[{"status":"public","_id":"1976","citation":{"apa":"Efremov, R., & Sazanov, L. A. (2012). The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2012.02.015","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2012. https://doi.org/10.1016/j.bbabio.2012.02.015.","ama":"Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 2012;1817(10):1785-1795. doi:10.1016/j.bbabio.2012.02.015","ieee":"R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex i - A structural and evolutionary perspective,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012.","short":"R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817 (2012) 1785–1795.","ista":"Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 1817(10), 1785–1795.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:10.1016/j.bbabio.2012.02.015."},"doi":"10.1016/j.bbabio.2012.02.015","acknowledgement":"The work in authors' laboratory was funded by the Medical Research Council.","date_created":"2018-12-11T11:55:00Z","date_updated":"2019-04-26T07:22:06Z","author":[{"full_name":"Efremov, Rouslan G","first_name":"Rouslan","last_name":"Efremov"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Leonid Sazanov","first_name":"Leonid A"}],"intvolume":" 1817","issue":"10","publist_id":"5108","abstract":[{"lang":"eng","text":"Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes."}],"page":"1785 - 1795","type":"review","title":"The coupling mechanism of respiratory complex i - A structural and evolutionary perspective","year":"2012","volume":1817,"month":"10","publication":"Biochimica et Biophysica Acta - Bioenergetics","publisher":"Elsevier","quality_controlled":0,"date_published":"2012-10-01T00:00:00Z","publication_status":"published","extern":1,"day":"01"},{"date_published":"2012-07-26T00:00:00Z","article_number":"116","publication":"BMC Plant Biology","file":[{"file_name":"IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf","relation":"main_file","creator":"system","file_size":1691436,"date_updated":"2020-07-14T12:46:35Z","content_type":"application/pdf","file_id":"4953","date_created":"2018-12-12T10:12:35Z","checksum":"0c629e36acd5f2878ff7dd088d67d494","access_level":"open_access"}],"publisher":"BioMed Central","day":"26","extern":"1","type":"journal_article","year":"2012","month":"07","date_updated":"2025-09-30T08:36:34Z","scopus_import":"1","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"}],"publist_id":"7328","article_processing_charge":"No","_id":"492","citation":{"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","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.","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.","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.","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"},"external_id":{"isi":["000309114300001"]},"date_created":"2018-12-11T11:46:46Z","doi":"10.1186/1471-2229-12-116","quality_controlled":"1","publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","title":"GiA Roots: Software for the high throughput analysis of plant root system architecture","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","volume":12,"author":[{"last_name":"Galkovskyi","full_name":"Galkovskyi, Taras","first_name":"Taras"},{"full_name":"Mileyko, Yuriy","first_name":"Yuriy","last_name":"Mileyko"},{"last_name":"Bucksch","full_name":"Bucksch, Alexander","first_name":"Alexander"},{"last_name":"Moore","first_name":"Brad","full_name":"Moore, Brad"},{"full_name":"Symonova, Olga","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","last_name":"Symonova"},{"last_name":"Price","first_name":"Charles","full_name":"Price, Charles"},{"last_name":"Topp","first_name":"Chrostopher","full_name":"Topp, Chrostopher"},{"last_name":"Iyer Pascuzzi","first_name":"Anjali","full_name":"Iyer Pascuzzi, Anjali"},{"last_name":"Zurek","first_name":"Paul","full_name":"Zurek, Paul"},{"full_name":"Fang, Suqin","first_name":"Suqin","last_name":"Fang"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"},{"full_name":"Benfey, Philip","first_name":"Philip","last_name":"Benfey"},{"last_name":"Weitz","full_name":"Weitz, Joshua","first_name":"Joshua"}],"has_accepted_license":"1","intvolume":" 12","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"946","isi":1,"ddc":["005","514","516"],"status":"public","oa":1},{"day":"13","publication":"Frontiers in Neuroscience","publisher":"Frontiers Research Foundation","file":[{"relation":"main_file","creator":"system","file_size":2693701,"date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf","checksum":"195238221c4b0b0f4035f6f6c16ea17c","access_level":"open_access","content_type":"application/pdf","file_id":"5356","date_created":"2018-12-12T10:18:34Z"}],"date_published":"2012-07-13T00:00:00Z","article_number":"55","year":"2012","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"month":"07","type":"journal_article","publist_id":"7327","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."}],"scopus_import":"1","date_updated":"2025-09-30T08:35:59Z","doi":"10.3389/fnins.2012.00055","date_created":"2018-12-11T11:46:46Z","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","external_id":{"isi":["000209165300066"]},"_id":"493","citation":{"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","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.","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.","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."},"article_processing_charge":"No","publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","quality_controlled":"1","volume":6,"oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Review of the BCI competition IV","intvolume":" 6","has_accepted_license":"1","author":[{"last_name":"Tangermann","first_name":"Michael","full_name":"Tangermann, Michael"},{"last_name":"Müller","full_name":"Müller, Klaus","first_name":"Klaus"},{"last_name":"Aertsen","full_name":"Aertsen, Ad","first_name":"Ad"},{"last_name":"Birbaumer","full_name":"Birbaumer, Niels","first_name":"Niels"},{"first_name":"Christoph","full_name":"Braun, Christoph","last_name":"Braun"},{"last_name":"Brunner","full_name":"Brunner, Clemens","first_name":"Clemens"},{"first_name":"Robert","full_name":"Leeb, Robert","last_name":"Leeb"},{"full_name":"Mehring, Carsten","first_name":"Carsten","last_name":"Mehring"},{"first_name":"Kai","full_name":"Miller, Kai","last_name":"Miller"},{"full_name":"Müller Putz, Gernot","first_name":"Gernot","last_name":"Müller Putz"},{"full_name":"Nolte, Guido","first_name":"Guido","last_name":"Nolte"},{"last_name":"Pfurtscheller","full_name":"Pfurtscheller, Gert","first_name":"Gert"},{"first_name":"Hubert","full_name":"Preissl, Hubert","last_name":"Preissl"},{"first_name":"Gerwin","full_name":"Schalk, Gerwin","last_name":"Schalk"},{"first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vidaurre","first_name":"Carmen","full_name":"Vidaurre, Carmen"},{"last_name":"Waldert","full_name":"Waldert, Stephan","first_name":"Stephan"},{"first_name":"Benjamin","full_name":"Blankertz, Benjamin","last_name":"Blankertz"}],"oa":1,"ddc":["004"],"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"945","isi":1},{"author":[{"last_name":"Kruckman","full_name":"Kruckman, Alex","first_name":"Alex"},{"full_name":"Rubin, Sasha","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin"},{"last_name":"Sheridan","first_name":"John","full_name":"Sheridan, John"},{"full_name":"Zax, Ben","first_name":"Ben","last_name":"Zax"}],"intvolume":" 96","has_accepted_license":"1","status":"public","ddc":["004"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"944","oa":1,"quality_controlled":"1","publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","page":"238 - 246","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A Myhill Nerode theorem for automata with advice","corr_author":"1","volume":96,"oa_version":"Published Version","scopus_import":1,"date_updated":"2024-10-09T20:55:00Z","conference":{"start_date":"2012-09-06","location":"Napoli, Italy","end_date":"2012-09-08","name":"GandALF: Games, Automata, Logics and Formal Verification"},"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."}],"publist_id":"7325","_id":"495","citation":{"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","ista":"Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246.","mla":"Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” Proceedings GandALF 2012, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:10.4204/EPTCS.96.18.","short":"A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246.","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.","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","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."},"doi":"10.4204/EPTCS.96.18","date_created":"2018-12-11T11:46:47Z","ec_funded":1,"publication":"Proceedings GandALF 2012","file":[{"access_level":"open_access","checksum":"56277f95edc9d531fa3bdc5f9579fda8","date_created":"2018-12-12T10:15:31Z","file_id":"5152","content_type":"application/pdf","date_updated":"2020-07-14T12:46:35Z","file_size":97736,"creator":"system","relation":"main_file","file_name":"IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf"}],"alternative_title":["EPTCS"],"publisher":"Open Publishing Association","date_published":"2012-10-07T00:00:00Z","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"day":"07","type":"conference","year":"2012","month":"10","department":[{"_id":"KrCh"}]},{"scopus_import":"1","conference":{"end_date":"2012-06-28","name":"LICS: Logic in Computer Science","start_date":"2012-06-25","location":"Dubrovnik, Croatia"},"date_updated":"2025-09-30T08:34:47Z","publist_id":"7324","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf","open_access":"1"}],"citation":{"apa":"Rabinovich, A., & Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.65","short":"A. Rabinovich, S. Rubin, in:, IEEE, 2012.","chicago":"Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. 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","ieee":"A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia, 2012.","ista":"Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Logic in Computer Science, LICS, , 6280474.","mla":"Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65."},"_id":"496","article_processing_charge":"No","doi":"10.1109/LICS.2012.65","ec_funded":1,"date_created":"2018-12-11T11:46:47Z","external_id":{"isi":["000309059900061"]},"publisher":"IEEE","alternative_title":["LICS"],"project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"date_published":"2012-01-01T00:00:00Z","article_number":"6280474","day":"01","type":"conference","department":[{"_id":"KrCh"}],"month":"01","year":"2012","author":[{"first_name":"Alexander","full_name":"Rabinovich, Alexander","last_name":"Rabinovich"},{"full_name":"Rubin, Sasha","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin"}],"status":"public","isi":1,"oa":1,"quality_controlled":"1","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"title":"Interpretations in trees with countably many branches","oa_version":"Preprint"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5378"}]},"scopus_import":1,"conference":{"name":"EACSL: European Association for Computer Science Logic","end_date":"2012-09-06","location":"Fontainebleau, France","start_date":"2012-09-03"},"date_updated":"2025-01-14T12:24:50Z","publist_id":"7323","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."}],"citation":{"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.","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","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. https://doi.org/10.4230/LIPIcs.CSL.2012.167.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.","short":"K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182.","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"},"_id":"497","doi":"10.4230/LIPIcs.CSL.2012.167","ec_funded":1,"date_created":"2018-12-11T11:46:48Z","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"content_type":"application/pdf","file_id":"4712","date_created":"2018-12-12T10:08:50Z","checksum":"f1b0dd99240800db2d7dbf9b5131fe5e","access_level":"open_access","file_name":"IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:46:35Z","file_size":471236}],"date_published":"2012-09-01T00:00:00Z","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"day":"01","type":"conference","department":[{"_id":"KrCh"}],"month":"09","year":"2012","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Chaubal","first_name":"Siddhesh","full_name":"Chaubal, Siddhesh"},{"last_name":"Kamath","full_name":"Kamath, Pritish","first_name":"Pritish"}],"intvolume":" 16","has_accepted_license":"1","status":"public","ddc":["004"],"pubrep_id":"943","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"page":"167 - 182","title":"Faster algorithms for alternating refinement relations","volume":16,"oa_version":"Published Version"},{"type":"journal_article","month":"12","department":[{"_id":"NiBa"}],"year":"2012","date_published":"2012-12-01T00:00:00Z","file":[{"file_id":"4821","date_created":"2018-12-12T10:10:33Z","content_type":"application/pdf","checksum":"233007138606aca5a2f75f7ae1742f43","access_level":"open_access","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","relation":"main_file"}],"publisher":"Wiley-Blackwell","publication":"Evolutionary Applications","day":"01","article_processing_charge":"No","citation":{"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.","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.","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","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.","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.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924."},"_id":"498","external_id":{"isi":["000312808900013"]},"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","date_created":"2018-12-11T11:46:48Z","doi":"10.1111/j.1752-4571.2012.00284.x","date_updated":"2025-09-30T08:33:55Z","abstract":[{"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.","lang":"eng"}],"publist_id":"7322","corr_author":"1","title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"913 - 924","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":5,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","isi":1,"pubrep_id":"942","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"status":"public","ddc":["576"],"oa":1,"author":[{"first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David"},{"first_name":"David","full_name":"Rowell, David","last_name":"Rowell"},{"first_name":"Andrew","full_name":"Young, Andrew","last_name":"Young"}],"has_accepted_license":"1","intvolume":" 5","issue":"8"},{"month":"07","department":[{"_id":"KrCh"}],"year":"2012","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"day":"02","date_published":"2012-07-02T00:00:00Z","file":[{"checksum":"a03c08c1589dbb0c96183a8bcf3ab240","access_level":"open_access","content_type":"application/pdf","file_id":"5522","date_created":"2018-12-12T11:54:00Z","creator":"system","relation":"main_file","file_size":592098,"date_updated":"2020-07-14T12:46:38Z","file_name":"IST-2012-002_IST-2012-0002.pdf"}],"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:38:59Z","doi":"10.15479/AT:IST-2012-0002","article_processing_charge":"No","citation":{"mla":"Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012, doi:10.15479/AT:IST-2012-0002.","ista":"Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.","ieee":"K. Chatterjee and Y. Velner, Mean-payoff pushdown games. IST Austria, 2012.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0002.","ama":"Chatterjee K, Velner Y. Mean-Payoff Pushdown Games. IST Austria; 2012. doi:10.15479/AT:IST-2012-0002","short":"K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.","apa":"Chatterjee, K., & Velner, Y. (2012). Mean-payoff pushdown games. IST Austria. https://doi.org/10.15479/AT:IST-2012-0002"},"_id":"5377","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"}],"date_updated":"2025-09-30T08:08:12Z","related_material":{"record":[{"id":"2956","status":"public","relation":"later_version"}]},"oa_version":"Published Version","title":"Mean-payoff pushdown games","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"33","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:38Z","publication_status":"published","oa":1,"pubrep_id":"10","status":"public","ddc":["000","005"],"has_accepted_license":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}]},{"day":"04","publisher":"IST Austria","file":[{"file_size":394256,"date_updated":"2020-07-14T12:46:39Z","creator":"system","relation":"main_file","file_name":"IST-2012-0001_IST-2012-0001.pdf","checksum":"ec8d1857cc7095d3de5107a0162ced37","access_level":"open_access","file_id":"5489","date_created":"2018-12-12T11:53:28Z","content_type":"application/pdf"}],"alternative_title":["IST Austria Technical Report"],"date_published":"2012-07-04T00:00:00Z","department":[{"_id":"KrCh"}],"month":"07","year":"2012","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"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."}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"497"}]},"date_updated":"2025-04-15T08:12:24Z","doi":"10.15479/AT:IST-2012-0001","date_created":"2018-12-12T11:38:59Z","citation":{"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","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0001.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating refinement relations. IST Austria, 2012.","ama":"Chatterjee K, Chaubal S, Kamath P. Faster Algorithms for Alternating Refinement Relations. IST Austria; 2012. doi:10.15479/AT:IST-2012-0001","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012."},"_id":"5378","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:39Z","publication_status":"published","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"21","language":[{"iso":"eng"}],"title":"Faster algorithms for alternating refinement relations","corr_author":"1","has_accepted_license":"1","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chaubal","full_name":"Chaubal, Siddhesh","first_name":"Siddhesh"},{"full_name":"Kamath, Pritish","first_name":"Pritish","last_name":"Kamath"}],"oa":1,"ddc":["000","005"],"status":"public","pubrep_id":"14"},{"year":"2012","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"month":"07","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"13","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","title":"Approximating marginals using discrete energy minimization","publication_status":"published","file_date_updated":"2020-07-14T12:46:44Z","day":"23","file":[{"file_id":"5490","date_created":"2018-12-12T11:53:29Z","content_type":"application/pdf","checksum":"7e0ba85ad123b13223aaf6cdde2d288c","access_level":"open_access","file_name":"IST-2012-0003_IST-2012-0003.pdf","date_updated":"2020-07-14T12:46:44Z","file_size":618744,"creator":"system","relation":"main_file"}],"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"date_published":"2012-07-23T00:00:00Z","doi":"10.15479/AT:IST-2012-0003","oa":1,"date_created":"2018-12-12T11:39:06Z","ddc":["000"],"_id":"5396","status":"public","citation":{"mla":"Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012, doi:10.15479/AT:IST-2012-0003.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p.","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.","ama":"Korc F, Kolmogorov V, Lampert C. Approximating Marginals Using Discrete Energy Minimization. IST Austria; 2012. doi:10.15479/AT:IST-2012-0003","short":"F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012.","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"},"pubrep_id":"36","has_accepted_license":"1","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."}],"related_material":{"record":[{"id":"3124","status":"public","relation":"earlier_version"}]},"date_updated":"2024-10-09T20:54:48Z","author":[{"first_name":"Filip","full_name":"Korc, Filip","last_name":"Korc","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"},{"full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert"}]},{"day":"12","publication_status":"published","file_date_updated":"2020-07-14T12:46:44Z","date_published":"2012-11-12T00:00:00Z","publisher":"IST Austria","file":[{"file_id":"5472","date_created":"2018-12-12T11:53:11Z","content_type":"application/pdf","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e","access_level":"open_access","file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","file_size":238544,"date_updated":"2020-07-14T12:46:44Z","creator":"system","relation":"main_file"}],"oa_version":"Published Version","year":"2012","department":[{"_id":"E-Lib"}],"month":"11","title":"Actual state of research data @ ISTAustria","language":[{"iso":"eng"}],"type":"report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","date_updated":"2020-07-14T23:04:49Z","author":[{"first_name":"Jana","full_name":"Porsche, Jana","last_name":"Porsche","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T11:39:06Z","oa":1,"pubrep_id":"103","status":"public","_id":"5398","ddc":["020"],"citation":{"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.","chicago":"Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012.","ama":"Porsche J. Actual State of Research Data @ ISTAustria. IST Austria; 2012.","short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","ieee":"J. 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Springer Nature, 2012. https://doi.org/10.1007/978-3-642-33386-6_10.","ama":"Gupta A. Improved single pass algorithms for resolution proof reduction. In: 10th International Symposium on Automated Technology for Verification and Analysis. Vol 7561. Springer Nature; 2012:107-121. doi:10.1007/978-3-642-33386-6_10","ieee":"A. Gupta, “Improved single pass algorithms for resolution proof reduction,” in 10th International Symposium on Automated Technology for Verification and Analysis, Thiruvananthapuram, Kerala, India, 2012, vol. 7561, pp. 107–121.","short":"A. Gupta, in:, 10th International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2012, pp. 107–121.","mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” 10th International Symposium on Automated Technology for Verification and Analysis, vol. 7561, Springer Nature, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10.","ista":"Gupta A. 2012. Improved single pass algorithms for resolution proof reduction. 10th International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 7561, 107–121.","apa":"Gupta, A. (2012). Improved single pass algorithms for resolution proof reduction. In 10th International Symposium on Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121). Thiruvananthapuram, Kerala, India: Springer Nature. https://doi.org/10.1007/978-3-642-33386-6_10"},"_id":"5745","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative\r\nReactive Modeling (QUAREM).","ec_funded":1,"date_created":"2018-12-18T13:01:46Z","doi":"10.1007/978-3-642-33386-6_10","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2012-10-06","location":"Thiruvananthapuram, Kerala, India","start_date":"2012-10-03"},"date_updated":"2025-04-15T07:56:27Z","scopus_import":"1","abstract":[{"text":"Unsatisfiability proofs find many applications in verification. Today, many SAT solvers are capable of producing resolution proofs of unsatisfiability. For efficiency smaller proofs are preferred over bigger ones. The solvers apply proof reduction methods to remove redundant parts of the proofs while and after generating the proofs. One method of reducing resolution proofs is redundant resolution reduction, i.e., removing repeated pivots in the paths of resolution proofs (aka Pivot recycle). The known single pass algorithm only tries to remove redundancies in the parts of the proof that are trees. In this paper, we present three modifications to improve the algorithm such that the redundancies can be found in the parts of the proofs that are DAGs. The first modified algorithm covers greater number of redundancies as compared to the known algorithm without incurring any additional cost. The second modified algorithm covers even greater number of the redundancies but it may have longer run times. Our third modified algorithm is parametrized and can trade off between run times and the coverage of the redundancies. We have implemented our algorithms in OpenSMT and applied them on unsatisfiability proofs of 198 examples from plain MUS track of SAT11 competition. The first and second algorithm additionally remove 0.89% and 10.57% of clauses respectively as compared to the original algorithm. For certain value of the parameter, the third algorithm removes almost as many clauses as the second algorithm but is significantly faster.","lang":"eng"}]},{"extern":"1","day":"01","publication":"Procedia Technology","file":[{"file_name":"2012_Procedia_Biswas.pdf","relation":"main_file","creator":"dernst","file_size":305426,"date_updated":"2020-07-14T12:47:12Z","content_type":"application/pdf","date_created":"2019-01-21T07:28:06Z","file_id":"5863","access_level":"open_access","checksum":"ba0185986b151d8c11201f48cd505ceb"}],"publisher":"Elsevier","date_published":"2012-05-01T00:00:00Z","year":"2012","month":"05","publication_identifier":{"issn":["2212-0173"]},"type":"journal_article","abstract":[{"lang":"eng","text":"Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two \r\nsignificant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe gradient image. Due to poor illumination, the region boundaries in an image may become vague, creating \r\nuncertainties in the gradient image. In this paper, we have proposed an algorithm based on the concept of type-2 fuzzy sets to handle uncertainties that automatically selects the threshold values needed to segment the gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). "}],"date_updated":"2021-01-12T08:03:43Z","doi":"10.1016/j.protcy.2012.05.134","date_created":"2019-01-17T11:54:21Z","_id":"5839","citation":{"ama":"Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 2012;4:820-824. doi:10.1016/j.protcy.2012.05.134","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.","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.","short":"R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824.","ista":"Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824.","mla":"Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology, vol. 4, Elsevier, 2012, pp. 820–24, doi:10.1016/j.protcy.2012.05.134.","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"},"publication_status":"published","file_date_updated":"2020-07-14T12:47:12Z","quality_controlled":"1","volume":4,"oa_version":"Published Version","language":[{"iso":"eng"}],"page":"820-824","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets","intvolume":" 4","has_accepted_license":"1","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","first_name":"Ranita"},{"full_name":"Sil, Jaya","first_name":"Jaya","last_name":"Sil"}],"oa":1,"ddc":["000"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"}},{"publication_status":"published","extern":"1","day":"13","publication":"Journal of Molecular Biology","publisher":"Elsevier","date_published":"2012-04-13T00:00:00Z","year":"2012","volume":417,"month":"04","oa_version":"None","page":"387 - 394","language":[{"iso":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly","intvolume":" 417","issue":"5","publist_id":"7208","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T08:05:21Z","author":[{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036"},{"full_name":"Taatjes, Dylan","first_name":"Dylan","last_name":"Taatjes"}],"doi":"10.1016/j.jmb.2012.02.014","oa":1,"date_created":"2018-12-11T11:47:24Z","_id":"596","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/","open_access":"1"}],"citation":{"ista":"Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 417(5), 387–394.","mla":"Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology, vol. 417, no. 5, Elsevier, 2012, pp. 387–94, doi:10.1016/j.jmb.2012.02.014.","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.","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.","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"},"article_processing_charge":"No"},{"day":"04","extern":"1","date_published":"2012-03-04T00:00:00Z","publisher":"Springer Nature","publication":"Nature Neuroscience","month":"03","year":"2012","type":"journal_article","publication_identifier":{"issn":["1097-6256","1546-1726"]},"abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T08:06:17Z","external_id":{"pmid":["22388961"]},"date_created":"2019-03-20T14:23:30Z","doi":"10.1038/nn.3061","citation":{"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.","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","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.","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.","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.","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.","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"},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/","open_access":"1"}],"_id":"6136","publication_status":"published","quality_controlled":"1","oa_version":"Submitted Version","volume":15,"title":"Tonic signaling from O2 sensors sets neural circuit activity and behavioral state","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"page":"581-591","intvolume":" 15","issue":"4","author":[{"last_name":"Busch","full_name":"Busch, Karl Emanuel","first_name":"Karl Emanuel"},{"last_name":"Laurent","full_name":"Laurent, Patrick","first_name":"Patrick"},{"last_name":"Soltesz","first_name":"Zoltan","full_name":"Soltesz, Zoltan"},{"last_name":"Murphy","first_name":"Robin Joseph","full_name":"Murphy, Robin Joseph"},{"last_name":"Faivre","full_name":"Faivre, Olivier","first_name":"Olivier"},{"last_name":"Hedwig","full_name":"Hedwig, Berthold","first_name":"Berthold"},{"full_name":"Thomas, Martin","first_name":"Martin","last_name":"Thomas"},{"last_name":"Smith","full_name":"Smith, Heather L","first_name":"Heather L"},{"full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono"}],"oa":1,"pmid":1,"status":"public"},{"intvolume":" 109","issue":"38","abstract":[{"text":"In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system.\n","lang":"eng"}],"publist_id":"5096","author":[{"last_name":"Schweizer","full_name":"Schweizer, Jakob","first_name":"Jakob"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Martin Loose","first_name":"Martin"},{"last_name":"Bonny","full_name":"Bonny, Mike ","first_name":"Mike"},{"last_name":"Kruse","full_name":"Kruse, Karsten","first_name":"Karsten"},{"last_name":"Mönch","first_name":"Ingolf","full_name":"Mönch, Ingolf"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "}],"date_updated":"2021-01-12T06:54:31Z","doi":"10.1073/pnas.1206953109","date_created":"2018-12-11T11:55:04Z","acknowledgement":"This work was supported by the Max-Planck-Society (P.S. and M.L.) and by the German Research Foundation as part of the Research Training Group “Nano- and Biotechnologies for Electronic Device Packaging” (GRK 1401) (J.S.) and by the Leibniz-Award (P.S.). ","citation":{"apa":"Schweizer, J., Loose, M., Bonny, M., Kruse, K., Mönch, I., & Schwille, P. (2012). Geometry sensing by self-organized protein patterns. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1206953109","ista":"Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. 2012. Geometry sensing by self-organized protein patterns. PNAS. 109(38), 15283–15288.","mla":"Schweizer, Jakob, et al. “Geometry Sensing by Self-Organized Protein Patterns.” PNAS, vol. 109, no. 38, National Academy of Sciences, 2012, pp. 15283–88, doi:10.1073/pnas.1206953109.","short":"J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, P. Schwille, PNAS 109 (2012) 15283–15288.","chicago":"Schweizer, Jakob, Martin Loose, Mike Bonny, Karsten Kruse, Ingolf Mönch, and Petra Schwille. “Geometry Sensing by Self-Organized Protein Patterns.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1206953109.","ieee":"J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, and P. Schwille, “Geometry sensing by self-organized protein patterns,” PNAS, vol. 109, no. 38. National Academy of Sciences, pp. 15283–15288, 2012.","ama":"Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. Geometry sensing by self-organized protein patterns. PNAS. 2012;109(38):15283-15288. doi:10.1073/pnas.1206953109"},"_id":"1987","status":"public","extern":1,"publication_status":"published","day":"18","publisher":"National Academy of Sciences","publication":"PNAS","quality_controlled":0,"date_published":"2012-09-18T00:00:00Z","month":"09","volume":109,"year":"2012","type":"journal_article","page":"15283 - 15288","title":"Geometry sensing by self-organized protein patterns"},{"status":"public","_id":"2073","citation":{"ista":"Zhou Q, Zhu H, Huang Q, Zhao L, Zhang G, Roy S, Vicoso B, Xuan Z, Ruan J, Zhang Y, Zhao R, Ye C, Zhang X, Wang J, Wang W, Bachtrog D. 2012. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 13(1).","mla":"Zhou, Qi, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” BMC Genomics, vol. 13, no. 1, BioMed Central, 2012, doi:10.1186/1471-2164-13-109.","short":"Q. Zhou, H. Zhu, Q. Huang, L. Zhao, G. Zhang, S. Roy, B. Vicoso, Z. Xuan, J. Ruan, Y. Zhang, R. Zhao, C. Ye, X. Zhang, J. Wang, W. Wang, D. Bachtrog, BMC Genomics 13 (2012).","ieee":"Q. Zhou et al., “Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans,” BMC Genomics, vol. 13, no. 1. BioMed Central, 2012.","chicago":"Zhou, Qi, Hongmei Zhu, Quanfei Huang, Li Zhao, Guo Zhang, Scott Roy, Beatriz Vicoso, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” BMC Genomics. BioMed Central, 2012. https://doi.org/10.1186/1471-2164-13-109.","ama":"Zhou Q, Zhu H, Huang Q, et al. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 2012;13(1). doi:10.1186/1471-2164-13-109","apa":"Zhou, Q., Zhu, H., Huang, Q., Zhao, L., Zhang, G., Roy, S., … Bachtrog, D. (2012). Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-13-109"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/1471-2164-13-109","date_created":"2018-12-11T11:55:33Z","date_updated":"2021-01-12T06:55:08Z","author":[{"last_name":"Zhou","first_name":"Qi","full_name":"Zhou, Qi"},{"first_name":"Hongmei","full_name":"Zhu, Hongmei","last_name":"Zhu"},{"full_name":"Huang, Quanfei","first_name":"Quanfei","last_name":"Huang"},{"last_name":"Zhao","first_name":"Li","full_name":"Zhao, Li"},{"first_name":"Guo","full_name":"Zhang, Guo J","last_name":"Zhang"},{"last_name":"Roy","full_name":"Roy, Scott W","first_name":"Scott"},{"full_name":"Beatriz Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"first_name":"Zhaolin","full_name":"Xuan, Zhaolin","last_name":"Xuan"},{"full_name":"Ruan, Jue","first_name":"Jue","last_name":"Ruan"},{"full_name":"Zhang, Yue","first_name":"Yue","last_name":"Zhang"},{"last_name":"Zhao","full_name":"Zhao, Ruoping","first_name":"Ruoping"},{"full_name":"Ye, Chen","first_name":"Chen","last_name":"Ye"},{"last_name":"Zhang","first_name":"Xiuqing","full_name":"Zhang, Xiuqing"},{"last_name":"Wang","full_name":"Wang, Jùn","first_name":"Jùn"},{"last_name":"Wang","first_name":"Wen","full_name":"Wang, Wen"},{"last_name":"Bachtrog","full_name":"Bachtrog, Doris","first_name":"Doris"}],"intvolume":" 13","issue":"1","publist_id":"4965","abstract":[{"text":"Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.","lang":"eng"}],"type":"journal_article","title":"Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans","year":"2012","volume":13,"month":"03","publication":"BMC Genomics","publisher":"BioMed Central","quality_controlled":0,"date_published":"2012-03-22T00:00:00Z","publication_status":"published","extern":1,"day":"22"},{"date_created":"2018-12-11T11:55:35Z","doi":"10.1111/j.1467-8659.2012.03037.x","_id":"2079","status":"public","citation":{"mla":"Hildebrand, Kristian, et al. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” Computer Graphics Forum, vol. 31, no. 2pt3, Wiley-Blackwell, 2012, pp. 583–92, doi:10.1111/j.1467-8659.2012.03037.x.","ista":"Hildebrand K, Bickel B, Alexa M. 2012. crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. 31(2pt3), 583–592.","short":"K. Hildebrand, B. Bickel, M. Alexa, Computer Graphics Forum 31 (2012) 583–592.","ama":"Hildebrand K, Bickel B, Alexa M. crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. 2012;31(2pt3):583-592. doi:10.1111/j.1467-8659.2012.03037.x","ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “crdbrd: Shape fabrication by sliding planar slices,” Computer Graphics Forum, vol. 31, no. 2pt3. Wiley-Blackwell, pp. 583–592, 2012.","chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” Computer Graphics Forum. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1467-8659.2012.03037.x.","apa":"Hildebrand, K., Bickel, B., & Alexa, M. (2012). crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2012.03037.x"},"abstract":[{"text":"We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes.","lang":"eng"}],"publist_id":"4959","intvolume":" 31","issue":"2pt3","date_updated":"2021-01-12T06:55:10Z","author":[{"full_name":"Hildebrand, Kristian","first_name":"Kristian","last_name":"Hildebrand"},{"first_name":"Bernd","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc","full_name":"Alexa, Marc","last_name":"Alexa"}],"volume":31,"year":"2012","month":"05","title":"crdbrd: Shape fabrication by sliding planar slices","page":"583 - 592","type":"journal_article","day":"01","publication_status":"published","extern":1,"quality_controlled":0,"date_published":"2012-05-01T00:00:00Z","publication":"Computer Graphics Forum","publisher":"Wiley-Blackwell"},{"doi":"10.1103/physrevlett.109.188101","article_type":"original","external_id":{"arxiv":["1206.3528"],"pmid":["23215334"]},"date_created":"2021-11-29T14:08:00Z","_id":"10387","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1206.3528"}],"citation":{"ista":"Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101.","mla":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:10.1103/physrevlett.109.188101.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.188101.","ieee":"A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” Physical Review Letters, vol. 109, no. 18. American Physical Society, 2012.","ama":"Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 2012;109(18). doi:10.1103/physrevlett.109.188101","apa":"Šarić, A., & Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.188101"},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process."}],"scopus_import":"1","date_updated":"2021-11-29T14:29:25Z","year":"2012","month":"10","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"type":"journal_article","extern":"1","day":"31","publication":"Physical Review Letters","publisher":"American Physical Society","date_published":"2012-10-31T00:00:00Z","article_number":"188101","pmid":1,"oa":1,"status":"public","intvolume":" 109","issue":"18","author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"volume":109,"oa_version":"Preprint","language":[{"iso":"eng"}],"keyword":["general physics and astronomy"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","arxiv":1,"title":"Mechanism of membrane tube formation induced by adhesive nanocomponents","publication_status":"published","quality_controlled":"1"},{"publication_status":"published","quality_controlled":"1","volume":108,"oa_version":"Preprint","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["general physics and astronomy"],"arxiv":1,"title":"Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles","issue":"11","intvolume":" 108","author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"pmid":1,"oa":1,"status":"public","extern":"1","day":"14","publication":"Physical Review Letters","publisher":"American Physical Society","date_published":"2012-03-14T00:00:00Z","article_number":"118101","year":"2012","month":"03","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"type":"journal_article","abstract":[{"text":"Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.","lang":"eng"}],"scopus_import":"1","date_updated":"2021-11-29T15:12:13Z","doi":"10.1103/physrevlett.108.118101","article_type":"original","date_created":"2021-11-29T14:30:05Z","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n","external_id":{"arxiv":["1201.0036"],"pmid":["22540513"]},"_id":"10388","citation":{"ama":"Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 2012;108(11). doi:10.1103/physrevlett.108.118101","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.108.118101.","ieee":"A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” Physical Review Letters, vol. 108, no. 11. American Physical Society, 2012.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:10.1103/physrevlett.108.118101.","ista":"Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.","apa":"Šarić, A., & Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.108.118101"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.0036"}],"article_processing_charge":"No"}]