[{"ddc":["000","005"],"file_date_updated":"2020-07-14T12:46:42Z","pubrep_id":"24","related_material":{"record":[{"status":"public","relation":"later_version","id":"3366"}]},"citation":{"short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>"},"page":"17","date_created":"2018-12-12T11:39:03Z","publication_status":"published","has_accepted_license":"1","doi":"10.15479/AT:IST-2010-0004","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_published":"2010-10-07T00:00:00Z","oa_version":"Published Version","type":"technical_report","title":"Quantitative synthesis for concurrent programs","oa":1,"publication_identifier":{"issn":["2664-1690"]},"status":"public","publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","alternative_title":["IST Austria Technical Report"],"day":"07","year":"2010","date_updated":"2023-02-23T11:24:08Z","abstract":[{"text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements.","lang":"eng"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":429101,"creator":"system","checksum":"da38782d2388a6fa32109d10bb9bad67","file_id":"5515","access_level":"open_access","date_updated":"2020-07-14T12:46:42Z","file_name":"IST-2010-0004_IST-2010-0004.pdf","date_created":"2018-12-12T11:53:53Z"}],"_id":"5388","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun"},{"full_name":"Singh, Rohit","first_name":"Rohit","last_name":"Singh"}]},{"publication_identifier":{"issn":["2664-1690"]},"oa":1,"title":"Simulation distances","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"month":"06","year":"2010","day":"04","abstract":[{"lang":"eng","text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation 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."}],"date_updated":"2023-02-23T12:09:16Z","_id":"5389","file":[{"file_size":367246,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"284ded99764e32a583a8ea83fcea254b","file_id":"5547","creator":"system","date_created":"2018-12-12T11:54:25Z","file_name":"IST-2010-0003_IST-2010-0003.pdf","date_updated":"2020-07-14T12:46:42Z"}],"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun"}],"ddc":["005"],"pubrep_id":"25","file_date_updated":"2020-07-14T12:46:42Z","related_material":{"record":[{"id":"3249","status":"public","relation":"later_version"},{"status":"public","relation":"later_version","id":"4393"}]},"citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>."},"date_created":"2018-12-12T11:39:03Z","page":"24","doi":"10.15479/AT:IST-2010-0003","publication_status":"published","has_accepted_license":"1","department":[{"_id":"ToHe"}],"date_published":"2010-06-04T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"technical_report"},{"month":"06","alternative_title":["IST Austria Technical Report"],"title":"Topological, automata-theoretic and logical characterization of finitary languages","oa":1,"publication_identifier":{"issn":["2664-1690"]},"status":"public","publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_id":"5532","checksum":"283d3604d76dd4d5161585d4c8625fbe","creator":"system","date_created":"2018-12-12T11:54:10Z","file_name":"IST-2010-0002_IST-2010-0002.pdf","date_updated":"2020-07-14T12:46:43Z","file_size":395662,"relation":"main_file","content_type":"application/pdf"}],"_id":"5390","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Nathanaël","last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël"}],"day":"04","year":"2010","date_updated":"2020-07-14T23:04:41Z","abstract":[{"lang":"eng","text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages."}],"citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010."},"ddc":["000"],"file_date_updated":"2020-07-14T12:46:43Z","pubrep_id":"26","language":[{"iso":"eng"}],"date_published":"2010-06-04T00:00:00Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","type":"technical_report","page":"21","date_created":"2018-12-12T11:39:03Z","publication_status":"published","has_accepted_license":"1","doi":"10.15479/AT:IST-2010-0002"},{"type":"technical_report","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"date_published":"2010-04-19T00:00:00Z","publication_status":"published","has_accepted_license":"1","doi":"10.15479/AT:IST-2010-0001","page":"27","date_created":"2018-12-12T11:39:04Z","citation":{"chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010."},"related_material":{"record":[{"id":"4390","status":"public","relation":"later_version"}]},"file_date_updated":"2020-07-14T12:46:43Z","pubrep_id":"27","ddc":["004"],"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien"},{"full_name":"Chaudhuri, Swarat","first_name":"Swarat","last_name":"Chaudhuri"},{"full_name":"Alur, Rajeev","first_name":"Rajeev","last_name":"Alur"}],"file":[{"date_created":"2018-12-12T11:53:44Z","file_name":"IST-2010-0001_IST-2010-0001.pdf","date_updated":"2020-07-14T12:46:43Z","access_level":"open_access","file_id":"5505","creator":"system","checksum":"986645caad7dd85a6a091488f6c646dc","file_size":372286,"relation":"main_file","content_type":"application/pdf"}],"_id":"5391","date_updated":"2023-02-23T12:09:09Z","abstract":[{"lang":"eng","text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable."}],"day":"19","year":"2010","month":"04","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Model checking of linearizability of concurrent list implementations","publication_identifier":{"issn":["2664-1690"]},"oa":1},{"article_processing_charge":"No","citation":{"short":"G. Juhás, I. Kazlov, A. Juhásová, in:, Applications and Theory of Petri Nets, Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, pp. 1–17.","ama":"Juhás G, Kazlov I, Juhásová A. Instance Deadlock: A Mystery behind Frozen Programs. In: <i>Applications and Theory of Petri Nets</i>. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010:1-17. doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>","ieee":"G. Juhás, I. Kazlov, and A. Juhásová, “Instance Deadlock: A Mystery behind Frozen Programs,” in <i>Applications and Theory of Petri Nets</i>, Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp. 1–17.","ista":"Juhás G, Kazlov I, Juhásová A. 2010.Instance Deadlock: A Mystery behind Frozen Programs. In: Applications and Theory of Petri Nets. , 1–17.","apa":"Juhás, G., Kazlov, I., &#38; Juhásová, A. (2010). Instance Deadlock: A Mystery behind Frozen Programs. In <i>Applications and Theory of Petri Nets</i> (pp. 1–17). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>","mla":"Juhás, Gabriel, et al. “Instance Deadlock: A Mystery behind Frozen Programs.” <i>Applications and Theory of Petri Nets</i>, Springer Berlin Heidelberg, 2010, pp. 1–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>.","chicago":"Juhás, Gabriel, Igor Kazlov, and Ana Juhásová. “Instance Deadlock: A Mystery behind Frozen Programs.” In <i>Applications and Theory of Petri Nets</i>, 1–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>."},"doi":"10.1007/978-3-642-13675-7_1","publication_status":"published","publication":"Applications and Theory of Petri Nets","date_created":"2019-02-08T09:33:41Z","page":"1-17","oa_version":"None","type":"book_chapter","date_published":"2010-01-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"4A997E50-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Berlin Heidelberg","status":"public","publication_identifier":{"isbn":["9783642136740","9783642136757"],"issn":["0302-9743","1611-3349"]},"title":"Instance Deadlock: A Mystery behind Frozen Programs","date_updated":"2022-04-01T13:45:24Z","extern":"1","year":"2010","author":[{"last_name":"Juhás","first_name":"Gabriel","full_name":"Juhás, Gabriel"},{"full_name":"Kazlov, Igor","last_name":"Kazlov","id":"4A997E50-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"full_name":"Juhásová, Ana","last_name":"Juhásová","first_name":"Ana"}],"place":"Berlin, Heidelberg","_id":"5940"},{"intvolume":"        17","citation":{"ista":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. 2010. P53 activates transcription by directing structural shifts in Mediator. Nature Structural and Molecular Biology. 17(6), 753–760.","apa":"Meyer, K., Lin, S., Bernecky, C., Gao, Y., &#38; Taatjes, D. (2010). P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>","mla":"Meyer, Krista, et al. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6, Nature Publishing Group, 2010, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>.","chicago":"Meyer, Krista, Shih Lin, Carrie Bernecky, Yuefeng Gao, and Dylan Taatjes. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>.","short":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, D. Taatjes, Nature Structural and Molecular Biology 17 (2010) 753–760.","ieee":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, and D. Taatjes, “P53 activates transcription by directing structural shifts in Mediator,” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6. Nature Publishing Group, pp. 753–760, 2010.","ama":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. 2010;17(6):753-760. doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>"},"volume":17,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932482/","open_access":"1"}],"publist_id":"7210","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2010-06-01T00:00:00Z","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:47:24Z","page":"753 - 760","publication":"Nature Structural and Molecular Biology","publication_status":"published","doi":"10.1038/nsmb.1816","month":"06","title":"P53 activates transcription by directing structural shifts in Mediator","oa":1,"publisher":"Nature Publishing Group","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"598","author":[{"full_name":"Meyer, Krista","last_name":"Meyer","first_name":"Krista"},{"last_name":"Lin","first_name":"Shih","full_name":"Lin, Shih"},{"orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"full_name":"Gao, Yuefeng","first_name":"Yuefeng","last_name":"Gao"},{"first_name":"Dylan","last_name":"Taatjes","full_name":"Taatjes, Dylan"}],"day":"01","extern":"1","year":"2010","date_updated":"2021-01-12T08:05:28Z","issue":"6","abstract":[{"text":"It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes.","lang":"eng"}]},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"11","extern":"1","pmid":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_size":578059,"file_name":"2010_PLOS_Weber.PDF","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-20T15:22:48Z","creator":"kschuh","file_id":"6143","checksum":"a01e6bbe15f044c0c79a26d7d881953e","access_level":"open_access"}],"author":[{"full_name":"Weber, Katherine P.","last_name":"Weber","first_name":"Katherine P."},{"last_name":"De","first_name":"Subhajyoti","full_name":"De, Subhajyoti"},{"full_name":"Kozarewa, Iwanka","first_name":"Iwanka","last_name":"Kozarewa"},{"full_name":"Turner, Daniel J.","first_name":"Daniel J.","last_name":"Turner"},{"full_name":"Babu, M. Madan","first_name":"M. Madan","last_name":"Babu"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443"}],"title":"Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2019-03-20T15:20:30Z","publication":"PLoS ONE","has_accepted_license":"1","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"pmid":["21085631"]},"quality_controlled":"1","volume":5,"year":"2010","date_updated":"2021-01-12T08:06:20Z","issue":"11","abstract":[{"text":"Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.","lang":"eng"}],"_id":"6142","article_number":"e13922","publication_identifier":{"issn":["1932-6203"]},"oa":1,"status":"public","month":"11","publication_status":"published","doi":"10.1371/journal.pone.0013922","date_published":"2010-11-11T00:00:00Z","oa_version":"Published Version","ddc":["570"],"file_date_updated":"2020-07-14T12:47:20Z","citation":{"chicago":"Weber, Katherine P., Subhajyoti De, Iwanka Kozarewa, Daniel J. Turner, M. Madan Babu, and Mario de Bono. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>.","ista":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. 2010. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS ONE. 5(11), e13922.","apa":"Weber, K. P., De, S., Kozarewa, I., Turner, D. J., Babu, M. M., &#38; de Bono, M. (2010). Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>","mla":"Weber, Katherine P., et al. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>, vol. 5, no. 11, e13922, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>.","short":"K.P. Weber, S. De, I. Kozarewa, D.J. Turner, M.M. Babu, M. de Bono, PLoS ONE 5 (2010).","ieee":"K. P. Weber, S. De, I. Kozarewa, D. J. Turner, M. M. Babu, and M. de Bono, “Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans,” <i>PLoS ONE</i>, vol. 5, no. 11. Public Library of Science, 2010.","ama":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. 2010;5(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>"},"intvolume":"         5"},{"_id":"619","author":[{"full_name":"Zacharasiewicz, Waldemar","first_name":"Waldemar","last_name":"Zacharasiewicz"},{"first_name":"Fritz","last_name":"Kirsch","full_name":"Kirsch, Fritz Peter"}],"year":"2010","extern":1,"day":"01","abstract":[{"text":"Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place.","lang":"eng"}],"date_updated":"2021-01-12T08:06:40Z","month":"01","title":"“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House","publisher":"Facultas.WUV","status":"public","date_published":"2010-01-01T00:00:00Z","type":"book_chapter","publication":"Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien","date_created":"2018-12-11T11:47:32Z","page":"173 - 179","publication_status":"published","citation":{"chicago":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” In <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, 173–79. Facultas.WUV, 2010.","mla":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, Facultas.WUV, 2010, pp. 173–79.","apa":"Zacharasiewicz, W., &#38; Kirsch, F. (2010). “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i> (pp. 173–179). Facultas.WUV.","ista":"Zacharasiewicz W, Kirsch F. 2010.“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien. , 173–179.","ieee":"W. Zacharasiewicz and F. Kirsch, “‘This is a fundamentalist town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House,” in <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i>, Facultas.WUV, 2010, pp. 173–179.","ama":"Zacharasiewicz W, Kirsch F. “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>. Facultas.WUV; 2010:173-179.","short":"W. Zacharasiewicz, F. Kirsch, in:, Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien, Facultas.WUV, 2010, pp. 173–179."},"quality_controlled":0,"publist_id":"7185"},{"publisher":"Nature Publishing Group","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95","publication_identifier":{"issn":["1078-8956","1546-170x"]},"month":"11","date_updated":"2021-01-12T08:06:43Z","abstract":[{"lang":"eng","text":"Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. "}],"pmid":1,"issue":"12","day":"21","year":"2010","extern":"1","author":[{"full_name":"Zhou, L","first_name":"L","last_name":"Zhou"},{"first_name":"F","last_name":"Li","full_name":"Li, F"},{"full_name":"Xu, Haibing","first_name":"Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"CX","last_name":"Luo","full_name":"Luo, CX"},{"first_name":"HY","last_name":"Wu","full_name":"Wu, HY"},{"first_name":"MM","last_name":"Zhu","full_name":"Zhu, MM"},{"first_name":"W","last_name":"Lu","full_name":"Lu, W"},{"first_name":"X","last_name":"Ji","full_name":"Ji, X"},{"full_name":"Zhou, QG","last_name":"Zhou","first_name":"QG"},{"last_name":"Zhu","first_name":"DY","full_name":"Zhu, DY"}],"_id":"6198","external_id":{"pmid":["21102461"]},"intvolume":"        16","citation":{"chicago":"Zhou, L, F Li, Haibing Xu, CX Luo, HY Wu, MM Zhu, W Lu, X Ji, QG Zhou, and DY Zhu. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>.","ista":"Zhou L, Li F, Xu H, Luo C, Wu H, Zhu M, Lu W, Ji X, Zhou Q, Zhu D. 2010. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nature Medicine. 16(12), 1439–1443.","apa":"Zhou, L., Li, F., Xu, H., Luo, C., Wu, H., Zhu, M., … Zhu, D. (2010). Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>","mla":"Zhou, L., et al. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>, vol. 16, no. 12, Nature Publishing Group, 2010, pp. 1439–43, doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>.","short":"L. Zhou, F. Li, H. Xu, C. Luo, H. Wu, M. Zhu, W. Lu, X. Ji, Q. Zhou, D. Zhu, Nature Medicine 16 (2010) 1439–1443.","ieee":"L. Zhou <i>et al.</i>, “Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95,” <i>Nature Medicine</i>, vol. 16, no. 12. Nature Publishing Group, pp. 1439–1443, 2010.","ama":"Zhou L, Li F, Xu H, et al. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. 2010;16(12):1439-1443. doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>"},"volume":16,"quality_controlled":"1","publication_status":"published","doi":"10.1038/nm.2245","page":"1439-1443","date_created":"2019-04-04T14:55:32Z","publication":"Nature Medicine","type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2010-11-21T00:00:00Z"},{"doi":"10.1515/crelle.2010.064","publication_status":"published","publication":"Crelles Journal","date_created":"2019-04-16T13:51:40Z","page":"1-44","type":"journal_article","oa_version":"Preprint","date_published":"2010-09-01T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0808.2340v2"}],"intvolume":"      2010","citation":{"short":"R. de la Bretèche, T.D. Browning, Crelles Journal 2010 (2010) 1–44.","ama":"Bretèche R de la, Browning TD. Le problème des diviseurs pour des formes binaires de degré 4. <i>Crelles Journal</i>. 2010;2010(646):1-44. doi:<a href=\"https://doi.org/10.1515/crelle.2010.064\">10.1515/crelle.2010.064</a>","ieee":"R. de la Bretèche and T. D. Browning, “Le problème des diviseurs pour des formes binaires de degré 4,” <i>Crelles Journal</i>, vol. 2010, no. 646. Walter de Gruyter GmbH, pp. 1–44, 2010.","apa":"Bretèche, R. de la, &#38; Browning, T. D. (2010). Le problème des diviseurs pour des formes binaires de degré 4. <i>Crelles Journal</i>. Walter de Gruyter GmbH. <a href=\"https://doi.org/10.1515/crelle.2010.064\">https://doi.org/10.1515/crelle.2010.064</a>","mla":"Bretèche, Régis de la, and Timothy D. Browning. “Le Problème Des Diviseurs Pour Des Formes Binaires de Degré 4.” <i>Crelles Journal</i>, vol. 2010, no. 646, Walter de Gruyter GmbH, 2010, pp. 1–44, doi:<a href=\"https://doi.org/10.1515/crelle.2010.064\">10.1515/crelle.2010.064</a>.","ista":"Bretèche R de la, Browning TD. 2010. Le problème des diviseurs pour des formes binaires de degré 4. Crelles Journal. 2010(646), 1–44.","chicago":"Bretèche, Régis de la, and Timothy D Browning. “Le Problème Des Diviseurs Pour Des Formes Binaires de Degré 4.” <i>Crelles Journal</i>. Walter de Gruyter GmbH, 2010. <a href=\"https://doi.org/10.1515/crelle.2010.064\">https://doi.org/10.1515/crelle.2010.064</a>."},"quality_controlled":"1","volume":2010,"external_id":{"arxiv":["0808.2340v2"]},"abstract":[{"lang":"eng","text":"We study the average order of the divisor function, as it ranges over the values of binary quartic forms that are reducible over ℚ."}],"issue":"646","arxiv":1,"date_updated":"2021-01-12T08:07:04Z","year":"2010","extern":"1","day":"01","author":[{"full_name":"Bretèche, Régis de la","last_name":"Bretèche","first_name":"Régis de la"},{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","first_name":"Timothy D","full_name":"Browning, Timothy D"}],"_id":"6320","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Walter de Gruyter GmbH","oa":1,"title":"Le problème des diviseurs pour des formes binaires de degré 4","month":"09"},{"status":"public","publisher":"Springer","title":"Kac's conjecture from Nakajima quiver varieties","oa":1,"month":"07","date_updated":"2021-01-12T06:50:56Z","issue":"1","abstract":[{"lang":"eng","text":"We prove a generating function formula for the Betti numbers of Nakajima quiver varieties. We prove that it is a q-deformation of the Weyl-Kac character formula. In particular this implies that the constant term of the polynomial counting the number of absolutely indecomposable representations of a quiver equals the multiplicity of a certain weight in the corresponding Kac-Moody algebra, which was conjectured by Kac in 1982."}],"acknowledgement":"This work has been supported by a Royal Society University Research Fellowship, NSF grants DMS-0305505 and DMS-0604775 and an Alfred Sloan Fellowship 2005-2007.","day":"01","year":"2010","extern":1,"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas","full_name":"Tamas Hausel"}],"_id":"1465","publist_id":"5730","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0811.1569"}],"volume":181,"intvolume":"       181","quality_controlled":0,"citation":{"short":"T. Hausel, Inventiones Mathematicae 181 (2010) 21–37.","ama":"Hausel T. Kac’s conjecture from Nakajima quiver varieties. <i>Inventiones Mathematicae</i>. 2010;181(1):21-37. doi:<a href=\"https://doi.org/10.1007/s00222-010-0241-3\">10.1007/s00222-010-0241-3</a>","ieee":"T. Hausel, “Kac’s conjecture from Nakajima quiver varieties,” <i>Inventiones Mathematicae</i>, vol. 181, no. 1. Springer, pp. 21–37, 2010.","chicago":"Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” <i>Inventiones Mathematicae</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00222-010-0241-3\">https://doi.org/10.1007/s00222-010-0241-3</a>.","apa":"Hausel, T. (2010). Kac’s conjecture from Nakajima quiver varieties. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-010-0241-3\">https://doi.org/10.1007/s00222-010-0241-3</a>","mla":"Hausel, Tamás. “Kac’s Conjecture from Nakajima Quiver Varieties.” <i>Inventiones Mathematicae</i>, vol. 181, no. 1, Springer, 2010, pp. 21–37, doi:<a href=\"https://doi.org/10.1007/s00222-010-0241-3\">10.1007/s00222-010-0241-3</a>.","ista":"Hausel T. 2010. Kac’s conjecture from Nakajima quiver varieties. Inventiones Mathematicae. 181(1), 21–37."},"publication_status":"published","doi":"10.1007/s00222-010-0241-3","page":"21 - 37","date_created":"2018-12-11T11:52:11Z","publication":"Inventiones Mathematicae","type":"journal_article","date_published":"2010-07-01T00:00:00Z"},{"month":"02","oa":1,"title":"Topology of character varieties and representations of quivers","publisher":"Elsevier","status":"public","_id":"1466","author":[{"full_name":"Tamas Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"full_name":"Letellier, Emmanuel","first_name":"Emmanuel","last_name":"Letellier"},{"last_name":"Rodríguez Villegas","first_name":"Fernando","full_name":"Rodríguez Villegas, Fernando"}],"extern":1,"year":"2010","day":"01","abstract":[{"text":"In Hausel et al. (2008) [10] we presented a conjecture generalizing the Cauchy formula for Macdonald polynomial. This conjecture encodes the mixed Hodge polynomials of the character varieties of representations of the fundamental group of a punctured Riemann surface of genus g. We proved several results which support this conjecture. Here we announce new results which are consequences of those in Hausel et al. (2008) [10].","lang":"eng"}],"issue":"3-4","date_updated":"2021-01-12T06:50:56Z","volume":348,"citation":{"ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Topology of character varieties and representations of quivers,” <i>Comptes Rendus Mathematique</i>, vol. 348, no. 3–4. Elsevier, pp. 131–135, 2010.","ama":"Hausel T, Letellier E, Rodríguez Villegas F. Topology of character varieties and representations of quivers. <i>Comptes Rendus Mathematique</i>. 2010;348(3-4):131-135. doi:<a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">10.1016/j.crma.2010.01.025</a>","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Comptes Rendus Mathematique 348 (2010) 131–135.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Topology of Character Varieties and Representations of Quivers.” <i>Comptes Rendus Mathematique</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">https://doi.org/10.1016/j.crma.2010.01.025</a>.","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2010). Topology of character varieties and representations of quivers. <i>Comptes Rendus Mathematique</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">https://doi.org/10.1016/j.crma.2010.01.025</a>","mla":"Hausel, Tamás, et al. “Topology of Character Varieties and Representations of Quivers.” <i>Comptes Rendus Mathematique</i>, vol. 348, no. 3–4, Elsevier, 2010, pp. 131–35, doi:<a href=\"https://doi.org/10.1016/j.crma.2010.01.025\">10.1016/j.crma.2010.01.025</a>.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2010. Topology of character varieties and representations of quivers. Comptes Rendus Mathematique. 348(3–4), 131–135."},"quality_controlled":0,"intvolume":"       348","main_file_link":[{"url":"http://arxiv.org/abs/0905.3491","open_access":"1"}],"publist_id":"5731","date_published":"2010-02-01T00:00:00Z","type":"journal_article","publication":"Comptes Rendus Mathematique","page":"131 - 135","date_created":"2018-12-11T11:52:11Z","doi":"10.1016/j.crma.2010.01.025","publication_status":"published"},{"month":"09","publisher":"Oxford University Press","status":"public","title":"S-Duality in HyperkäHler Hodge Theory","oa":1,"author":[{"full_name":"Tamas Hausel","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas"}],"_id":"1468","date_updated":"2021-01-12T06:50:57Z","abstract":[{"text":"This chapter surveys the motivations, related results, and progress made towards the following problem, raised by Hitchin in 1995: What is the space of L2 harmonic forms on the moduli space of Higgs bundles on a Riemann surface?","lang":"eng"}],"day":"01","extern":1,"year":"2010","citation":{"short":"T. Hausel, in:, The Many Facets of Geometry: A Tribute to Nigel Hitchin, Oxford University Press, 2010.","ieee":"T. Hausel, “S-Duality in HyperkäHler Hodge Theory,” in <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>, Oxford University Press, 2010.","ama":"Hausel T. S-Duality in HyperkäHler Hodge Theory. In: <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press; 2010. doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">10.1093/acprof:oso/9780199534920.003.0016</a>","chicago":"Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” In <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press, 2010. <a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">https://doi.org/10.1093/acprof:oso/9780199534920.003.0016</a>.","apa":"Hausel, T. (2010). S-Duality in HyperkäHler Hodge Theory. In <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">https://doi.org/10.1093/acprof:oso/9780199534920.003.0016</a>","mla":"Hausel, Tamás. “S-Duality in HyperkäHler Hodge Theory.” <i>The Many Facets of Geometry: A Tribute to Nigel Hitchin</i>, Oxford University Press, 2010, doi:<a href=\"https://doi.org/10.1093/acprof:oso/9780199534920.003.0016\">10.1093/acprof:oso/9780199534920.003.0016</a>.","ista":"Hausel T. 2010.S-Duality in HyperkäHler Hodge Theory. In: The Many Facets of Geometry: A Tribute to Nigel Hitchin. ."},"quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/0709.0504","open_access":"1"}],"publist_id":"5729","type":"book_chapter","date_published":"2010-09-01T00:00:00Z","publication_status":"published","doi":"10.1093/acprof:oso/9780199534920.003.0016","date_created":"2018-12-11T11:52:12Z","publication":"The Many Facets of Geometry: A Tribute to Nigel Hitchin"},{"alternative_title":["The Frontiers Collection"],"series_title":"FRONTCOLL","edition":"1","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Adaptive Methods in BCI Research - An Introductory Tutorial","author":[{"orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"last_name":"Vidaurre","first_name":"Carmen","full_name":"Vidaurre, Carmen"},{"first_name":"Klaus-Robert","last_name":"Müller","full_name":"Müller, Klaus-Robert"}],"acknowledgement":"This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5 Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore, we thank Matthias Krauledat for fruitful discussions and tools for generating Fig. 5.","day":"06","quality_controlled":"1","editor":[{"full_name":"Graimann, Bernhard","last_name":"Graimann","first_name":"Bernhard"},{"full_name":"Pfurtscheller, Gert","first_name":"Gert","last_name":"Pfurtscheller"},{"full_name":"Allison, Brendan","first_name":"Brendan","last_name":"Allison"}],"article_processing_charge":"No","type":"book_chapter","language":[{"iso":"eng"}],"department":[{"_id":"ScienComp"}],"date_created":"2024-02-14T09:56:00Z","page":"331-355","publication":"Brain-Computer Interfaces","month":"09","status":"public","publication_identifier":{"issn":["1612-3018"],"isbn":["9783642020902"],"eisbn":["9783642020919"]},"place":"Berlin, Heidelberg","_id":"14983","date_updated":"2024-02-19T09:47:25Z","abstract":[{"text":"This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data.","lang":"eng"}],"year":"2010","citation":{"chicago":"Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods in BCI Research - An Introductory Tutorial.” In <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed., 331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>.","apa":"Schlögl, A., Vidaurre, C., &#38; Müller, K.-R. (2010). Adaptive Methods in BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &#38; B. Allison (Eds.), <i>Brain-Computer Interfaces</i> (1st ed., pp. 331–355). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>","mla":"Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory Tutorial.” <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann et al., 1st ed., Springer, 2010, pp. 331–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>.","ista":"Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research - An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection, , 331–355.","ama":"Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. <i>Brain-Computer Interfaces</i>. 1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>","ieee":"A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in <i>Brain-Computer Interfaces</i>, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355.","short":"A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller, B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg, 2010, pp. 331–355."},"oa_version":"None","date_published":"2010-09-06T00:00:00Z","publication_status":"published","doi":"10.1007/978-3-642-02091-9_18"},{"_id":"13409","date_updated":"2023-08-08T07:58:13Z","abstract":[{"text":"The immobilization of molecular switches onto inorganic supports has recently become a hot topic as it can give rise to novel hybrid materials in which the properties of the two components are mutually enhanced. Even more attractive is the concept of “transferring” the switchable characteristics of single layers of organic molecules onto the underlying inorganic components, rendering them responsive to external stimuli as well. Of the various molecular switches studied, azobenzene (AB) has arguably attracted most attention due to its simple molecular structure, and because its “trigger” (light) is a noninvasive one, it can be delivered instantaneously, and into a precise location. In order to fully realize its potential, however, it is necessary to immobilize AB onto solid supports. It is the goal of this manuscript to comprehensively yet concisely review such hybrid systems which comprise AB forming well-defined self-assembled monolayers (SAMs) on planar and curved (colloidal and nanoporous) inorganic surfaces. I discuss methods to immobilize AB derivatives onto surfaces, strategies to ensure efficient AB isomerization, ways to monitor the switching process, properties of these switchable hybrid materials, and, last but not least, their emerging applications.","lang":"eng"}],"issue":"12","year":"2010","month":"10","status":"public","publication_identifier":{"issn":["0033-4545"],"eissn":["1365-3075"]},"oa":1,"oa_version":"Published Version","date_published":"2010-10-15T00:00:00Z","publication_status":"published","doi":"10.1351/pac-con-10-09-04","citation":{"short":"R. Klajn, Pure and Applied Chemistry 82 (2010) 2247–2279.","ama":"Klajn R. Immobilized azobenzenes for the construction of photoresponsive materials. <i>Pure and Applied Chemistry</i>. 2010;82(12):2247-2279. doi:<a href=\"https://doi.org/10.1351/pac-con-10-09-04\">10.1351/pac-con-10-09-04</a>","ieee":"R. Klajn, “Immobilized azobenzenes for the construction of photoresponsive materials,” <i>Pure and Applied Chemistry</i>, vol. 82, no. 12. De Gruyter, pp. 2247–2279, 2010.","ista":"Klajn R. 2010. Immobilized azobenzenes for the construction of photoresponsive materials. Pure and Applied Chemistry. 82(12), 2247–2279.","apa":"Klajn, R. (2010). Immobilized azobenzenes for the construction of photoresponsive materials. <i>Pure and Applied Chemistry</i>. De Gruyter. <a href=\"https://doi.org/10.1351/pac-con-10-09-04\">https://doi.org/10.1351/pac-con-10-09-04</a>","mla":"Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive Materials.” <i>Pure and Applied Chemistry</i>, vol. 82, no. 12, De Gruyter, 2010, pp. 2247–79, doi:<a href=\"https://doi.org/10.1351/pac-con-10-09-04\">10.1351/pac-con-10-09-04</a>.","chicago":"Klajn, Rafal. “Immobilized Azobenzenes for the Construction of Photoresponsive Materials.” <i>Pure and Applied Chemistry</i>. De Gruyter, 2010. <a href=\"https://doi.org/10.1351/pac-con-10-09-04\">https://doi.org/10.1351/pac-con-10-09-04</a>."},"intvolume":"        82","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1351/pac-con-10-09-04","open_access":"1"}],"author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"}],"day":"15","extern":"1","publisher":"De Gruyter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Immobilized azobenzenes for the construction of photoresponsive materials","type":"journal_article","language":[{"iso":"eng"}],"page":"2247-2279","date_created":"2023-08-01T09:48:11Z","publication":"Pure and Applied Chemistry","keyword":["General Chemical Engineering","General Chemistry"],"volume":82,"quality_controlled":"1","article_type":"original","article_processing_charge":"No"},{"article_type":"original","article_processing_charge":"No","external_id":{"pmid":["20218598"]},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"volume":132,"quality_controlled":"1","date_created":"2023-08-01T09:48:27Z","page":"4310-4320","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"type":"journal_article","title":"Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory","publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"31","extern":"1","pmid":1,"author":[{"full_name":"Coskun, Ali","first_name":"Ali","last_name":"Coskun"},{"first_name":"Paul J.","last_name":"Wesson","full_name":"Wesson, Paul J."},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"},{"last_name":"Trabolsi","first_name":"Ali","full_name":"Trabolsi, Ali"},{"first_name":"Lei","last_name":"Fang","full_name":"Fang, Lei"},{"full_name":"Olson, Mark A.","last_name":"Olson","first_name":"Mark A."},{"first_name":"Sanjeev K.","last_name":"Dey","full_name":"Dey, Sanjeev K."},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"},{"last_name":"Stoddart","first_name":"J. Fraser","full_name":"Stoddart, J. Fraser"}],"scopus_import":"1","citation":{"apa":"Coskun, A., Wesson, P. J., Klajn, R., Trabolsi, A., Fang, L., Olson, M. A., … Stoddart, J. F. (2010). Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja9102327\">https://doi.org/10.1021/ja9102327</a>","mla":"Coskun, Ali, et al. “Molecular-Mechanical Switching at the Nanoparticle−solvent Interface: Practice and Theory.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 12, American Chemical Society, 2010, pp. 4310–20, doi:<a href=\"https://doi.org/10.1021/ja9102327\">10.1021/ja9102327</a>.","ista":"Coskun A, Wesson PJ, Klajn R, Trabolsi A, Fang L, Olson MA, Dey SK, Grzybowski BA, Stoddart JF. 2010. Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. Journal of the American Chemical Society. 132(12), 4310–4320.","chicago":"Coskun, Ali, Paul J. Wesson, Rafal Klajn, Ali Trabolsi, Lei Fang, Mark A. Olson, Sanjeev K. Dey, Bartosz A. Grzybowski, and J. Fraser Stoddart. “Molecular-Mechanical Switching at the Nanoparticle−solvent Interface: Practice and Theory.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja9102327\">https://doi.org/10.1021/ja9102327</a>.","short":"A. Coskun, P.J. Wesson, R. Klajn, A. Trabolsi, L. Fang, M.A. Olson, S.K. Dey, B.A. Grzybowski, J.F. Stoddart, Journal of the American Chemical Society 132 (2010) 4310–4320.","ama":"Coskun A, Wesson PJ, Klajn R, et al. Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory. <i>Journal of the American Chemical Society</i>. 2010;132(12):4310-4320. doi:<a href=\"https://doi.org/10.1021/ja9102327\">10.1021/ja9102327</a>","ieee":"A. Coskun <i>et al.</i>, “Molecular-mechanical switching at the nanoparticle−solvent interface: Practice and theory,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 12. American Chemical Society, pp. 4310–4320, 2010."},"intvolume":"       132","publication_status":"published","doi":"10.1021/ja9102327","date_published":"2010-03-31T00:00:00Z","oa_version":"None","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"status":"public","month":"03","year":"2010","date_updated":"2023-08-08T08:00:31Z","issue":"12","abstract":[{"lang":"eng","text":"A range (Au, Pt, Pd) of metal nanoparticles (MNPs) has been prepared and functionalized with (a) redox-active stalks containing tetrathiafulvalene (TTF) units, (b) [2]pseudorotaxanes formed between these stalks and cyclobis(paraquat-p-phenylene) (CBPQT4+) rings, and (c) bistable [2]rotaxane molecules where the dumbbell component contains a 1,5-dioxynaphthalene (DNP) unit, as well as a TTF unit, encircled by a CBPQT4+ ring. It transpires that the molecules present in (a) and (c) and the supermolecules described in (b) retain their switching characteristics, previously observed in solution, when they are immobilized onto MNPs. Moreover, their oxidation potentials depend on the fraction, χ, of the molecules or supermolecules on the surface of the nanoparticles. A variation in χ affects the oxidation potentials of the TTF units to the extent that switching can be subjected to fine tuning as a result. Specifically, increasing χ results in positive shifts (i) in the oxidation potentials of the TTF unit in (a)−(c) and (ii) the reduction potentials of the CBPQT4+ rings in (c). These shifts can be attributed to an increase in the electrostatic potential surrounding the MNPs. Both the magnitude and the direction of these shifts are reproduced by a model, based on the Poisson−Boltzmann equation coupled with charge-regulating boundary conditions. Furthermore, the kinetics of relaxation from the metastable state coconformation (MSCC) to the ground-state coconformation (GSCC) of the bistable [2]rotaxane molecules also depends on χ, as well as on the nanoparticle diameter. Increasing either of these parameters accelerates the rate of relaxation from the MSCC to the GSCC. This rate is a function of (i) the activation energy for the relaxation process associated with the bistable [2]rotaxane molecules in solution and (ii) the electrostatic potential surrounding the MNPs. The electrostatic potential depends on (i) the diameter of the MNPs, (ii) the amount of the bistable [2]rotaxane molecules on the surface of the MNPs, and (iii) the equilibrium distribution of the CBPQT4+ rings between the DNP and TTF recognition sites in the GSCC. This electrostatic potential has also been quantified using the Poisson−Boltzmann equation, leading to faithful estimates of the rate constants."}],"_id":"13410"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","title":"Nanoparticles that “remember” temperature","author":[{"full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"},{"last_name":"Browne","first_name":"Kevin P.","full_name":"Browne, Kevin P."},{"full_name":"Soh, Siowling","last_name":"Soh","first_name":"Siowling"},{"first_name":"Bartosz A.","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A."}],"pmid":1,"extern":"1","day":"05","quality_controlled":"1","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"volume":6,"external_id":{"pmid":["20521264"]},"article_type":"original","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"publication":"Small","date_created":"2023-08-01T09:48:38Z","page":"1385-1387","month":"07","status":"public","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"_id":"13411","abstract":[{"text":"Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide a basis for sensors that “remember” whether the sample has ever exceeded the melting temperature of the matrix. The operation of these sensors rests on the ability to photoinduce metastable electric dipoles on NP surfaces – upon melting, these dipoles drive NP aggregation, precipitation, and crosslinking. These events are manifested by a pronounced color change.","lang":"eng"}],"issue":"13","date_updated":"2023-08-08T08:15:25Z","year":"2010","citation":{"short":"R. Klajn, K.P. Browne, S. Soh, B.A. Grzybowski, Small 6 (2010) 1385–1387.","ieee":"R. Klajn, K. P. Browne, S. Soh, and B. A. Grzybowski, “Nanoparticles that ‘remember’ temperature,” <i>Small</i>, vol. 6, no. 13. Wiley, pp. 1385–1387, 2010.","ama":"Klajn R, Browne KP, Soh S, Grzybowski BA. Nanoparticles that “remember” temperature. <i>Small</i>. 2010;6(13):1385-1387. doi:<a href=\"https://doi.org/10.1002/smll.200902272\">10.1002/smll.200902272</a>","chicago":"Klajn, Rafal, Kevin P. Browne, Siowling Soh, and Bartosz A. Grzybowski. “Nanoparticles That ‘Remember’ Temperature.” <i>Small</i>. Wiley, 2010. <a href=\"https://doi.org/10.1002/smll.200902272\">https://doi.org/10.1002/smll.200902272</a>.","mla":"Klajn, Rafal, et al. “Nanoparticles That ‘Remember’ Temperature.” <i>Small</i>, vol. 6, no. 13, Wiley, 2010, pp. 1385–87, doi:<a href=\"https://doi.org/10.1002/smll.200902272\">10.1002/smll.200902272</a>.","ista":"Klajn R, Browne KP, Soh S, Grzybowski BA. 2010. Nanoparticles that “remember” temperature. Small. 6(13), 1385–1387.","apa":"Klajn, R., Browne, K. P., Soh, S., &#38; Grzybowski, B. A. (2010). Nanoparticles that “remember” temperature. <i>Small</i>. Wiley. <a href=\"https://doi.org/10.1002/smll.200902272\">https://doi.org/10.1002/smll.200902272</a>"},"intvolume":"         6","scopus_import":"1","oa_version":"None","date_published":"2010-07-05T00:00:00Z","doi":"10.1002/smll.200902272","publication_status":"published"},{"doi":"10.1039/b920377j","publication_status":"published","date_published":"2010-04-21T00:00:00Z","oa_version":"None","scopus_import":"1","intvolume":"        39","citation":{"short":"R. Klajn, J.F. Stoddart, B.A. Grzybowski, Chemical Society Reviews 39 (2010) 2203–2237.","ama":"Klajn R, Stoddart JF, Grzybowski BA. Nanoparticles functionalised with reversible molecular and supramolecular switches. <i>Chemical Society Reviews</i>. 2010;39(6):2203-2237. doi:<a href=\"https://doi.org/10.1039/b920377j\">10.1039/b920377j</a>","ieee":"R. Klajn, J. F. Stoddart, and B. A. Grzybowski, “Nanoparticles functionalised with reversible molecular and supramolecular switches,” <i>Chemical Society Reviews</i>, vol. 39, no. 6. Royal Society of Chemistry, pp. 2203–2237, 2010.","apa":"Klajn, R., Stoddart, J. F., &#38; Grzybowski, B. A. (2010). Nanoparticles functionalised with reversible molecular and supramolecular switches. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/b920377j\">https://doi.org/10.1039/b920377j</a>","ista":"Klajn R, Stoddart JF, Grzybowski BA. 2010. Nanoparticles functionalised with reversible molecular and supramolecular switches. Chemical Society Reviews. 39(6), 2203–2237.","mla":"Klajn, Rafal, et al. “Nanoparticles Functionalised with Reversible Molecular and Supramolecular Switches.” <i>Chemical Society Reviews</i>, vol. 39, no. 6, Royal Society of Chemistry, 2010, pp. 2203–37, doi:<a href=\"https://doi.org/10.1039/b920377j\">10.1039/b920377j</a>.","chicago":"Klajn, Rafal, J. Fraser Stoddart, and Bartosz A. Grzybowski. “Nanoparticles Functionalised with Reversible Molecular and Supramolecular Switches.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2010. <a href=\"https://doi.org/10.1039/b920377j\">https://doi.org/10.1039/b920377j</a>."},"year":"2010","abstract":[{"text":"Nanoparticles (NPs) and molecular/supramolecular switches have attracted considerable interest during the past decade on account of their unique properties and prominent roles in the fields of organic chemistry and materials science. Materials derived from the combination of these two components are now emerging in the literature. This critical review evaluates materials which comprise NPs functionalised with well-defined self-assembled monolayers of molecular and supramolecular switches. We draw attention to the fact that immobilisation of switches on NPs does not, in general, hamper their switching ability, although it can impart new properties on the supporting particles. This premise leads us to the discussion of systems in which switching on the surfaces of NPs can be used to modulate reversibly a range of NP properties—optical, fluorescent, electrical, magnetic—as well as the controlled release of small molecules. Finally, we discuss examples in which molecular switches direct reversible self-assembly of NPs (308 references).","lang":"eng"}],"issue":"6","date_updated":"2023-08-08T08:19:00Z","_id":"13412","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]},"status":"public","month":"04","publication":"Chemical Society Reviews","page":"2203-2237","date_created":"2023-08-01T09:49:07Z","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","keyword":["General Chemistry"],"quality_controlled":"1","volume":39,"external_id":{"pmid":["20407689"]},"extern":"1","day":"21","pmid":1,"author":[{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Stoddart, J. Fraser","last_name":"Stoddart","first_name":"J. Fraser"},{"last_name":"Grzybowski","first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A."}],"title":"Nanoparticles functionalised with reversible molecular and supramolecular switches","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society of Chemistry"},{"date_updated":"2021-01-12T08:21:46Z","abstract":[{"lang":"eng","text":"Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst)."}],"acknowledgement":"We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.","day":"31","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2010","extern":1,"author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"}],"_id":"901","publisher":"BioMed Central","status":"public","title":"Mitochondrial pathogenic mutations are population-specific","month":"12","publication_status":"published","doi":"10.1186/1745-6150-5-68","date_created":"2018-12-11T11:49:06Z","publication":"Biology Direct","type":"journal_article","date_published":"2010-12-31T00:00:00Z","publist_id":"6749","volume":5,"citation":{"apa":"Breen, M., &#38; Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>","ista":"Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.","mla":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>.","chicago":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>.","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010).","ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","ama":"Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>"},"intvolume":"         5","quality_controlled":0},{"publisher":"American Physical Society","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","author":[{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"},{"last_name":"Abécassis","first_name":"Benjamin","full_name":"Abécassis, Benjamin"},{"last_name":"Cottin-Bizonne","first_name":"Cécile","full_name":"Cottin-Bizonne, Cécile"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"pmid":1,"day":"02","extern":"1","external_id":{"pmid":["20481918"],"arxiv":["1004.1256 "]},"volume":104,"quality_controlled":"1","article_processing_charge":"No","article_type":"letter_note","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2021-01-19T10:25:04Z","publication":"Physical Review Letters","month":"04","status":"public","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"oa":1,"article_number":"138302","_id":"9012","date_updated":"2023-02-23T13:46:40Z","arxiv":1,"abstract":[{"text":"In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.","lang":"eng"}],"issue":"13","year":"2010","citation":{"apa":"Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>","ista":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal motility and pattern formation under rectified diffusiophoresis. Physical Review Letters. 104(13), 138302.","mla":"Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>, vol. 104, no. 13, 138302, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>.","chicago":"Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>.","ieee":"J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Colloidal motility and pattern formation under rectified diffusiophoresis,” <i>Physical Review Letters</i>, vol. 104, no. 13. American Physical Society, 2010.","ama":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. 2010;104(13). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010)."},"intvolume":"       104","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"oa_version":"Preprint","date_published":"2010-04-02T00:00:00Z","publication_status":"published","doi":"10.1103/physrevlett.104.138302"}]