26Z day: '14' department: - _id: XiFe doi: 10.1126/science.1224839 external_id: pmid: - '22984074' intvolume: ' 337' issue: '6100' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/ month: '09' oa: 1 oa_version: Published Version page: 1360-1364 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 337 year: '2012' ... --- _id: '6588' abstract: - lang: eng text: First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions. acknowledgement: "This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n" article_processing_charge: No article_type: original author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Pausinger F. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 2012;8(1):63-78. apa: Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. B. Verkin Institute for Low Temperature Physics and Engineering. chicago: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” Journal of Mathematical Physics, Analysis, Geometry. B. Verkin Institute for Low Temperature Physics and Engineering, 2012. ieee: F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,” Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1. B. Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012. ista: Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78. mla: Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” Journal of Mathematical Physics, Analysis, Geometry, vol. 8, no. 1, B. Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78. short: F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78. date_created: 2019-06-27T08:16:56Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-10-16T09:41:31Z day: '01' department: - _id: HeEd external_id: isi: - '000301173600004' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://mi.mathnet.ru/eng/jmag525 month: '01' oa: 1 oa_version: Published Version page: 63-78 publication: Journal of Mathematical Physics, Analysis, Geometry publication_identifier: issn: - 1812-9471 publication_status: published publisher: B. Verkin Institute for Low Temperature Physics and Engineering quality_controlled: '1' scopus_import: '1' status: public title: Elementary solutions of the Bernstein problem on two intervals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3123' abstract: - lang: eng text: We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation. acknowledgement: This work was funded by NSF grant IIS-1017014 and CCF- 0917093. alternative_title: - Eurographics article_processing_charge: No author: - first_name: Jihun full_name: Yu, Jihun last_name: Yu - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Greg full_name: Turk, Greg last_name: Turk - first_name: Chee full_name: Yap, Chee last_name: Yap citation: ama: 'Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids. In: Computer Graphics Forum. Vol 31. Wiley; 2012:815-824. doi:10.1111/j.1467-8659.2012.03062.x' apa: 'Yu, J., Wojtan, C., Turk, G., & Yap, C. (2012). Explicit mesh surfaces for particle based fluids. In Computer Graphics Forum (Vol. 31, pp. 815–824). Cagliari, Sardinia, Italy: Wiley. https://doi.org/10.1111/j.1467-8659.2012.03062.x' chicago: Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces for Particle Based Fluids.” In Computer Graphics Forum, 31:815–24. Wiley, 2012. https://doi.org/10.1111/j.1467-8659.2012.03062.x. ieee: J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle based fluids,” in Computer Graphics Forum, Cagliari, Sardinia, Italy, 2012, vol. 31, no. 2, pp. 815–824. ista: 'Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association for Computer Graphics, Eurographics, vol. 31, 815–824.' mla: Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” Computer Graphics Forum, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:10.1111/j.1467-8659.2012.03062.x. short: J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012, pp. 815–824. conference: end_date: 2012-05-18 location: Cagliari, Sardinia, Italy name: 'EUROGRAPHICS: Conference on European Association for Computer Graphics' start_date: 2012-05-13 date_created: 2018-12-11T12:01:31Z date_published: 2012-05-01T00:00:00Z date_updated: 2023-10-16T09:54:40Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/j.1467-8659.2012.03062.x file: - access_level: open_access checksum: acb325dd1e31859bedd30e013f61d0b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:39Z date_updated: 2020-07-14T12:46:00Z file_id: '5092' file_name: IST-2016-601-v1+1_meshSPH.pdf file_size: 5740527 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 31' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 815 - 824 publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley publist_id: '3576' pubrep_id: '601' quality_controlled: '1' scopus_import: '1' status: public title: Explicit mesh surfaces for particle based fluids type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2012' ... --- _id: '3244' abstract: - lang: eng text: "Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen.\r\n" article_processing_charge: No article_type: letter_note author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 citation: ama: Danowski P. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und Information. 2012;64(4):284. apa: Danowski, P. (2012). Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und Information. Fachzeitschrift des BIB – Berufsverband Information Bibliothek. chicago: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum Bibliothek und Information. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012. ieee: P. Danowski, “Die Zeit des Abwartens ist vorbei!,” BuB - Forum Bibliothek und Information, vol. 64, no. 4. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, p. 284, 2012. ista: Danowski P. 2012. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und Information. 64(4), 284. mla: Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” BuB - Forum Bibliothek und Information, vol. 64, no. 4, Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012, p. 284. short: P. Danowski, BuB - Forum Bibliothek und Information 64 (2012) 284. date_created: 2018-12-11T12:02:13Z date_published: 2012-04-15T00:00:00Z date_updated: 2023-10-16T10:19:14Z day: '15' department: - _id: E-Lib intvolume: ' 64' issue: '4' language: - iso: ger main_file_link: - open_access: '1' url: https://www.b-u-b.de/fileadmin/archiv/imports/pdf_files/2012/bub_2012_04_284.pdf month: '04' oa: 1 oa_version: Published Version page: '284' popular_science: '1' publication: BuB - Forum Bibliothek und Information publication_identifier: issn: - 1869 -1137 publication_status: published publisher: Fachzeitschrift des BIB – Berufsverband Information Bibliothek publist_id: '3432' status: public title: Die Zeit des Abwartens ist vorbei! type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2012' ... --- _id: '3243' abstract: - lang: eng text: 'Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick Danowski gibt seine Einschätzung ab. ' article_processing_charge: No article_type: letter_note author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 citation: ama: Danowski P. Zwischen Technologie und Information. Büchereiperspektiven. 2012;2012(1):11. apa: Danowski, P. (2012). Zwischen Technologie und Information. Büchereiperspektiven. Büchereiverband Österreichs. chicago: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven. Büchereiverband Österreichs, 2012. ieee: P. Danowski, “Zwischen Technologie und Information,” Büchereiperspektiven, vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012. ista: Danowski P. 2012. Zwischen Technologie und Information. Büchereiperspektiven. 2012(1), 11. mla: Danowski, Patrick. “Zwischen Technologie und Information.” Büchereiperspektiven, vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11. short: P. Danowski, Büchereiperspektiven 2012 (2012) 11. date_created: 2018-12-11T12:02:13Z date_published: 2012-03-01T00:00:00Z date_updated: 2023-10-16T10:40:18Z day: '01' department: - _id: E-Lib intvolume: ' 2012' issue: '1' language: - iso: ger main_file_link: - open_access: '1' url: https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf month: '03' oa: 1 oa_version: Published Version page: '11' popular_science: '1' publication: Büchereiperspektiven publication_identifier: issn: - 1607-7172 publication_status: published publisher: Büchereiverband Österreichs publist_id: '3433' status: public title: Zwischen Technologie und Information type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2012 year: '2012' ... --- _id: '2915' acknowledgement: "The project receives funding from the European Community’s Seventh Framework Programme under grant agreement\r\nno. ICT- 248273 GeRT." article_processing_charge: No author: - first_name: Oliver full_name: Kroemer, Oliver last_name: Kroemer - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Jan full_name: Peters, Jan last_name: Peters citation: ama: 'Kroemer O, Lampert C, Peters J. Multi-modal learning for dynamic tactile sensing. In: Deutsches Zentrum für Luft und Raumfahrt; 2012.' apa: Kroemer, O., Lampert, C., & Peters, J. (2012). Multi-modal learning for dynamic tactile sensing. Deutsches Zentrum für Luft und Raumfahrt. chicago: Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Multi-Modal Learning for Dynamic Tactile Sensing.” Deutsches Zentrum für Luft und Raumfahrt, 2012. ieee: O. Kroemer, C. Lampert, and J. Peters, “Multi-modal learning for dynamic tactile sensing,” 2012. ista: Kroemer O, Lampert C, Peters J. 2012. Multi-modal learning for dynamic tactile sensing mla: Kroemer, Oliver, et al. Multi-Modal Learning for Dynamic Tactile Sensing. Deutsches Zentrum für Luft und Raumfahrt, 2012. short: O. Kroemer, C. Lampert, J. Peters, in:, Deutsches Zentrum für Luft und Raumfahrt, 2012. date_created: 2018-12-11T12:00:19Z date_published: 2012-10-11T00:00:00Z date_updated: 2023-10-17T07:58:59Z day: '11' department: - _id: ChLa language: - iso: eng month: '10' oa_version: None publication_status: published publisher: Deutsches Zentrum für Luft und Raumfahrt publist_id: '3828' quality_controlled: '1' status: public title: Multi-modal learning for dynamic tactile sensing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2912' article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Nataliya full_name: Strelkova, Nataliya last_name: Strelkova citation: ama: Edelsbrunner H, Strelkova N. On the configuration space for the shortest networks. Russian Mathematical Surveys. 2012;67(6):1167–1168. doi:10.4213/rm9503 apa: Edelsbrunner, H., & Strelkova, N. (2012). On the configuration space for the shortest networks. Russian Mathematical Surveys. Russian Academy of Sciences. https://doi.org/10.4213/rm9503 chicago: Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space for the Shortest Networks.” Russian Mathematical Surveys. Russian Academy of Sciences, 2012. https://doi.org/10.4213/rm9503. ieee: H. Edelsbrunner and N. Strelkova, “On the configuration space for the shortest networks,” Russian Mathematical Surveys, vol. 67, no. 6. Russian Academy of Sciences, pp. 1167–1168, 2012. ista: Edelsbrunner H, Strelkova N. 2012. On the configuration space for the shortest networks. Russian Mathematical Surveys. 67(6), 1167–1168. mla: Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space for the Shortest Networks.” Russian Mathematical Surveys, vol. 67, no. 6, Russian Academy of Sciences, 2012, pp. 1167–1168, doi:10.4213/rm9503. short: H. Edelsbrunner, N. Strelkova, Russian Mathematical Surveys 67 (2012) 1167–1168. date_created: 2018-12-11T12:00:18Z date_published: 2012-10-01T00:00:00Z date_updated: 2023-10-17T11:40:39Z day: '01' department: - _id: HeEd doi: 10.4213/rm9503 intvolume: ' 67' issue: '6' language: - iso: eng month: '10' oa_version: None page: 1167–1168 publication: Russian Mathematical Surveys publication_status: published publisher: Russian Academy of Sciences publist_id: '3831' quality_controlled: '1' status: public title: On the configuration space for the shortest networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2012' ... --- _id: '3127' abstract: - lang: eng text: "When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations." article_processing_charge: No author: - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: 'Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: Proceedings of the 29th International Conference on Machine Learning. ML Research Press; 2012:211-218.' apa: 'Quadrianto, N., Lampert, C., & Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In Proceedings of the 29th International Conference on Machine Learning (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.' chicago: Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In Proceedings of the 29th International Conference on Machine Learning, 211–18. ML Research Press, 2012. ieee: N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in Proceedings of the 29th International Conference on Machine Learning, Edinburgh, United Kingdom, 2012, pp. 211–218. ista: 'Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218.' mla: Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–18. short: N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218. conference: end_date: 2012-07-01 location: Edinburgh, United Kingdom name: 'ICML: International Conference on Machine Learning' start_date: 2012-06-26 date_created: 2018-12-11T12:01:33Z date_published: 2012-06-01T00:00:00Z date_updated: 2023-10-17T11:55:06Z day: '01' department: - _id: ChLa - _id: HeEd language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1206.4652 month: '06' oa: 1 oa_version: Preprint page: 211-218 publication: Proceedings of the 29th International Conference on Machine Learning publication_status: published publisher: ML Research Press publist_id: '3572' quality_controlled: '1' scopus_import: '1' status: public title: The most persistent soft-clique in a set of sampled graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2904' abstract: - lang: eng text: Generalized van der Corput sequences are onedimensional, infinite sequences in the unit interval. They are generated from permutations in integer base b and are the building blocks of the multi-dimensional Halton sequences. Motivated by recent progress of Atanassov on the uniform distribution behavior of Halton sequences, we study, among others, permutations of the form P(i) = ai (mod b) for coprime integers a and b. We show that multipliers a that either divide b - 1 or b + 1 generate van der Corput sequences with weak distribution properties. We give explicit lower bounds for the asymptotic distribution behavior of these sequences and relate them to sequences generated from the identity permutation in smaller bases, which are, due to Faure, the weakest distributed generalized van der Corput sequences. - lang: fre text: Les suites de Van der Corput généralisées sont dessuites unidimensionnelles et infinies dans l’intervalle de l’unité.Elles sont générées par permutations des entiers de la basebetsont les éléments constitutifs des suites multi-dimensionnelles deHalton. Suites aux progrès récents d’Atanassov concernant le com-portement de distribution uniforme des suites de Halton nous nousintéressons aux permutations de la formuleP(i) =ai(modb)pour les entiers premiers entre euxaetb. Dans cet article nousidentifions des multiplicateursagénérant des suites de Van derCorput ayant une mauvaise distribution. Nous donnons les bornesinférieures explicites pour cette distribution asymptotique asso-ciée à ces suites et relions ces dernières aux suites générées parpermutation d’identité, qui sont, selon Faure, les moins bien dis-tribuées des suites généralisées de Van der Corput dans une basedonnée. article_processing_charge: No article_type: original author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Pausinger F. Weak multipliers for generalized van der Corput sequences. Journal de Theorie des Nombres des Bordeaux. 2012;24(3):729-749. doi:10.5802/jtnb.819 apa: Pausinger, F. (2012). Weak multipliers for generalized van der Corput sequences. Journal de Theorie Des Nombres Des Bordeaux. Université de Bordeaux. https://doi.org/10.5802/jtnb.819 chicago: Pausinger, Florian. “Weak Multipliers for Generalized van Der Corput Sequences.” Journal de Theorie Des Nombres Des Bordeaux. Université de Bordeaux, 2012. https://doi.org/10.5802/jtnb.819. ieee: F. Pausinger, “Weak multipliers for generalized van der Corput sequences,” Journal de Theorie des Nombres des Bordeaux, vol. 24, no. 3. Université de Bordeaux, pp. 729–749, 2012. ista: Pausinger F. 2012. Weak multipliers for generalized van der Corput sequences. Journal de Theorie des Nombres des Bordeaux. 24(3), 729–749. mla: Pausinger, Florian. “Weak Multipliers for Generalized van Der Corput Sequences.” Journal de Theorie Des Nombres Des Bordeaux, vol. 24, no. 3, Université de Bordeaux, 2012, pp. 729–49, doi:10.5802/jtnb.819. short: F. Pausinger, Journal de Theorie Des Nombres Des Bordeaux 24 (2012) 729–749. date_created: 2018-12-11T12:00:15Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-10-18T07:53:47Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.5802/jtnb.819 file: - access_level: open_access checksum: 6954bfe9d7f4119fbdda7a11cf0f5c67 content_type: application/pdf creator: dernst date_created: 2020-05-11T12:40:39Z date_updated: 2020-07-14T12:45:52Z file_id: '7819' file_name: JTNB_2012__24_3_729_0.pdf file_size: 819275 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 24' issue: '3' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 729 - 749 publication: Journal de Theorie des Nombres des Bordeaux publication_identifier: eissn: - 2118-8572 issn: - 1246-7405 publication_status: published publisher: Université de Bordeaux publist_id: '3843' quality_controlled: '1' scopus_import: '1' status: public title: Weak multipliers for generalized van der Corput sequences type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '2902' abstract: - lang: eng text: 'We present an algorithm for simplifying linear cartographic objects and results obtained with a computer program implementing this algorithm. ' article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Oleg full_name: Musin, Oleg last_name: Musin - first_name: Alexey full_name: Ukhalov, Alexey last_name: Ukhalov - first_name: Olga full_name: Yakimova, Olga last_name: Yakimova - first_name: Vladislav full_name: Alexeev, Vladislav last_name: Alexeev - first_name: Victoriya full_name: Bogaevskaya, Victoriya last_name: Bogaevskaya - first_name: Andrey full_name: Gorohov, Andrey last_name: Gorohov - first_name: Margarita full_name: Preobrazhenskaya, Margarita last_name: Preobrazhenskaya citation: ama: Edelsbrunner H, Musin O, Ukhalov A, et al. Fractal and computational geometry for generalizing cartographic objects. Modeling and Analysis of Information Systems. 2012;19(6):152-160. apa: Edelsbrunner, H., Musin, O., Ukhalov, A., Yakimova, O., Alexeev, V., Bogaevskaya, V., … Preobrazhenskaya, M. (2012). Fractal and computational geometry for generalizing cartographic objects. Modeling and Analysis of Information Systems. Russian Academy of Sciences. chicago: Edelsbrunner, Herbert, Oleg Musin, Alexey Ukhalov, Olga Yakimova, Vladislav Alexeev, Victoriya Bogaevskaya, Andrey Gorohov, and Margarita Preobrazhenskaya. “Fractal and computational geometry for generalizing cartographic objects.” Modeling and Analysis of Information Systems. Russian Academy of Sciences, 2012. ieee: H. Edelsbrunner et al., “Fractal and computational geometry for generalizing cartographic objects,” Modeling and Analysis of Information Systems, vol. 19, no. 6. Russian Academy of Sciences, pp. 152–160, 2012. ista: Edelsbrunner H, Musin O, Ukhalov A, Yakimova O, Alexeev V, Bogaevskaya V, Gorohov A, Preobrazhenskaya M. 2012. Fractal and computational geometry for generalizing cartographic objects. Modeling and Analysis of Information Systems. 19(6), 152–160. mla: Edelsbrunner, Herbert, et al. “Fractal and computational geometry for generalizing cartographic objects.” Modeling and Analysis of Information Systems, vol. 19, no. 6, Russian Academy of Sciences, 2012, pp. 152–60. short: H. Edelsbrunner, O. Musin, A. Ukhalov, O. Yakimova, V. Alexeev, V. Bogaevskaya, A. Gorohov, M. Preobrazhenskaya, Modeling and Analysis of Information Systems 19 (2012) 152–160. date_created: 2018-12-11T12:00:15Z date_published: 2012-12-01T00:00:00Z date_updated: 2023-10-18T07:34:45Z day: '01' department: - _id: HeEd intvolume: ' 19' issue: '6' language: - iso: rus main_file_link: - open_access: '1' url: http://mi.mathnet.ru/eng/mais280 month: '12' oa: 1 oa_version: Published Version page: 152 - 160 publication: Modeling and Analysis of Information Systems publication_status: published publisher: Russian Academy of Sciences publist_id: '3845' quality_controlled: '1' status: public title: Fractal and computational geometry for generalizing cartographic objects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2012' ... --- _id: '10389' abstract: - lang: eng text: We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies and William L. Miller for helpful discussions. article_number: '8324' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 2011;7(18). doi:10.1039/c1sm05773a apa: Šarić, A., & Cacciuto, A. (2011). Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm05773a chicago: Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1sm05773a. ieee: A. Šarić and A. Cacciuto, “Soft elastic surfaces as a platform for particle self-assembly,” Soft Matter, vol. 7, no. 18. Royal Society of Chemistry, 2011. ista: Šarić A, Cacciuto A. 2011. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 7(18), 8324. mla: Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter, vol. 7, no. 18, 8324, Royal Society of Chemistry, 2011, doi:10.1039/c1sm05773a. short: A. Šarić, A. Cacciuto, Soft Matter 7 (2011). date_created: 2021-11-29T14:33:18Z date_published: 2011-08-08T00:00:00Z date_updated: 2021-11-29T15:12:10Z day: '08' doi: 10.1039/c1sm05773a extern: '1' external_id: arxiv: - '1106.2995' intvolume: ' 7' issue: '18' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1106.2995 month: '08' oa: 1 oa_version: Preprint publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Soft elastic surfaces as a platform for particle self-assembly type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 7 year: '2011' ... --- _id: '1050' abstract: - lang: eng text: We present experimentally derived potential curves 1?and spin-orbit interaction functions for the strongly perturbed AΣu+ 3?and bΠu states of the cesium dimer. The results are based on data from several sources. Laser-induced fluorescence Fourier transform spectroscopy (LIF FTS) was used some time ago in the Laboratoire Aimé Cotton primarily to study the XΣg+ state. More recent work at Tsinghua University provides information from moderate 3?resolution spectroscopy on the lowest levels of the bΠ0u± state as well as additional high-resolution data. From Innsbruck University, we have precision data obtained with cold Cs2 molecules. Recent data from Temple University was obtained using the optical-optical double resonance polarization spectroscopy technique, and finally, a group at the University of Latvia has added additional LIF FTS data. In the Hamiltonian matrix, we have used analytic potentials (the expanded Morse oscillator form) with both finite-difference (FD) coupled-channel and discrete variable representation (DVR) calculations of the term values. Fitted diagonal and off-diagonal spin-orbit functions are obtained and compared with ab initio results from Temple and Moscow State universities. acknowledgement: The work in Temple University was supported by NSF grant no. PHY-0855502. S.K. acknowledges support from AFOSR and from NSF grant no. PHY-1005453. S.A., C.M., and J.H. were supported by NSF grants no. PHY-0652938 and PHY-0968898. The work at Stony Brook was supported by NSF grants no. PHY-0652459 and PHY-0968905. The work in Tsinghua University was supported by NSFC of China, under grant no. 20773072. The Moscow team thanks the Russian Foundation for Basic Researches by the grant no. 10-03-00195 and MSU Priority Direction 2.3. M.T. and R.F. are grateful to Ilze Klincare, Olga Nikolayeva, and Artis Kruzins for their help in spectra analysis, as well as appreciate the support from the ESF 2009/0223/1DP/1.1.1.2.0/09/APIA/VIAA/008 project. article_processing_charge: No author: - first_name: Jianmei full_name: Bai, Jianmei last_name: Bai - first_name: Ergin full_name: Ahmed, Ergin last_name: Ahmed - first_name: Bediha full_name: Beser, Bediha last_name: Beser - first_name: Yafei full_name: Guan, Yafei last_name: Guan - first_name: Svetlana full_name: Kotochigova, Svetlana last_name: Kotochigova - first_name: Marjatta full_name: Lyyra, Marjatta last_name: Lyyra - first_name: Seth full_name: Ashman, Seth last_name: Ashman - first_name: Christopher full_name: Wolfe, Christopher last_name: Wolfe - first_name: John full_name: Huennekens, John last_name: Huennekens - first_name: Feng full_name: Xie, Feng last_name: Xie - first_name: Dan full_name: Li, Dan last_name: Li - first_name: Li full_name: Li, Li last_name: Li - first_name: Maris full_name: Tamanis, Maris last_name: Tamanis - first_name: Ruvin full_name: Ferber, Ruvin last_name: Ferber - first_name: Anastasia full_name: Drozdova, Anastasia last_name: Drozdova - first_name: Elena full_name: Pazyuk, Elena last_name: Pazyuk - first_name: Andrey full_name: Stolyarov, Andrey last_name: Stolyarov - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl - first_name: Nadia full_name: Bouloufa, Nadia last_name: Bouloufa - first_name: Olivier full_name: Dulieu, Olivier last_name: Dulieu - first_name: Claude full_name: Amiot, Claude last_name: Amiot - first_name: Houssam full_name: Salami, Houssam last_name: Salami - first_name: Thomas full_name: Bergeman, Thomas last_name: Bergeman citation: ama: Bai J, Ahmed E, Beser B, et al. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(3). doi:10.1103/PhysRevA.83.032514 apa: Bai, J., Ahmed, E., Beser, B., Guan, Y., Kotochigova, S., Lyyra, M., … Bergeman, T. (2011). Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.032514 chicago: Bai, Jianmei, Ergin Ahmed, Bediha Beser, Yafei Guan, Svetlana Kotochigova, Marjatta Lyyra, Seth Ashman, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.032514. ieee: J. Bai et al., “Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 3. American Physical Society, 2011. ista: Bai J, Ahmed E, Beser B, Guan Y, Kotochigova S, Lyyra M, Ashman S, Wolfe C, Huennekens J, Xie F, Li D, Li L, Tamanis M, Ferber R, Drozdova A, Pazyuk E, Stolyarov A, Danzl JG, Nägerl H, Bouloufa N, Dulieu O, Amiot C, Salami H, Bergeman T. 2011. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. Physical Review A - Atomic, Molecular, and Optical Physics. 83(3). mla: Bai, Jianmei, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 3, American Physical Society, 2011, doi:10.1103/PhysRevA.83.032514. short: J. Bai, E. Ahmed, B. Beser, Y. Guan, S. Kotochigova, M. Lyyra, S. Ashman, C. Wolfe, J. Huennekens, F. Xie, D. Li, L. Li, M. Tamanis, R. Ferber, A. Drozdova, E. Pazyuk, A. Stolyarov, J.G. Danzl, H. Nägerl, N. Bouloufa, O. Dulieu, C. Amiot, H. Salami, T. Bergeman, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011). date_created: 2018-12-11T11:49:53Z date_published: 2011-03-28T00:00:00Z date_updated: 2021-01-12T06:47:55Z day: '28' doi: 10.1103/PhysRevA.83.032514 extern: '1' external_id: arxiv: - '1101.5412' intvolume: ' 83' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1101.5412 month: '03' oa: 1 oa_version: Preprint publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_status: published publisher: American Physical Society publist_id: '6339' status: public title: Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2011' ... --- _id: '1048' abstract: - lang: eng text: We produce an ultracold and dense sample of rovibronic ground state Cs 2 molecules close to the regime of quantum degeneracy, in a single hyperfine level, in the presence of an optical lattice. The molecules are individually trapped, in the motional ground state of an optical lattice well, with a lifetime of 8 s. For preparation, we start with a zero-temperature atomic Mott-insulator state with optimized double-site occupancy and efficiently associate weakly-bound dimer molecules on a Feshbach resonance. Despite extremely weak Franck-Condon wavefunction overlap, the molecules are subsequently transferred with >50% efficiency to the rovibronic ground state by a stimulated four-photon process. Our results present a crucial step towards the generation of Bose-Einstein condensates of ground-state molecules and, when suitably generalized to polar heteronuclear molecules such as RbCs, the realization of dipolar many-body quantum-gas phases in periodic potentials. acknowledgement: "We thank H. Ritsch, N. Bouloufa, O. Dulieu, J. Aldegunde, J. M. Hutson, H. Salami, T. Bergeman, S. D ̈urr, and K. Bergmann for valuable discussions and H. Telle, H. Schnatz, B. Lipphardt, and J. Alnis for sharing technical expertise. We are indebted to R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Ministry of Science and\r\nResearch (Bundesministerium f ̈ur Wissenschaft und Forschung) and the Austrian Science Fund\r\n(Fonds zur F ̈orderung der wissenschaftlichen Forschung) in the form of a START prize grant\r\nand by the European Science Foundation within the framework of the EuroQUASAR collective\r\nresearch project QuDeGPM (Project I 153-N16) and within the framework of the EuroQUAM\r\ncollective research project QuDipMol (Project I 124-N16). R.H. was supported by a Marie Curie\r\nInternational Incoming Fellowship within the 7th European Community Framework Programme" article_processing_charge: No author: - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Mattias full_name: Gustavsson, Mattias last_name: Gustavsson - first_name: Russell full_name: Hart, Russell last_name: Hart - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: 'Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. 2011;264(1). doi:10.1088/1742-6596/264/1/012015' apa: 'Nägerl, H., Mark, M., Haller, E., Gustavsson, M., Hart, R., & Danzl, J. G. (2011). Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/264/1/012015' chicago: 'Nägerl, Hanns, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Johann G Danzl. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” Journal of Physics: Conference Series. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1742-6596/264/1/012015.' ieee: 'H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and J. G. Danzl, “Ultracold and dense samples of ground-state molecules in lattice potentials,” Journal of Physics: Conference Series, vol. 264, no. 1. IOP Publishing Ltd., 2011.' ista: 'Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. 2011. Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. 264(1).' mla: 'Nägerl, Hanns, et al. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” Journal of Physics: Conference Series, vol. 264, no. 1, IOP Publishing Ltd., 2011, doi:10.1088/1742-6596/264/1/012015.' short: 'H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J.G. Danzl, Journal of Physics: Conference Series 264 (2011).' date_created: 2018-12-11T11:49:52Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:47:54Z day: '01' doi: 10.1088/1742-6596/264/1/012015 extern: '1' external_id: arxiv: - '1011.0179' intvolume: ' 264' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1011.0179 month: '01' oa: 1 oa_version: Preprint publication: 'Journal of Physics: Conference Series' publication_status: published publisher: IOP Publishing Ltd. publist_id: '6340' status: public title: Ultracold and dense samples of ground-state molecules in lattice potentials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 264 year: '2011' ... --- _id: '1052' abstract: - lang: eng text: The present paper aims at finding optimal parameters for trapping of Cs 2 molecules in optical lattices, with the perspective of creating a quantum degenerate gas of ground-state molecules. We have calculated dynamic polarizabilities of Cs 2 molecules subject to an oscillating electric field, using accurate potential curves and electronic transition dipole moments. We show that for some particular wavelengths of the optical lattice, called "magic wavelengths", the polarizability of the ground-state molecules is equal to the one of a Feshbach molecule. As the creation of the sample of ground-state molecules relies on an adiabatic population transfer from weakly-bound molecules created on a Feshbach resonance, such a coincidence ensures that both the initial and final states are favorably trapped by the lattice light, allowing optimized transfer in agreement with the experimental observation. acknowledgement: "We thank E. Haller for important contributions to the experimental work and R. Grimm for generous support. We acknowledge funding by the Austrian \ Science Fund (FWF) within\r\nproject Quantum Gases of Ground-State Molecules, \ project\r\nnumber P 21555-N20." article_processing_charge: No author: - first_name: Romain full_name: Vexiau, Romain last_name: Vexiau - first_name: Nadia full_name: Bouloufa, Nadia last_name: Bouloufa - first_name: Mireille full_name: Aymar, Mireille last_name: Aymar - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl - first_name: Olivier full_name: Dulieu, Olivier last_name: Dulieu citation: ama: Vexiau R, Bouloufa N, Aymar M, et al. Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. European Physical Journal D. 2011;65(1-2):243-250. doi:10.1140/epjd/e2011-20085-4 apa: Vexiau, R., Bouloufa, N., Aymar, M., Danzl, J. G., Mark, M., Nägerl, H., & Dulieu, O. (2011). Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. European Physical Journal D. Springer. https://doi.org/10.1140/epjd/e2011-20085-4 chicago: Vexiau, Romain, Nadia Bouloufa, Mireille Aymar, Johann G Danzl, Manfred Mark, Hanns Nägerl, and Olivier Dulieu. “Optimal Trapping Wavelengths of Cs 2 Molecules in an Optical Lattice.” European Physical Journal D. Springer, 2011. https://doi.org/10.1140/epjd/e2011-20085-4. ieee: R. Vexiau et al., “Optimal trapping wavelengths of Cs 2 molecules in an optical lattice,” European Physical Journal D, vol. 65, no. 1–2. Springer, pp. 243–250, 2011. ista: Vexiau R, Bouloufa N, Aymar M, Danzl JG, Mark M, Nägerl H, Dulieu O. 2011. Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. European Physical Journal D. 65(1–2), 243–250. mla: Vexiau, Romain, et al. “Optimal Trapping Wavelengths of Cs 2 Molecules in an Optical Lattice.” European Physical Journal D, vol. 65, no. 1–2, Springer, 2011, pp. 243–50, doi:10.1140/epjd/e2011-20085-4. short: R. Vexiau, N. Bouloufa, M. Aymar, J.G. Danzl, M. Mark, H. Nägerl, O. Dulieu, European Physical Journal D 65 (2011) 243–250. date_created: 2018-12-11T11:49:53Z date_published: 2011-11-01T00:00:00Z date_updated: 2021-01-12T06:47:56Z day: '01' doi: 10.1140/epjd/e2011-20085-4 extern: '1' external_id: arxiv: - '1102.1793' intvolume: ' 65' issue: 1-2 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1102.1793 month: '11' oa: 1 oa_version: Preprint page: 243 - 250 publication: European Physical Journal D publication_status: published publisher: Springer publist_id: '6336' status: public title: Optimal trapping wavelengths of Cs 2 molecules in an optical lattice type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2011' ... --- _id: '1051' abstract: - lang: eng text: We demonstrate the temporal Talbot effect for trapped matter waves using ultracold atoms in an optical lattice. We investigate the phase evolution of an array of essentially non-interacting matter waves and observe matter-wave collapse and revival in the form of a Talbot interference pattern. By using long expansion times, we image momentum space with sub-recoil resolution, allowing us to observe fractional Talbot fringes up to tenth order. acknowledgement: We are indebted to R Grimm for generous support and we thank A Daley for valuable discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within project I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM. article_processing_charge: No author: - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Katharina full_name: Lauber, Katharina last_name: Lauber - first_name: Mattias full_name: Gustavsson, Mattias last_name: Gustavsson - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Mark M, Haller E, Danzl JG, Lauber K, Gustavsson M, Nägerl H. Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. New Journal of Physics. 2011;13. doi:10.1088/1367-2630/13/8/085008 apa: Mark, M., Haller, E., Danzl, J. G., Lauber, K., Gustavsson, M., & Nägerl, H. (2011). Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/13/8/085008 chicago: Mark, Manfred, Elmar Haller, Johann G Danzl, Katharina Lauber, Mattias Gustavsson, and Hanns Nägerl. “Demonstration of the Temporal Matter-Wave Talbot Effect for Trapped Matter Waves.” New Journal of Physics. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1367-2630/13/8/085008. ieee: M. Mark, E. Haller, J. G. Danzl, K. Lauber, M. Gustavsson, and H. Nägerl, “Demonstration of the temporal matter-wave Talbot effect for trapped matter waves,” New Journal of Physics, vol. 13. IOP Publishing Ltd., 2011. ista: Mark M, Haller E, Danzl JG, Lauber K, Gustavsson M, Nägerl H. 2011. Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. New Journal of Physics. 13. mla: Mark, Manfred, et al. “Demonstration of the Temporal Matter-Wave Talbot Effect for Trapped Matter Waves.” New Journal of Physics, vol. 13, IOP Publishing Ltd., 2011, doi:10.1088/1367-2630/13/8/085008. short: M. Mark, E. Haller, J.G. Danzl, K. Lauber, M. Gustavsson, H. Nägerl, New Journal of Physics 13 (2011). date_created: 2018-12-11T11:49:53Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T06:47:56Z day: '01' doi: 10.1088/1367-2630/13/8/085008 extern: '1' intvolume: ' 13' language: - iso: eng month: '08' oa_version: None publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '6338' status: public title: Demonstration of the temporal matter-wave Talbot effect for trapped matter waves type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2011' ... --- _id: '1053' abstract: - lang: eng text: We perform precision measurements on a Mott-insulator quantum state of ultracold atoms with tunable interactions. We probe the dependence of the superfluid-to-Mott-insulator transition on the interaction strength and explore the limits of the standard Bose-Hubbard model description. By tuning the on-site interaction energies to values comparable to the interband separation, we are able to quantitatively measure number-dependent shifts in the excitation spectrum caused by effective multibody interactions. acknowledgement: We are indebted to R. Grimm for generous support. We thank D. Boyanovsky, H. Büchler, P. Johnson, W. Niedenzu, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within project I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM. article_processing_charge: No author: - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Katharina full_name: Lauber, Katharina last_name: Lauber - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Andrew full_name: Daley, Andrew last_name: Daley - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Mark M, Haller E, Lauber K, Danzl JG, Daley A, Nägerl H. Precision measurements on a tunable Mott insulator of ultracold atoms. Physical Review Letters. 2011;107(17). doi:10.1103/PhysRevLett.107.175301 apa: Mark, M., Haller, E., Lauber, K., Danzl, J. G., Daley, A., & Nägerl, H. (2011). Precision measurements on a tunable Mott insulator of ultracold atoms. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.175301 chicago: Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Andrew Daley, and Hanns Nägerl. “Precision Measurements on a Tunable Mott Insulator of Ultracold Atoms.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.175301. ieee: M. Mark, E. Haller, K. Lauber, J. G. Danzl, A. Daley, and H. Nägerl, “Precision measurements on a tunable Mott insulator of ultracold atoms,” Physical Review Letters, vol. 107, no. 17. American Physical Society, 2011. ista: Mark M, Haller E, Lauber K, Danzl JG, Daley A, Nägerl H. 2011. Precision measurements on a tunable Mott insulator of ultracold atoms. Physical Review Letters. 107(17). mla: Mark, Manfred, et al. “Precision Measurements on a Tunable Mott Insulator of Ultracold Atoms.” Physical Review Letters, vol. 107, no. 17, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.175301. short: M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Daley, H. Nägerl, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:49:54Z date_published: 2011-10-18T00:00:00Z date_updated: 2021-01-12T06:47:56Z day: '18' doi: 10.1103/PhysRevLett.107.175301 extern: '1' external_id: arxiv: - '1107.1803' intvolume: ' 107' issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1107.1803 month: '10' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6337' status: public title: Precision measurements on a tunable Mott insulator of ultracold atoms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2011' ... --- _id: '1054' abstract: - lang: eng text: We investigate local three-body correlations for bosonic particles in three dimensions and one dimension as a function of the interaction strength. The three-body correlation function g(3) is determined by measuring the three-body recombination rate in an ultracold gas of Cs atoms. In three dimensions, we measure the dependence of g(3) on the gas parameter in a BEC, finding good agreement with the theoretical prediction accounting for beyond-mean-field effects. In one dimension, we observe a reduction of g( 3) by several orders of magnitude upon increasing interactions from the weakly interacting BEC to the strongly interacting Tonks-Girardeau regime, in good agreement with predictions from the Lieb-Liniger model for all strengths of interaction. acknowledgement: We thank R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM. G. P. acknowledges funding from the EU through NAME-QUAM and AQUTE. article_processing_charge: No author: - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Mahmoud full_name: Rabie, Mahmoud last_name: Rabie - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Russell full_name: Hart, Russell last_name: Hart - first_name: Katharina full_name: Lauber, Katharina last_name: Lauber - first_name: Guido full_name: Pupillo, Guido last_name: Pupillo - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Haller E, Rabie M, Mark M, et al. Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. Physical Review Letters. 2011;107(23). doi:10.1103/PhysRevLett.107.230404 apa: Haller, E., Rabie, M., Mark, M., Danzl, J. G., Hart, R., Lauber, K., … Nägerl, H. (2011). Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.230404 chicago: Haller, Elmar, Mahmoud Rabie, Manfred Mark, Johann G Danzl, Russell Hart, Katharina Lauber, Guido Pupillo, and Hanns Nägerl. “Three-Body Correlation Functions and Recombination Rates for Bosons in Three Dimensions and One Dimension.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.230404. ieee: E. Haller et al., “Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension,” Physical Review Letters, vol. 107, no. 23. American Physical Society, 2011. ista: Haller E, Rabie M, Mark M, Danzl JG, Hart R, Lauber K, Pupillo G, Nägerl H. 2011. Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. Physical Review Letters. 107(23). mla: Haller, Elmar, et al. “Three-Body Correlation Functions and Recombination Rates for Bosons in Three Dimensions and One Dimension.” Physical Review Letters, vol. 107, no. 23, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.230404. short: E. Haller, M. Rabie, M. Mark, J.G. Danzl, R. Hart, K. Lauber, G. Pupillo, H. Nägerl, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:49:54Z date_published: 2011-12-02T00:00:00Z date_updated: 2021-01-12T06:47:57Z day: '02' doi: 10.1103/PhysRevLett.107.230404 extern: '1' external_id: arxiv: - '1107.4516' intvolume: ' 107' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1107.4516 month: '12' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6335' status: public title: Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2011' ... --- _id: '11094' abstract: - lang: eng text: Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly. article_processing_charge: No article_type: original author: - first_name: Jessica A. full_name: Talamas, Jessica A. last_name: Talamas - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Talamas JA, Hetzer M. POM121 and Sun1 play a role in early steps of interphase NPC assembly. Journal of Cell Biology. 2011;194(1):27-37. doi:10.1083/jcb.201012154 apa: Talamas, J. A., & Hetzer, M. (2011). POM121 and Sun1 play a role in early steps of interphase NPC assembly. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201012154 chicago: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” Journal of Cell Biology. Rockefeller University Press, 2011. https://doi.org/10.1083/jcb.201012154. ieee: J. A. Talamas and M. Hetzer, “POM121 and Sun1 play a role in early steps of interphase NPC assembly,” Journal of Cell Biology, vol. 194, no. 1. Rockefeller University Press, pp. 27–37, 2011. ista: Talamas JA, Hetzer M. 2011. POM121 and Sun1 play a role in early steps of interphase NPC assembly. Journal of Cell Biology. 194(1), 27–37. mla: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” Journal of Cell Biology, vol. 194, no. 1, Rockefeller University Press, 2011, pp. 27–37, doi:10.1083/jcb.201012154. short: J.A. Talamas, M. Hetzer, Journal of Cell Biology 194 (2011) 27–37. date_created: 2022-04-07T07:52:18Z date_published: 2011-07-04T00:00:00Z date_updated: 2022-07-18T08:53:46Z day: '04' doi: 10.1083/jcb.201012154 extern: '1' external_id: pmid: - '21727197' intvolume: ' 194' issue: '1' keyword: - Cell Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1083/jcb.201012154 month: '07' oa: 1 oa_version: Published Version page: 27-37 pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: POM121 and Sun1 play a role in early steps of interphase NPC assembly type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 194 year: '2011' ... --- _id: '11096' abstract: - lang: eng text: As the gatekeepers of the eukaryotic cell nucleus, nuclear pore complexes (NPCs) mediate all molecular trafficking between the nucleoplasm and the cytoplasm. In recent years, transport-independent functions of NPC components, nucleoporins, have been identified including roles in chromatin organization and gene regulation. Here, we summarize our current view of the NPC as a dynamic hub for the integration of chromatin regulation and nuclear trafficking and discuss the functional interplay between nucleoporins and the nuclear genome. article_processing_charge: No article_type: original author: - first_name: Yun full_name: Liang, Yun last_name: Liang - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Liang Y, Hetzer M. Functional interactions between nucleoporins and chromatin. Current Opinion in Cell Biology. 2011;23(1):65-70. doi:10.1016/j.ceb.2010.09.008 apa: Liang, Y., & Hetzer, M. (2011). Functional interactions between nucleoporins and chromatin. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2010.09.008 chicago: Liang, Yun, and Martin Hetzer. “Functional Interactions between Nucleoporins and Chromatin.” Current Opinion in Cell Biology. Elsevier, 2011. https://doi.org/10.1016/j.ceb.2010.09.008. ieee: Y. Liang and M. Hetzer, “Functional interactions between nucleoporins and chromatin,” Current Opinion in Cell Biology, vol. 23, no. 1. Elsevier, pp. 65–70, 2011. ista: Liang Y, Hetzer M. 2011. Functional interactions between nucleoporins and chromatin. Current Opinion in Cell Biology. 23(1), 65–70. mla: Liang, Yun, and Martin Hetzer. “Functional Interactions between Nucleoporins and Chromatin.” Current Opinion in Cell Biology, vol. 23, no. 1, Elsevier, 2011, pp. 65–70, doi:10.1016/j.ceb.2010.09.008. short: Y. Liang, M. Hetzer, Current Opinion in Cell Biology 23 (2011) 65–70. date_created: 2022-04-07T07:52:37Z date_published: 2011-02-01T00:00:00Z date_updated: 2022-07-18T08:53:48Z day: '01' doi: 10.1016/j.ceb.2010.09.008 extern: '1' external_id: pmid: - '21030234' intvolume: ' 23' issue: '1' keyword: - Cell Biology language: - iso: eng month: '02' oa_version: None page: 65-70 pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: issn: - 0955-0674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Functional interactions between nucleoporins and chromatin type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 23 year: '2011' ... --- _id: '11095' article_processing_charge: No article_type: letter_note author: - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Giacomo full_name: Cavalli, Giacomo last_name: Cavalli citation: ama: Hetzer M, Cavalli G. Editorial overview. Current Opinion in Cell Biology. 2011;23(3):255-257. doi:10.1016/j.ceb.2011.04.013 apa: Hetzer, M., & Cavalli, G. (2011). Editorial overview. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.04.013 chicago: Hetzer, Martin, and Giacomo Cavalli. “Editorial Overview.” Current Opinion in Cell Biology. Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.04.013. ieee: M. Hetzer and G. Cavalli, “Editorial overview,” Current Opinion in Cell Biology, vol. 23, no. 3. Elsevier, pp. 255–257, 2011. ista: Hetzer M, Cavalli G. 2011. Editorial overview. Current Opinion in Cell Biology. 23(3), 255–257. mla: Hetzer, Martin, and Giacomo Cavalli. “Editorial Overview.” Current Opinion in Cell Biology, vol. 23, no. 3, Elsevier, 2011, pp. 255–57, doi:10.1016/j.ceb.2011.04.013. short: M. Hetzer, G. Cavalli, Current Opinion in Cell Biology 23 (2011) 255–257. date_created: 2022-04-07T07:52:27Z date_published: 2011-06-01T00:00:00Z date_updated: 2022-07-18T08:39:40Z day: '01' doi: 10.1016/j.ceb.2011.04.013 extern: '1' external_id: pmid: - '21592757' intvolume: ' 23' issue: '3' keyword: - Cell Biology language: - iso: eng month: '06' oa_version: None page: 255-257 pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: issn: - 0955-0674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Editorial overview type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 23 year: '2011' ...