[{"oa":1,"publisher":"BioMed Central","quality_controlled":"1","date_created":"2018-12-11T11:46:46Z","doi":"10.1186/1471-2229-12-116","date_published":"2012-07-26T00:00:00Z","publication":"BMC Plant Biology","day":"26","year":"2012","has_accepted_license":"1","article_number":"116","title":"GiA Roots: Software for the high throughput analysis of plant root system architecture","article_processing_charge":"No","publist_id":"7328","author":[{"first_name":"Taras","full_name":"Galkovskyi, Taras","last_name":"Galkovskyi"},{"first_name":"Yuriy","full_name":"Mileyko, Yuriy","last_name":"Mileyko"},{"first_name":"Alexander","full_name":"Bucksch, Alexander","last_name":"Bucksch"},{"first_name":"Brad","last_name":"Moore","full_name":"Moore, Brad"},{"full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"last_name":"Price","full_name":"Price, Charles","first_name":"Charles"},{"first_name":"Chrostopher","full_name":"Topp, Chrostopher","last_name":"Topp"},{"last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali"},{"full_name":"Zurek, Paul","last_name":"Zurek","first_name":"Paul"},{"last_name":"Fang","full_name":"Fang, Suqin","first_name":"Suqin"},{"first_name":"John","last_name":"Harer","full_name":"Harer, John"},{"first_name":"Philip","last_name":"Benfey","full_name":"Benfey, Philip"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology, vol. 12, 116, BioMed Central, 2012, doi:10.1186/1471-2229-12-116.","short":"T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C. Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC Plant Biology 12 (2012).","ieee":"T. Galkovskyi et al., “GiA Roots: Software for the high throughput analysis of plant root system architecture,” BMC Plant Biology, vol. 12. BioMed Central, 2012.","ama":"Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 2012;12. doi:10.1186/1471-2229-12-116","apa":"Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-12-116","chicago":"Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology. BioMed Central, 2012. https://doi.org/10.1186/1471-2229-12-116.","ista":"Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C, Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 12, 116."},"intvolume":" 12","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.","lang":"eng"}],"volume":12,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:35Z","file_name":"IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":1691436,"creator":"system","file_id":"4953","checksum":"0c629e36acd5f2878ff7dd088d67d494","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","pubrep_id":"946","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"492","file_date_updated":"2020-07-14T12:46:35Z","ddc":["005","514","516"],"extern":"1","date_updated":"2022-08-25T14:59:17Z"},{"quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"acknowledgement":"The studies were in part or completely supported by the Bundesministerium für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631 and 216886, the World Class University Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008), the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415 (Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk), the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830, German Research Foundation grants 550/B5 and C6, and by a scholarship from the German National Academic Foundation. This paper only reflects the authors’ views and funding agencies are not liable for any use that may be made of the information contained herein.\r\n","doi":"10.3389/fnins.2012.00055","date_published":"2012-07-13T00:00:00Z","date_created":"2018-12-11T11:46:46Z","day":"13","publication":"Frontiers in Neuroscience","has_accepted_license":"1","year":"2012","article_number":"55","title":"Review of the BCI competition IV","publist_id":"7327","author":[{"last_name":"Tangermann","full_name":"Tangermann, Michael","first_name":"Michael"},{"last_name":"Müller","full_name":"Müller, Klaus","first_name":"Klaus"},{"first_name":"Ad","last_name":"Aertsen","full_name":"Aertsen, Ad"},{"last_name":"Birbaumer","full_name":"Birbaumer, Niels","first_name":"Niels"},{"first_name":"Christoph","full_name":"Braun, Christoph","last_name":"Braun"},{"first_name":"Clemens","full_name":"Brunner, Clemens","last_name":"Brunner"},{"first_name":"Robert","last_name":"Leeb","full_name":"Leeb, Robert"},{"full_name":"Mehring, Carsten","last_name":"Mehring","first_name":"Carsten"},{"last_name":"Miller","full_name":"Miller, Kai","first_name":"Kai"},{"first_name":"Gernot","full_name":"Müller Putz, Gernot","last_name":"Müller Putz"},{"last_name":"Nolte","full_name":"Nolte, Guido","first_name":"Guido"},{"first_name":"Gert","last_name":"Pfurtscheller","full_name":"Pfurtscheller, Gert"},{"first_name":"Hubert","full_name":"Preissl, Hubert","last_name":"Preissl"},{"first_name":"Gerwin","full_name":"Schalk, Gerwin","last_name":"Schalk"},{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Vidaurre","full_name":"Vidaurre, Carmen","first_name":"Carmen"},{"last_name":"Waldert","full_name":"Waldert, Stephan","first_name":"Stephan"},{"last_name":"Blankertz","full_name":"Blankertz, Benjamin","first_name":"Benjamin"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R, Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition IV. Frontiers in Neuroscience. 6, 55.","chicago":"Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.” Frontiers in Neuroscience. Frontiers Research Foundation, 2012. https://doi.org/10.3389/fnins.2012.00055.","apa":"Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner, C., … Blankertz, B. (2012). Review of the BCI competition IV. Frontiers in Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnins.2012.00055","ama":"Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV. Frontiers in Neuroscience. 2012;6. doi:10.3389/fnins.2012.00055","short":"M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner, R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H. Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers in Neuroscience 6 (2012).","ieee":"M. Tangermann et al., “Review of the BCI competition IV,” Frontiers in Neuroscience, vol. 6. Frontiers Research Foundation, 2012.","mla":"Tangermann, Michael, et al. “Review of the BCI Competition IV.” Frontiers in Neuroscience, vol. 6, 55, Frontiers Research Foundation, 2012, doi:10.3389/fnins.2012.00055."},"month":"07","intvolume":" 6","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs."}],"volume":6,"file":[{"checksum":"195238221c4b0b0f4035f6f6c16ea17c","file_id":"5356","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:18:34Z","file_name":"IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf","creator":"system","date_updated":"2020-07-14T12:46:35Z","file_size":2693701}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"945","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"493","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"ddc":["004"],"date_updated":"2021-01-12T08:01:03Z"},{"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"citation":{"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.","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.","short":"A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246.","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.","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","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alex","full_name":"Kruckman, Alex","last_name":"Kruckman"},{"full_name":"Rubin, Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"},{"full_name":"Sheridan, John","last_name":"Sheridan","first_name":"John"},{"first_name":"Ben","full_name":"Zax, Ben","last_name":"Zax"}],"publist_id":"7325","title":"A Myhill Nerode theorem for automata with advice","oa":1,"publisher":"Open Publishing Association","quality_controlled":"1","year":"2012","has_accepted_license":"1","publication":"Proceedings GandALF 2012","day":"07","page":"238 - 246","date_created":"2018-12-11T11:46:47Z","date_published":"2012-10-07T00:00:00Z","doi":"10.4204/EPTCS.96.18","_id":"495","conference":{"name":"GandALF: Games, Automata, Logics and Formal Verification","location":"Napoli, Italy","end_date":"2012-09-08","start_date":"2012-09-06"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"944","status":"public","date_updated":"2021-01-12T08:01:04Z","ddc":["004"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:35Z","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."}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["EPTCS"],"intvolume":" 96","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":97736,"date_updated":"2020-07-14T12:46:35Z","creator":"system","file_name":"IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf","date_created":"2018-12-12T10:15:31Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"56277f95edc9d531fa3bdc5f9579fda8","file_id":"5152"}],"ec_funded":1,"volume":96},{"author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Rowell","full_name":"Rowell, David"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"}],"publist_id":"7322","title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","citation":{"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.","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.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924.","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","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","page":"913 - 924","date_created":"2018-12-11T11:46:48Z","date_published":"2012-12-01T00:00:00Z","doi":"10.1111/j.1752-4571.2012.00284.x","year":"2012","has_accepted_license":"1","publication":"Evolutionary Applications","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","pubrep_id":"942","status":"public","_id":"498","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:35Z","date_updated":"2021-01-12T08:01:06Z","ddc":["576"],"intvolume":" 5","month":"12","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."}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"8","volume":5,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"233007138606aca5a2f75f7ae1742f43","file_id":"4821","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:33Z","file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":396136,"creator":"system"}]},{"year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"doi":"10.1109/LICS.2012.65","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:46:47Z","ec_funded":1,"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."}],"oa_version":"Preprint","alternative_title":["LICS"],"publisher":"IEEE","scopus_import":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf"}],"oa":1,"month":"01","date_updated":"2021-01-12T08:01:05Z","citation":{"short":"A. Rabinovich, S. Rubin, in:, IEEE, 2012.","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.","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","ama":"Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:10.1109/LICS.2012.65","mla":"Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65.","ista":"Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.","chicago":"Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. https://doi.org/10.1109/LICS.2012.65."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Rabinovich","full_name":"Rabinovich, Alexander","first_name":"Alexander"},{"first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin","full_name":"Rubin, Sasha"}],"publist_id":"7324","title":"Interpretations in trees with countably many branches","department":[{"_id":"KrCh"}],"_id":"496","article_number":"6280474","type":"conference","conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2012-06-25","location":"Dubrovnik, Croatia","end_date":"2012-06-28"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"status":"public"},{"_id":"494","article_number":"29","type":"journal_article","status":"public","citation":{"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.","short":"U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13 (2012).","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","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.","ista":"Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29.","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."},"date_updated":"2021-01-12T08:01:03Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"publist_id":"7326","title":"Translating to Co-Büchi made tight, unified, and useful","department":[{"_id":"ToHe"}],"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."}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"ACM","month":"10","intvolume":" 13","year":"2012","publication_status":"published","day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","language":[{"iso":"eng"}],"date_published":"2012-10-01T00:00:00Z","issue":"4","doi":"10.1145/2362355.2362357","volume":13,"date_created":"2018-12-11T11:46:47Z"},{"publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2012","day":"30","publication":"Journal of Cell Biology","page":"347 - 349","doi":"10.1083/jcb.201204039","date_published":"2012-04-30T00:00:00Z","date_created":"2018-12-11T11:46:51Z","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","short":"M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349.","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.","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.","ista":"Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7314","author":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Cell migration: Fibroblasts find a new way to get ahead","oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 197","publication_status":"published","file":[{"file_name":"2012_CellBiology_Sixt.pdf","date_created":"2019-02-12T09:03:09Z","creator":"kschuh","file_size":986566,"date_updated":"2020-07-14T12:46:36Z","file_id":"5957","checksum":"45c02be33ebd99fc3077d60b9c90bdfa","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"3","volume":197,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"506","type":"journal_article","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","date_updated":"2021-01-12T08:01:11Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:46:36Z"},{"title":"Faster algorithms for alternating refinement relations","publist_id":"7323","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chaubal, Siddhesh","last_name":"Chaubal","first_name":"Siddhesh"},{"first_name":"Pritish","last_name":"Kamath","full_name":"Kamath, Pritish"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182.","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","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.","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.","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."},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_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"}],"doi":"10.4230/LIPIcs.CSL.2012.167","date_published":"2012-09-01T00:00:00Z","date_created":"2018-12-11T11:46:48Z","page":"167 - 182","day":"01","has_accepted_license":"1","year":"2012","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:35Z","ddc":["004"],"date_updated":"2023-02-23T12:23:32Z","status":"public","pubrep_id":"943","type":"conference","conference":{"location":"Fontainebleau, France","end_date":"2012-09-06","start_date":"2012-09-03","name":"EACSL: European Association for Computer Science Logic"},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"497","volume":16,"related_material":{"record":[{"relation":"earlier_version","id":"5378","status":"public"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4712","checksum":"f1b0dd99240800db2d7dbf9b5131fe5e","file_size":471236,"date_updated":"2020-07-14T12:46:35Z","creator":"system","file_name":"IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf","date_created":"2018-12-12T10:08:50Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 16","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","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."}]},{"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."}],"oa_version":"None","main_file_link":[{"url":"https://arxiv.org/abs/1109.5018","open_access":"1"}],"month":"01","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"2141"},{"relation":"earlier_version","status":"public","id":"5379"}]},"_id":"3165","conference":{"end_date":"2012-01-19","location":"Kyoto, Japan","start_date":"2012-01-17","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","pubrep_id":"15","status":"public","date_updated":"2023-02-23T12:23:35Z","department":[{"_id":"KrCh"}],"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.","oa":1,"publisher":"SIAM","quality_controlled":"1","year":"2012","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","page":"1386 - 1399","date_created":"2018-12-11T12:01:46Z","date_published":"2012-01-01T00:00:00Z","doi":"10.1137/1.9781611973099.109","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"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"citation":{"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.","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.","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","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","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.","short":"K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1109.5018"]},"article_processing_charge":"No","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"}],"publist_id":"3519","title":"An O(n2) time algorithm for alternating Büchi games"},{"month":"08","quality_controlled":"1","publisher":"IEEE","scopus_import":1,"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.","oa_version":"None","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"date_created":"2018-12-11T12:00:32Z","date_published":"2012-08-23T00:00:00Z","related_material":{"record":[{"id":"5377","status":"public","relation":"earlier_version"}]},"doi":"10.1109/LICS.2012.30","language":[{"iso":"eng"}],"publication":"Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science","day":"23","year":"2012","publication_status":"published","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_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","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"start_date":"2012-06-25","location":"Dubrovnik, Croatia ","end_date":"2012-06-28","name":"LICS: Logic in Computer Science"},"type":"conference","article_number":"6280438","_id":"2956","department":[{"_id":"KrCh"}],"title":"Mean payoff pushdown games","publist_id":"3770","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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."},"date_updated":"2023-02-23T12:23:30Z"},{"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"07","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"day":"02","file":[{"creator":"system","date_updated":"2020-07-14T12:46:38Z","file_size":592098,"date_created":"2018-12-12T11:54:00Z","file_name":"IST-2012-002_IST-2012-0002.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a03c08c1589dbb0c96183a8bcf3ab240","file_id":"5522"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","year":"2012","publication_status":"published","related_material":{"record":[{"id":"2956","status":"public","relation":"later_version"}]},"doi":"10.15479/AT:IST-2012-0002","date_published":"2012-07-02T00:00:00Z","date_created":"2018-12-12T11:38:59Z","page":"33","_id":"5377","status":"public","pubrep_id":"10","type":"technical_report","ddc":["000","005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T11:05:50Z","citation":{"ista":"Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.","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.","short":"K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.","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","mla":"Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012, doi:10.15479/AT:IST-2012-0002."},"title":"Mean-payoff pushdown games","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}]},{"doi":"10.15479/AT:IST-2012-0001","date_published":"2012-07-04T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"497"}]},"date_created":"2018-12-12T11:38:59Z","page":"21","file":[{"file_name":"IST-2012-0001_IST-2012-0001.pdf","date_created":"2018-12-12T11:53:28Z","file_size":394256,"date_updated":"2020-07-14T12:46:39Z","creator":"system","file_id":"5489","checksum":"ec8d1857cc7095d3de5107a0162ced37","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"day":"04","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","publication_status":"published","year":"2012","month":"07","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"oa_version":"Published Version","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."}],"file_date_updated":"2020-07-14T12:46:39Z","title":"Faster algorithms for alternating refinement relations","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Siddhesh","last_name":"Chaubal","full_name":"Chaubal, Siddhesh"},{"last_name":"Kamath","full_name":"Kamath, Pritish","first_name":"Pritish"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"date_updated":"2023-02-23T12:21:38Z","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","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating refinement relations. IST Austria, 2012.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001.","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","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."},"status":"public","pubrep_id":"14","type":"technical_report","_id":"5378"},{"article_number":"6280436","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","short":"K. Chatterjee, L. Doyen, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012.","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.","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."},"title":"Partial-observation stochastic games: How to win when belief fails","external_id":{"arxiv":["1107.2141"]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"publist_id":"3771","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.","oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science","day":"23","year":"2012","date_created":"2018-12-11T12:00:32Z","doi":"10.1109/LICS.2012.28","date_published":"2012-08-23T00:00:00Z","_id":"2955","status":"public","conference":{"location":"Dubrovnik, Croatia","end_date":"2012-06-28","start_date":"2012-06-25","name":"LICS: Logic in Computer Science"},"type":"conference","date_updated":"2023-02-23T12:23:43Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1107.2141","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"2211"},{"relation":"earlier_version","id":"5381","status":"public"}]}},{"_id":"3341","status":"public","conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","end_date":"2012-04-01","location":"Tallinn, Estonia","start_date":"2012-03-24"},"type":"conference","date_updated":"2023-02-23T12:23:46Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"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).","lang":"eng"}],"intvolume":" 7213","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2009"}],"scopus_import":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":7213,"related_material":{"record":[{"id":"5382","status":"public","relation":"earlier_version"}]},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","short":"K. Chatterjee, in:, Springer, 2012, pp. 270–285."},"title":"Robustness of structurally equivalent concurrent parity games","external_id":{"arxiv":["1107.2009"]},"publist_id":"3284","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"Springer","day":"22","year":"2012","date_created":"2018-12-11T12:02:46Z","date_published":"2012-03-22T00:00:00Z","doi":"10.1007/978-3-642-28729-9_18","page":"270 - 285"},{"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1107.2091"}],"month":"08","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."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","id":"5384","status":"public"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"LICS: Logic in Computer Science","location":"Dubrovnik, Croatia ","end_date":"2012-06-28","start_date":"2012-06-25"},"status":"public","_id":"2957","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T12:23:51Z","quality_controlled":"1","publisher":"IEEE","oa":1,"date_published":"2012-08-23T00:00:00Z","doi":"10.1109/LICS.2012.29","date_created":"2018-12-11T12:00:33Z","year":"2012","day":"23","publication":"Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_number":"6280437","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu","last_name":"Tracol"}],"publist_id":"3769","external_id":{"arxiv":["1107.2091"]},"title":"Decidable problems for probabilistic automata on infinite words","citation":{"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.","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.","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.","short":"K. Chatterjee, M. Tracol, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 413","month":"01","scopus_import":1,"oa_version":"None","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"volume":413,"issue":"1","related_material":{"record":[{"id":"4393","status":"public","relation":"earlier_version"},{"relation":"earlier_version","id":"5389","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","pubrep_id":"42","status":"public","type":"journal_article","_id":"3249","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T12:24:04Z","quality_controlled":"1","publisher":"Elsevier","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.","date_created":"2018-12-11T12:02:15Z","doi":"10.1016/j.tcs.2011.08.002","date_published":"2012-01-06T00:00:00Z","page":"21 - 35","publication":"Theoretical Computer Science","day":"06","year":"2012","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"title":"Simulation distances","publist_id":"3408","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A. 2012. Simulation distances. Theoretical Computer Science. 413(1), 21–35.","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.","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","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” Theoretical Computer Science, vol. 413, no. 1. Elsevier, pp. 21–35, 2012.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 413 (2012) 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."}},{"publisher":"ICML","alternative_title":["Inferning 2012"],"quality_controlled":"1","oa":1,"month":"06","abstract":[{"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","lang":"eng"}],"oa_version":"Submitted Version","related_material":{"record":[{"status":"public","id":"5396","relation":"later_version"}]},"date_published":"2012-06-30T00:00:00Z","date_created":"2018-12-11T12:01:31Z","has_accepted_license":"1","publication_status":"published","year":"2012","day":"30","file":[{"file_name":"IST-2016-565-v1+1_DM-inferning2012.pdf","date_created":"2018-12-12T10:11:34Z","creator":"system","file_size":305836,"date_updated":"2020-07-14T12:46:00Z","checksum":"3d0d4246548c736857302aadb2ff5d15","file_id":"4889","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2012-07-01","location":"Edinburgh, Scotland","start_date":"2012-06-26","name":"ICML: International Conference on Machine Learning"},"status":"public","pubrep_id":"565","_id":"3124","author":[{"first_name":"Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Korc","full_name":"Korc, Filip"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publist_id":"3575","department":[{"_id":"ChLa"},{"_id":"VlKo"}],"title":"Approximating marginals using discrete energy minimization","file_date_updated":"2020-07-14T12:46:00Z","citation":{"ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” 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.","ama":"Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.","short":"F. Korc, V. Kolmogorov, C. Lampert, in:, 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.","mla":"Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. ICML, 2012."},"date_updated":"2023-02-23T12:24:24Z","ddc":["000"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2012-07-23T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3124"}]},"doi":"10.15479/AT:IST-2012-0003","date_created":"2018-12-12T11:39:06Z","page":"13","day":"23","file":[{"file_size":618744,"date_updated":"2020-07-14T12:46:44Z","creator":"system","file_name":"IST-2012-0003_IST-2012-0003.pdf","date_created":"2018-12-12T11:53:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7e0ba85ad123b13223aaf6cdde2d288c","file_id":"5490"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","publication_status":"published","year":"2012","month":"07","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"oa_version":"Published Version","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."}],"department":[{"_id":"VlKo"},{"_id":"ChLa"}],"title":"Approximating marginals using discrete energy minimization","file_date_updated":"2020-07-14T12:46:44Z","author":[{"last_name":"Korc","full_name":"Korc, Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Filip"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T11:13:22Z","citation":{"mla":"Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012, doi:10.15479/AT:IST-2012-0003.","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","short":"F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012.","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, Approximating marginals using discrete energy minimization. IST Austria, 2012.","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.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p."},"status":"public","pubrep_id":"36","type":"technical_report","_id":"5396"},{"_id":"5398","status":"public","pubrep_id":"103","type":"report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"date_updated":"2020-07-14T23:04:49Z","citation":{"chicago":"Porsche, Jana. 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.","ieee":"J. Porsche, Actual state of research data @ ISTAustria. IST Austria, 2012.","short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","ama":"Porsche J. Actual State of Research Data @ ISTAustria. IST Austria; 2012.","apa":"Porsche, J. (2012). Actual state of research data @ ISTAustria. IST Austria."},"file_date_updated":"2020-07-14T12:46:44Z","department":[{"_id":"E-Lib"}],"title":"Actual state of research data @ ISTAustria","author":[{"full_name":"Porsche, Jana","last_name":"Porsche","first_name":"Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","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."}],"month":"11","publisher":"IST Austria","oa":1,"file":[{"file_id":"5472","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","date_created":"2018-12-12T11:53:11Z","file_size":238544,"date_updated":"2020-07-14T12:46:44Z","creator":"system"}],"day":"12","language":[{"iso":"eng"}],"has_accepted_license":"1","year":"2012","publication_status":"published","date_published":"2012-11-12T00:00:00Z","date_created":"2018-12-12T11:39:06Z"},{"_id":"5839","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","ddc":["000"],"extern":"1","date_updated":"2021-01-12T08:03:43Z","file_date_updated":"2020-07-14T12:47:12Z","oa_version":"Published Version","abstract":[{"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). ","lang":"eng"}],"intvolume":" 4","month":"05","language":[{"iso":"eng"}],"file":[{"file_size":305426,"date_updated":"2020-07-14T12:47:12Z","creator":"dernst","file_name":"2012_Procedia_Biswas.pdf","date_created":"2019-01-21T07:28:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5863","checksum":"ba0185986b151d8c11201f48cd505ceb"}],"publication_status":"published","publication_identifier":{"issn":["2212-0173"]},"volume":4,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824.","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.","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","short":"R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824.","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.","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."},"title":"An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets","author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jaya","last_name":"Sil","full_name":"Sil, Jaya"}],"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Procedia Technology","day":"01","year":"2012","has_accepted_license":"1","date_created":"2019-01-17T11:54:21Z","doi":"10.1016/j.protcy.2012.05.134","date_published":"2012-05-01T00:00:00Z","page":"820-824"},{"date_created":"2018-12-11T11:47:24Z","issue":"5","volume":417,"doi":"10.1016/j.jmb.2012.02.014","date_published":"2012-04-13T00:00:00Z","page":"387 - 394","publication":"Journal of Molecular Biology","language":[{"iso":"eng"}],"day":"13","year":"2012","publication_status":"published","intvolume":" 417","month":"04","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/","open_access":"1"}],"oa":1,"publisher":"Elsevier","oa_version":"None","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."}],"title":"Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly","article_processing_charge":"No","publist_id":"7208","author":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dylan","full_name":"Taatjes, Dylan","last_name":"Taatjes"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:05:21Z","citation":{"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.","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","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","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.","short":"C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394.","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.","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."},"status":"public","type":"journal_article","_id":"596"},{"oa_version":"Submitted Version","pmid":1,"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."}],"month":"03","intvolume":" 15","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1097-6256","1546-1726"]},"publication_status":"published","volume":15,"issue":"4","_id":"6136","status":"public","type":"journal_article","extern":"1","date_updated":"2021-01-12T08:06:17Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"04","publication":"Nature Neuroscience","year":"2012","date_published":"2012-03-04T00:00:00Z","doi":"10.1038/nn.3061","date_created":"2019-03-20T14:23:30Z","page":"581-591","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"title":"Tonic signaling from O2 sensors sets neural circuit activity and behavioral state","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"},{"last_name":"Murphy","full_name":"Murphy, Robin Joseph","first_name":"Robin Joseph"},{"last_name":"Faivre","full_name":"Faivre, Olivier","first_name":"Olivier"},{"last_name":"Hedwig","full_name":"Hedwig, Berthold","first_name":"Berthold"},{"last_name":"Thomas","full_name":"Thomas, Martin","first_name":"Martin"},{"first_name":"Heather L","full_name":"Smith, Heather L","last_name":"Smith"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono"}],"external_id":{"pmid":["22388961"]}},{"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."}],"oa_version":"None","publisher":"IEEE","quality_controlled":"1","month":"07","publication_status":"published","year":"2012","publication_identifier":{"issn":["1520-6149"]},"language":[{"iso":"eng"}],"publication":"2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","day":"31","page":"2905-2908","date_created":"2019-07-31T09:14:48Z","date_published":"2012-07-31T00:00:00Z","doi":"10.1109/icassp.2012.6288524","_id":"6746","conference":{"name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing","end_date":"2012-03-30","location":"Kyoto, Japan","start_date":"2012-03-25"},"type":"conference","status":"public","citation":{"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.","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.","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","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","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.","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."},"date_updated":"2021-01-12T08:08:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Zhou, Qi","last_name":"Zhou","first_name":"Qi"},{"last_name":"Ma","full_name":"Ma, Xiaoli","first_name":"Xiaoli"},{"last_name":"Lottici","full_name":"Lottici, Vincenzo","first_name":"Vincenzo"}],"title":"A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems"},{"day":"01","publication":"Journal of Materials Science","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-4803"],"issn":["0022-2461"]},"publication_status":"published","year":"2012","date_published":"2012-08-01T00:00:00Z","issue":"15","volume":47,"doi":"10.1007/s10853-012-6463-6","date_created":"2019-11-19T13:36:54Z","page":"5729-5734","oa_version":"None","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."}],"month":"08","intvolume":" 47","quality_controlled":"1","publisher":"Springer Nature","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"K.C. Lukas, G. Joshi, K.A. Modic, Z.F. Ren, C.P. Opeil, Journal of Materials Science 47 (2012) 5729–5734.","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.","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."},"date_updated":"2021-01-12T08:11:43Z","title":"Thermoelectric properties of Ho-doped Bi0.88Sb0.12","author":[{"first_name":"K. C.","last_name":"Lukas","full_name":"Lukas, K. C."},{"first_name":"G.","last_name":"Joshi","full_name":"Joshi, G."},{"last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A"},{"first_name":"Z. F.","last_name":"Ren","full_name":"Ren, Z. F."},{"last_name":"Opeil","full_name":"Opeil, C. P.","first_name":"C. P."}],"article_processing_charge":"No","_id":"7074","status":"public","type":"journal_article","article_type":"original"},{"_id":"7308","article_type":"original","type":"journal_article","status":"public","citation":{"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.","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.","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.","short":"M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, P.G. Bruce, Journal of the American Chemical Society 135 (2012) 494–500.","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","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"},"date_updated":"2021-01-12T08:12:56Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ottakam Thotiyl, Muhammed M.","last_name":"Ottakam Thotiyl","first_name":"Muhammed M."},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"first_name":"Zhangquan","full_name":"Peng, Zhangquan","last_name":"Peng"},{"last_name":"Bruce","full_name":"Bruce, Peter G.","first_name":"Peter G."}],"article_processing_charge":"No","title":"The carbon electrode in nonaqueous Li–O2 cells","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."}],"oa_version":"None","publisher":"ACS","quality_controlled":"1","month":"11","intvolume":" 135","publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","year":"2012","day":"28","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","page":"494-500","date_published":"2012-11-28T00:00:00Z","issue":"1","doi":"10.1021/ja310258x","volume":135,"date_created":"2020-01-15T12:18:57Z"},{"title":"Challenges facing Lithium batteries and electrical double-layer capacitors","author":[{"first_name":"Nam-Soon","last_name":"Choi","full_name":"Choi, Nam-Soon"},{"last_name":"Chen","full_name":"Chen, Zonghai","first_name":"Zonghai"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"last_name":"Ji","full_name":"Ji, Xiulei","first_name":"Xiulei"},{"full_name":"Sun, Yang-Kook","last_name":"Sun","first_name":"Yang-Kook"},{"full_name":"Amine, Khalil","last_name":"Amine","first_name":"Khalil"},{"first_name":"Gleb","last_name":"Yushin","full_name":"Yushin, Gleb"},{"last_name":"Nazar","full_name":"Nazar, Linda F.","first_name":"Linda F."},{"first_name":"Jaephil","last_name":"Cho","full_name":"Cho, Jaephil"},{"last_name":"Bruce","full_name":"Bruce, Peter G.","first_name":"Peter G."}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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","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."},"date_updated":"2021-01-12T08:12:56Z","status":"public","article_type":"original","type":"journal_article","_id":"7309","date_published":"2012-10-01T00:00:00Z","volume":51,"doi":"10.1002/anie.201201429","issue":"40","date_created":"2020-01-15T12:19:11Z","page":"9994-10024","day":"01","language":[{"iso":"eng"}],"publication":"Angewandte Chemie International Edition","publication_identifier":{"issn":["1433-7851"]},"year":"2012","publication_status":"published","month":"10","intvolume":" 51","publisher":"Wiley","quality_controlled":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}]},{"publication_identifier":{"issn":["0036-8075","1095-9203"]},"publication_status":"published","year":"2012","day":"03","publication":"Science","language":[{"iso":"eng"}],"page":"563-566","volume":337,"issue":"6094","doi":"10.1126/science.1223985","date_published":"2012-08-03T00:00:00Z","date_created":"2020-01-15T12:19:23Z","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."}],"oa_version":"None","publisher":"AAAS","quality_controlled":"1","month":"08","intvolume":" 337","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","short":"Z. Peng, S.A. Freunberger, Y. Chen, P.G. Bruce, Science 337 (2012) 563–566.","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.","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.","ista":"Peng Z, Freunberger SA, Chen Y, Bruce PG. 2012. A reversible and higher-rate Li-O2 battery. Science. 337(6094), 563–566.","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."},"date_updated":"2021-01-12T08:12:57Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Peng, Z.","last_name":"Peng","first_name":"Z."},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"full_name":"Chen, Y.","last_name":"Chen","first_name":"Y."},{"last_name":"Bruce","full_name":"Bruce, P. G.","first_name":"P. G."}],"article_processing_charge":"No","title":"A reversible and higher-rate Li-O2 battery","_id":"7310","type":"journal_article","article_type":"original","status":"public"},{"author":[{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"last_name":"Peng","full_name":"Peng, Zhangquan","first_name":"Zhangquan"},{"first_name":"Fanny","full_name":"Bardé, Fanny","last_name":"Bardé"},{"last_name":"Bruce","full_name":"Bruce, Peter G.","first_name":"Peter G."}],"article_processing_charge":"No","title":"Li–O2 battery with a dimethylformamide electrolyte","date_updated":"2021-01-12T08:12:58Z","citation":{"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.","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.","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","short":"Y. Chen, S.A. Freunberger, Z. Peng, F. Bardé, P.G. Bruce, Journal of the American Chemical Society 134 (2012) 7952–7957.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"original","status":"public","_id":"7311","page":"7952-7957","volume":134,"date_published":"2012-04-19T00:00:00Z","issue":"18","doi":"10.1021/ja302178w","date_created":"2020-01-15T12:19:36Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","year":"2012","day":"19","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","publisher":"ACS","quality_controlled":"1","month":"04","intvolume":" 134","abstract":[{"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.","lang":"eng"}],"oa_version":"None"},{"date_updated":"2023-02-23T13:12:27Z","citation":{"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.","short":"D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, G. Losa, in:, ACM, 2012, pp. 298–307.","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","mla":"Alistarh, Dan-Adrian, et al. On the Cost of Composing Shared-Memory Algorithms. ACM, 2012, pp. 298–307, doi:10.1145/2312005.2312057.","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"},{"full_name":"Kuznetsov, Petr","last_name":"Kuznetsov","first_name":"Petr"},{"first_name":"Giuliano","last_name":"Losa","full_name":"Losa, Giuliano"}],"publist_id":"6892","article_processing_charge":"No","title":"On the cost of composing shared-memory algorithms","_id":"762","type":"conference","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"status":"public","year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"page":"298 - 307","doi":"10.1145/2312005.2312057","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:48:22Z","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."}],"oa_version":"None","publisher":"ACM","month":"01"},{"title":"Early deciding synchronous renaming in O(log f) rounds or less","publist_id":"6893","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Attiya, Hagit","last_name":"Attiya","first_name":"Hagit"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"last_name":"Travers","full_name":"Travers, Corentin","first_name":"Corentin"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:12:41Z","citation":{"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.","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.","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","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","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.","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."},"status":"public","type":"conference","conference":{"name":"SIROCCO: Structural Information and Communication Complexity"},"_id":"763","doi":"10.1007/978-3-642-31104-8_17","date_published":"2012-01-01T00:00:00Z","volume":"7355 LNCS","date_created":"2018-12-11T11:48:22Z","page":"195 - 206","day":"01","language":[{"iso":"eng"}],"year":"2012","publication_status":"published","month":"01","alternative_title":["LNCS"],"publisher":"Springer","oa_version":"None","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","abstract":[{"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].","lang":"eng"}]},{"page":"595 - 629","date_published":"2012-02-01T00:00:00Z","issue":"1-2","volume":62,"doi":"10.1007/s00453-011-9581-7","date_created":"2018-12-11T11:48:23Z","year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Algorithmica (New York)","publisher":"Springer","month":"02","intvolume":" 62","abstract":[{"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.","lang":"eng"}],"oa_version":"None","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.","publist_id":"6894","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Gilbert","full_name":"Gilbert, Seth","first_name":"Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"article_processing_charge":"No","title":"Of choices, failures and asynchrony: the many faces of set agreement","citation":{"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.","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.","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.","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","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"},"date_updated":"2023-02-23T13:13:02Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"764"},{"month":"01","publisher":"IEEE","oa_version":"None","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."}],"doi":"10.1109/FOCS.2012.41","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:48:23Z","page":"331 - 340","day":"01","language":[{"iso":"eng"}],"publication_status":"published","year":"2012","status":"public","type":"conference","conference":{"name":"FOCS: Foundations of Computer Science"},"_id":"766","title":"How to allocate tasks asynchronously","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Bender","full_name":"Bender, Michael","first_name":"Michael"},{"first_name":"Seth","full_name":"Gilbert, Seth","last_name":"Gilbert"},{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"}],"publist_id":"6890","article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:13:27Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE, 2012, pp. 331–40, 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","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","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.","short":"D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340.","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.","ista":"Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks asynchronously. FOCS: Foundations of Computer Science, 331–340."}},{"issue":"4","doi":"10.1007/s00224-012-9407-2","volume":51,"date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:48:23Z","page":"404 - 424","day":"01","language":[{"iso":"eng"}],"publication":"Theory of Computing Systems","year":"2012","publication_status":"published","month":"01","intvolume":" 51","publisher":"Elsevier","oa_version":"None","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.","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."}],"title":"Generating Fast Indulgent Algorithms","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Gilbert, Seth","last_name":"Gilbert","first_name":"Seth"},{"first_name":"Rachid","full_name":"Guerraoui, Rachid","last_name":"Guerraoui"},{"first_name":"Corentin","full_name":"Travers, Corentin","last_name":"Travers"}],"publist_id":"6891","article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424.","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","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","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.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424.","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."},"date_updated":"2023-02-23T13:13:40Z","status":"public","type":"journal_article","_id":"767"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"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.","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.","short":"M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266.","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.","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","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."},"date_updated":"2021-01-12T08:15:16Z","title":"Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants","article_processing_charge":"No","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Mar","full_name":"Mar, Khyne U","first_name":"Khyne U"},{"first_name":"Virpi","full_name":"Lummaa, Virpi","last_name":"Lummaa"}],"_id":"7749","status":"public","type":"journal_article","article_type":"original","publication":"Ecology Letters","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2012","publication_identifier":{"issn":["1461-023X"]},"date_created":"2020-04-30T11:01:26Z","date_published":"2012-03-01T00:00:00Z","doi":"10.1111/j.1461-0248.2011.01735.x","volume":15,"issue":"3","page":"260-266","oa_version":"None","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."}],"intvolume":" 15","month":"03","publisher":"Wiley","quality_controlled":"1"},{"_id":"7748","status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:15:15Z","citation":{"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.","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.","short":"M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618.","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","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","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.","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."},"title":"Environment-dependent selection on mate choice in a natural population of birds","article_processing_charge":"No","author":[{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Sander van Doorn, G.","last_name":"Sander van Doorn","first_name":"G."},{"first_name":"Lars","full_name":"Gustafsson, Lars","last_name":"Gustafsson"},{"full_name":"Qvarnström, Anna","last_name":"Qvarnström","first_name":"Anna"}],"oa_version":"None","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."}],"intvolume":" 15","month":"06","publisher":"Wiley","quality_controlled":"1","publication":"Ecology Letters","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2012","publication_identifier":{"issn":["1461-023X"]},"date_created":"2020-04-30T11:01:07Z","volume":15,"doi":"10.1111/j.1461-0248.2012.01780.x","date_published":"2012-06-01T00:00:00Z","issue":"6","page":"611-618"},{"date_created":"2020-04-30T11:44:12Z","volume":109,"date_published":"2012-08-27T00:00:00Z","doi":"10.1103/physrevlett.109.095704","issue":"9","language":[{"iso":"eng"}],"publication":"Physical Review Letters","day":"27","publication_status":"published","year":"2012","publication_identifier":{"issn":["0031-9007","1079-7114"]},"intvolume":" 109","month":"08","publisher":"American Physical Society","quality_controlled":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}],"title":"Finite-size scaling at the jamming transition","article_processing_charge":"No","author":[{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"last_name":"Nagel","full_name":"Nagel, Sidney R.","first_name":"Sidney R."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"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.","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","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","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012).","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.","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.","ista":"Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704."},"date_updated":"2021-01-12T08:15:27Z","status":"public","article_type":"original","type":"journal_article","article_number":"095704","_id":"7776"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":287,"issue":"53","oa_version":"None","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 287","month":"12","scopus_import":"1","extern":"1","date_updated":"2022-03-21T07:57:14Z","_id":"801","status":"public","article_type":"original","type":"journal_article","publication":"Journal of Biological Chemistry","day":"28","year":"2012","date_created":"2018-12-11T11:48:34Z","date_published":"2012-12-28T00:00:00Z","doi":"10.1074/jbc.M112.398321","page":"44418 - 44424","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft.","publisher":"American Society for Biochemistry and Molecular Biology","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","short":"J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424."},"title":"Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose","article_processing_charge":"No","external_id":{"pmid":["23139423"]},"publist_id":"6852","author":[{"full_name":"Engel, Jakob","last_name":"Engel","first_name":"Jakob"},{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S","orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S","last_name":"Schmalhorst"},{"last_name":"Routier","full_name":"Routier, Françoise","first_name":"Françoise"}]},{"article_number":"011909","citation":{"ista":"Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 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.","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012).","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","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."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","external_id":{"pmid":["23005454"]},"article_processing_charge":"No","author":[{"first_name":"Guillaume","last_name":"Hennequin","full_name":"Hennequin, Guillaume"},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"first_name":"Wulfram","last_name":"Gerstner","full_name":"Gerstner, Wulfram"}],"title":"Non-normal amplification in random balanced neuronal networks","quality_controlled":"1","publisher":"American Physical Society","year":"2012","publication":"Physical Review E","day":"11","date_created":"2020-06-25T13:09:06Z","date_published":"2012-06-11T00:00:00Z","doi":"10.1103/physreve.86.011909","_id":"8024","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T08:16:35Z","extern":"1","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."}],"pmid":1,"oa_version":"None","intvolume":" 86","month":"06","publication_status":"published","publication_identifier":{"issn":["1539-3755"],"eisbn":["1550-2376"]},"language":[{"iso":"eng"}],"volume":86,"issue":"1"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5956","checksum":"2f59e15cc3a85bb500a9887cef2aab67","date_updated":"2020-07-14T12:48:09Z","file_size":3326073,"creator":"kschuh","date_created":"2019-02-12T08:54:51Z","file_name":"2012_Biologists_Vinzenz.pdf"}],"issue":"11","volume":125,"abstract":[{"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.","lang":"eng"}],"oa_version":"None","intvolume":" 125","month":"06","date_updated":"2021-01-12T08:16:47Z","ddc":["570"],"extern":"1","file_date_updated":"2020-07-14T12:48:09Z","_id":"808","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","status":"public","year":"2012","has_accepted_license":"1","publication":"Journal of Cell Science","day":"01","page":"2775 - 2785","date_created":"2018-12-11T11:48:37Z","date_published":"2012-06-01T00:00:00Z","doi":"10.1242/jcs.107623","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.","oa":1,"quality_controlled":"1","publisher":"Company of Biologists","citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Vinzenz","full_name":"Vinzenz, Marlene","first_name":"Marlene"},{"full_name":"Nemethova, Maria","last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur"},{"last_name":"Mueller","full_name":"Mueller, Jan","first_name":"Jan"},{"full_name":"Narita, Akihiro","last_name":"Narita","first_name":"Akihiro"},{"first_name":"Edit","last_name":"Urban","full_name":"Urban, Edit"},{"last_name":"Winkler","full_name":"Winkler, Christoph","first_name":"Christoph"},{"last_name":"Schmeiser","full_name":"Schmeiser, Christian","first_name":"Christian"},{"first_name":"Stefan","last_name":"Koestler","full_name":"Koestler, Stefan"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"full_name":"Resch, Guenter","last_name":"Resch","first_name":"Guenter"},{"first_name":"Yuichiro","last_name":"Maéda","full_name":"Maéda, Yuichiro"},{"last_name":"Small","full_name":"Small, John","first_name":"John"}],"publist_id":"6842","title":"Actin branching in the initiation and maintenance of lamellipodia"},{"extern":"1","date_updated":"2021-01-12T08:17:43Z","_id":"8246","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0378-1097"]},"publication_status":"published","volume":333,"issue":"2","pmid":1,"oa_version":"None","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."}],"month":"08","intvolume":" 333","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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"},"title":"Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response","author":[{"first_name":"Vanina","full_name":"Dengler, Vanina","last_name":"Dengler"},{"first_name":"Patricia Stutzmann","last_name":"Meier","full_name":"Meier, Patricia Stutzmann"},{"last_name":"Heusser","full_name":"Heusser, Ronald","first_name":"Ronald"},{"first_name":"Peter","last_name":"Kupferschmied","full_name":"Kupferschmied, Peter"},{"last_name":"Fazekas","full_name":"Fazekas, Judit","orcid":"0000-0002-8777-3502","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarah","full_name":"Friebe, Sarah","last_name":"Friebe"},{"first_name":"Sibylle Burger","last_name":"Staufer","full_name":"Staufer, Sibylle Burger"},{"first_name":"Paul A.","full_name":"Majcherczyk, Paul A.","last_name":"Majcherczyk"},{"full_name":"Moreillon, Philippe","last_name":"Moreillon","first_name":"Philippe"},{"first_name":"Brigitte","full_name":"Berger-Bächi, Brigitte","last_name":"Berger-Bächi"},{"full_name":"McCallum, Nadine","last_name":"McCallum","first_name":"Nadine"}],"article_processing_charge":"No","external_id":{"pmid":["22640011"]},"day":"01","publication":"FEMS Microbiology Letters","year":"2012","date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1574-6968.2012.02603.x","date_created":"2020-08-10T11:54:47Z","page":"109-120","quality_controlled":"1","publisher":"Oxford University Press"},{"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.","quality_controlled":0,"publisher":"Annual Reviews","month":"11","intvolume":" 28","year":"2012","publication_status":"published","day":"01","publication":"Annual Review of Cell and Developmental Biology","page":"463 - 487","doi":"10.1146/annurev-cellbio-101011-155741","date_published":"2012-11-01T00:00:00Z","volume":28,"date_created":"2018-12-11T11:48:43Z","_id":"826","type":"journal_article","status":"public","citation":{"ista":"Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.","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.","short":"M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487.","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","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."},"date_updated":"2021-01-12T08:17:46Z","extern":1,"author":[{"first_name":"Marleen","full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"}],"publist_id":"6822","title":"Hormonal interactions in the regulation of plant development"},{"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.","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."}],"month":"10","intvolume":" 24","quality_controlled":0,"publisher":"American Society of Plant Biologists","day":"01","publication":"The Plant Cell","year":"2012","publication_status":"published","doi":"10.1105/tpc.112.103044","date_published":"2012-10-01T00:00:00Z","volume":24,"issue":"10","date_created":"2018-12-11T11:48:43Z","page":"3967 - 3981","_id":"829","status":"public","type":"journal_article","extern":1,"citation":{"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.","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.","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.","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.","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","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"},"date_updated":"2021-01-12T08:17:55Z","title":"Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin","author":[{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Katerina","full_name":"Podlesakova, Katerina","last_name":"Podlesakova"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","orcid":"0000-0001-5227-5741","full_name":"Peter Marhavy"},{"first_name":"Jérôme","last_name":"Duclercq","full_name":"Duclercq, Jérôme"},{"last_name":"Cuesta","full_name":"Candela Cuesta","orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Muller","full_name":"Muller, Bruno","first_name":"Bruno"},{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"full_name":"Tarkowski, Petr","last_name":"Tarkowski","first_name":"Petr"},{"last_name":"Benková","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6819"},{"_id":"846","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"extern":1,"citation":{"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.","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.","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","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","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.","short":"O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222."},"date_updated":"2021-01-12T08:19:25Z","title":"Estimating the rate of irreversibility in protein evolution","author":[{"last_name":"Soylemez","full_name":"Soylemez, Onuralp","first_name":"Onuralp"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"publist_id":"6802","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.","abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 4","quality_controlled":0,"publisher":"Oxford University Press","day":"01","publication":"Genome Biology and Evolution","publication_status":"published","year":"2012","volume":4,"doi":"10.1093/gbe/evs096","date_published":"2012-01-01T00:00:00Z","issue":"12","date_created":"2018-12-11T11:48:49Z","page":"1213 - 1222"},{"year":"2012","publication_status":"published","publication_identifier":{"issn":["0925-2738","1573-5001"]},"publication":"Journal of Biomolecular NMR","language":[{"iso":"eng"}],"day":"23","page":"155-168","date_created":"2020-09-18T10:09:18Z","volume":54,"doi":"10.1007/s10858-012-9659-9","date_published":"2012-08-23T00:00:00Z","issue":"2","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."}],"oa_version":"None","quality_controlled":"1","publisher":"Springer Nature","intvolume":" 54","month":"08","date_updated":"2021-01-12T08:19:27Z","citation":{"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.","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.","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.","short":"S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"first_name":"Sam","last_name":"Asami","full_name":"Asami, Sam"},{"last_name":"Szekely","full_name":"Szekely, Kathrin","first_name":"Kathrin"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Meier","full_name":"Meier, Beat H.","first_name":"Beat H."},{"first_name":"Bernd","last_name":"Reif","full_name":"Reif, Bernd"}],"title":"Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency","_id":"8463","article_type":"original","type":"journal_article","status":"public"},{"_id":"8465","article_type":"original","type":"journal_article","status":"public","citation":{"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.","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","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.","short":"M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807.","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.","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."},"date_updated":"2021-01-12T08:19:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"full_name":"Tollinger, Martin","last_name":"Tollinger","first_name":"Martin"},{"first_name":"Astrid C.","full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen"},{"first_name":"Beat H.","full_name":"Meier, Beat H.","last_name":"Meier"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"title":"Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy","abstract":[{"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.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"American Chemical Society","intvolume":" 134","month":"08","year":"2012","publication_status":"published","publication_identifier":{"issn":["0002-7863","1520-5126"]},"language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","day":"21","page":"14800-14807","date_created":"2020-09-18T10:10:20Z","date_published":"2012-08-21T00:00:00Z","doi":"10.1021/ja303591y","issue":"36","volume":134},{"author":[{"first_name":"Enrico","full_name":"Rennella, Enrico","last_name":"Rennella"},{"first_name":"Thomas","full_name":"Cutuil, Thomas","last_name":"Cutuil"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"last_name":"Ayala","full_name":"Ayala, Isabel","first_name":"Isabel"},{"first_name":"Vincent","last_name":"Forge","full_name":"Forge, Vincent"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"article_processing_charge":"No","title":"Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate","citation":{"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","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","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.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 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.","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.","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."},"date_updated":"2021-01-12T08:19:28Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","type":"journal_article","status":"public","_id":"8466","page":"8066-8069","issue":"19","doi":"10.1021/ja302598j","date_published":"2012-05-03T00:00:00Z","volume":134,"date_created":"2020-09-18T10:10:28Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"year":"2012","publication_status":"published","day":"03","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"publisher":"American Chemical Society","quality_controlled":"1","month":"05","intvolume":" 134","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."}],"oa_version":"None"},{"quality_controlled":"1","publisher":"Elsevier","intvolume":" 214","month":"01","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."}],"oa_version":"None","page":"76-80","date_created":"2020-09-18T10:10:36Z","date_published":"2012-01-01T00:00:00Z","volume":214,"doi":"10.1016/j.jmr.2011.10.010","publication_status":"published","year":"2012","publication_identifier":{"issn":["1090-7807"]},"language":[{"iso":"eng"}],"publication":"Journal of Magnetic Resonance","day":"01","article_type":"original","type":"journal_article","status":"public","_id":"8467","article_processing_charge":"No","author":[{"full_name":"Huber, Matthias","last_name":"Huber","first_name":"Matthias"},{"first_name":"Oliver","last_name":"With","full_name":"With, Oliver"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"René","last_name":"Verel","full_name":"Verel, René"},{"last_name":"Ernst","full_name":"Ernst, Matthias","first_name":"Matthias"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."}],"title":"A supplementary coil for 2H decoupling with commercial HCN MAS probes","citation":{"short":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80.","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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T08:19:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"_id":"8502","type":"journal_article","article_type":"original","status":"public","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"citation":{"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.","short":"V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697.","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","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.","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.","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."},"date_updated":"2021-01-12T08:19:44Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Maria","last_name":"Saprykina","full_name":"Saprykina, Maria"}],"article_processing_charge":"No","title":"An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension","abstract":[{"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.","lang":"eng"}],"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","month":"11","intvolume":" 315","publication_identifier":{"issn":["0010-3616","1432-0916"]},"publication_status":"published","year":"2012","day":"01","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"page":"643-697","date_published":"2012-11-01T00:00:00Z","issue":"3","volume":315,"doi":"10.1007/s00220-012-1532-x","date_created":"2020-09-18T10:47:16Z"},{"date_created":"2018-12-11T11:48:52Z","volume":7,"doi":"10.1186/1745-6150-7-30","date_published":"2012-09-01T00:00:00Z","publication":"Biology Direct","day":"01","publication_status":"published","year":"2012","intvolume":" 7","month":"09","publisher":"BioMed Central","quality_controlled":0,"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.\n","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."}],"title":"Stop codons in bacteria are not selectively equivalent","publist_id":"6792","author":[{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Alice","full_name":"Ledda, Alice","last_name":"Ledda"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter K"}],"extern":1,"date_updated":"2021-01-12T08:20:08Z","citation":{"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","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","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.","short":"I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).","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.","ista":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.","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."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"858"},{"publist_id":"6748","author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"first_name":"Carsten","last_name":"Kemena","full_name":"Kemena, Carsten"},{"last_name":"Vlasov","full_name":"Vlasov, Peter K","first_name":"Peter"},{"last_name":"Notredame","full_name":"Notredame, Cédric","first_name":"Cédric"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"title":"Epistasis as the primary factor in molecular evolution","citation":{"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.","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.","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.","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","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"},"date_updated":"2021-01-12T08:21:45Z","extern":1,"type":"journal_article","status":"public","_id":"900","page":"535 - 538","date_created":"2018-12-11T11:49:06Z","issue":"7421","doi":"10.1038/nature11510","volume":490,"date_published":"2012-10-25T00:00:00Z","year":"2012","publication_status":"published","publication":"Nature","day":"25","publisher":"Nature Publishing Group","quality_controlled":0,"intvolume":" 490","month":"10","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.\n"}]