[{"publist_id":"4630","author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi","full_name":"Dragoi, Cezara"},{"first_name":"Constantin","full_name":"Enea, Constantin","last_name":"Enea"},{"first_name":"Mihaela","full_name":"Sighireanu, Mihaela","last_name":"Sighireanu"}],"oa_version":"Submitted Version","file":[{"file_size":299004,"creator":"system","relation":"main_file","date_created":"2018-12-12T10:10:36Z","file_id":"4824","access_level":"open_access","content_type":"application/pdf","checksum":"907edd33a5892e3af093365f1fd57ed7","file_name":"IST-2014-196-v1+1_sas13.pdf","date_updated":"2020-07-14T12:45:37Z"}],"ec_funded":1,"department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:37Z","type":"conference","_id":"2298","date_published":"2013-01-01T00:00:00Z","doi":"10.1007/978-3-642-38856-9_10","conference":{"start_date":"2013-06-20","name":"SAS: Static Analysis Symposium","location":"Seattle, WA, United States","end_date":"2013-06-22"},"month":"01","publication_status":"published","quality_controlled":"1","oa":1,"intvolume":"      7935","volume":7935,"year":"2013","date_created":"2018-12-11T11:56:50Z","page":"150 - 171","status":"public","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"title":"Local shape analysis for overlaid data structures","ddc":["000","004"],"publisher":"Springer","date_updated":"2021-01-12T06:56:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"196","day":"01","citation":{"mla":"Dragoi, Cezara, et al. <i>Local Shape Analysis for Overlaid Data Structures</i>. Vol. 7935, Springer, 2013, pp. 150–71, doi:<a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">10.1007/978-3-642-38856-9_10</a>.","ieee":"C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.","short":"C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171.","ista":"Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.","chicago":"Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">https://doi.org/10.1007/978-3-642-38856-9_10</a>.","apa":"Dragoi, C., Enea, C., &#38; Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">https://doi.org/10.1007/978-3-642-38856-9_10</a>","ama":"Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:<a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">10.1007/978-3-642-38856-9_10</a>"},"abstract":[{"text":"We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.\r\n","lang":"eng"}],"has_accepted_license":"1","scopus_import":1},{"has_accepted_license":"1","scopus_import":1,"day":"01","citation":{"mla":"Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:<a href=\"https://doi.org/10.1007/s10009-011-0207-9\">10.1007/s10009-011-0207-9</a>.","ieee":"Y. Godhal, K. Chatterjee, and T. A. Henzinger, “Synthesis of AMBA AHB from formal specification: A case study,” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 15, no. 5–6. Springer, pp. 585–601, 2013.","short":"Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 15 (2013) 585–601.","apa":"Godhal, Y., Chatterjee, K., &#38; Henzinger, T. A. (2013). Synthesis of AMBA AHB from formal specification: A case study. <i>International Journal on Software Tools for Technology Transfer</i>. Springer. <a href=\"https://doi.org/10.1007/s10009-011-0207-9\">https://doi.org/10.1007/s10009-011-0207-9</a>","chicago":"Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” <i>International Journal on Software Tools for Technology Transfer</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10009-011-0207-9\">https://doi.org/10.1007/s10009-011-0207-9</a>.","ista":"Godhal Y, Chatterjee K, Henzinger TA. 2013. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 15(5–6), 585–601.","ama":"Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification: A case study. <i>International Journal on Software Tools for Technology Transfer</i>. 2013;15(5-6):585-601. doi:<a href=\"https://doi.org/10.1007/s10009-011-0207-9\">10.1007/s10009-011-0207-9</a>"},"abstract":[{"text":"The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.","lang":"eng"}],"title":"Synthesis of AMBA AHB from formal specification: A case study","ddc":["000"],"pubrep_id":"87","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:37Z","publisher":"Springer","volume":15,"date_created":"2018-12-11T11:56:51Z","year":"2013","page":"585 - 601","status":"public","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2013-10-01T00:00:00Z","doi":"10.1007/s10009-011-0207-9","_id":"2299","month":"10","quality_controlled":"1","publication_status":"published","publication":"International Journal on Software Tools for Technology Transfer","intvolume":"        15","oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:37Z","type":"journal_article","issue":"5-6","file":[{"creator":"system","file_size":277372,"file_id":"4910","date_created":"2018-12-12T10:11:53Z","relation":"main_file","date_updated":"2020-07-14T12:45:37Z","file_name":"IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf","access_level":"open_access","checksum":"57b06a732dd8d6349190dba6b5b0d33b","content_type":"application/pdf"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"oa_version":"Submitted Version","author":[{"first_name":"Yashdeep","id":"5B547124-EB61-11E9-8887-89D9C04DBDF5","full_name":"Godhal, Yashdeep","last_name":"Godhal"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"publist_id":"4629"},{"department":[{"_id":"RoSe"}],"publist_id":"4627","oa_version":"Preprint","author":[{"first_name":"Alessandro","full_name":"Giuliani, Alessandro","last_name":"Giuliani"},{"last_name":"Lieb","full_name":"Lieb, Élliott","first_name":"Élliott"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","quality_controlled":"1","oa":1,"publication":"Physical Review B","intvolume":"        88","_id":"2300","doi":"10.1103/PhysRevB.88.064401","date_published":"2013-08-01T00:00:00Z","external_id":{"arxiv":["1305.5323"]},"arxiv":1,"month":"08","language":[{"iso":"eng"}],"issue":"6","type":"journal_article","date_updated":"2021-01-12T06:56:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","article_number":"064401","title":"Realization of stripes and slabs in two and three dimensions","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1305.5323","open_access":"1"}],"volume":88,"year":"2013","date_created":"2018-12-11T11:56:51Z","scopus_import":1,"abstract":[{"text":"We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.","lang":"eng"}],"day":"01","citation":{"mla":"Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” <i>Physical Review B</i>, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">10.1103/PhysRevB.88.064401</a>.","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” <i>Physical Review B</i>, vol. 88, no. 6. American Physical Society, 2013.","short":"A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).","ama":"Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. <i>Physical Review B</i>. 2013;88(6). doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">10.1103/PhysRevB.88.064401</a>","apa":"Giuliani, A., Lieb, É., &#38; Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">https://doi.org/10.1103/PhysRevB.88.064401</a>","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” <i>Physical Review B</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">https://doi.org/10.1103/PhysRevB.88.064401</a>.","ista":"Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401."}},{"day":"01","citation":{"short":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331.","ista":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Languages Design and Implementation, 321–331.","ama":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>. ACM; 2013:321-331. doi:<a href=\"https://doi.org/10.1145/2491956.2462184\">10.1145/2491956.2462184</a>","apa":"Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., &#38; Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i> (pp. 321–331). Seattle, WA, United States: ACM. <a href=\"https://doi.org/10.1145/2491956.2462184\">https://doi.org/10.1145/2491956.2462184</a>","chicago":"Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, 321–31. ACM, 2013. <a href=\"https://doi.org/10.1145/2491956.2462184\">https://doi.org/10.1145/2491956.2462184</a>.","mla":"Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, ACM, 2013, pp. 321–31, doi:<a href=\"https://doi.org/10.1145/2491956.2462184\">10.1145/2491956.2462184</a>.","ieee":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Seattle, WA, United States, 2013, pp. 321–331."},"language":[{"iso":"eng"}],"abstract":[{"text":"We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to &quot;close&quot; the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P.","lang":"eng"}],"type":"conference","_id":"2301","date_published":"2013-06-01T00:00:00Z","doi":"10.1145/2491956.2462184","scopus_import":1,"conference":{"start_date":"2013-06-16","name":"PLDI: Programming Languages Design and Implementation","location":"Seattle, WA, United States","end_date":"2013-06-19"},"month":"06","publication_status":"published","quality_controlled":"1","publication":"Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation","year":"2013","date_created":"2018-12-11T11:56:52Z","page":"321 - 331","publist_id":"4626","status":"public","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"oa_version":"None","author":[{"first_name":"Ankush","last_name":"Desai","full_name":"Desai, Ankush"},{"first_name":"Vivek","full_name":"Gupta, Vivek","last_name":"Gupta"},{"first_name":"Ethan","last_name":"Jackson","full_name":"Jackson, Ethan"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736"}],"main_file_link":[{"url":"http://research.microsoft.com/pubs/191069/pldi212_desai.pdf"}],"ec_funded":1,"title":"P: Safe asynchronous event-driven programming","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","date_updated":"2021-01-12T06:56:38Z"},{"acknowledgement":"This work was supported by IST Austria institutional funds.","volume":8,"year":"2013","date_created":"2018-12-11T11:56:52Z","page":"557 - 568","status":"public","publist_id":"4624","author":[{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"article_type":"review","oa_version":"None","department":[{"_id":"SiHi"}],"title":"Dissection of gene function at clonal level using mosaic analysis with double markers","publisher":"Springer","date_updated":"2021-01-12T06:56:39Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"03","citation":{"short":"S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.","apa":"Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. <i>Frontiers in Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11515-013-1279-6\">https://doi.org/10.1007/s11515-013-1279-6</a>","ama":"Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. <i>Frontiers in Biology</i>. 2013;8(6):557-568. doi:<a href=\"https://doi.org/10.1007/s11515-013-1279-6\">10.1007/s11515-013-1279-6</a>","chicago":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” <i>Frontiers in Biology</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s11515-013-1279-6\">https://doi.org/10.1007/s11515-013-1279-6</a>.","ista":"Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568.","mla":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” <i>Frontiers in Biology</i>, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:<a href=\"https://doi.org/10.1007/s11515-013-1279-6\">10.1007/s11515-013-1279-6</a>.","ieee":"S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” <i>Frontiers in Biology</i>, vol. 8, no. 6. Springer, pp. 557–568, 2013."},"language":[{"iso":"eng"}],"issue":"6","abstract":[{"lang":"eng","text":"MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools."}],"type":"journal_article","_id":"2303","date_published":"2013-09-03T00:00:00Z","doi":"10.1007/s11515-013-1279-6","scopus_import":1,"month":"09","publication_status":"published","quality_controlled":"1","publication":"Frontiers in Biology","intvolume":"         8"},{"volume":43,"acknowledgement":"This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria).","date_created":"2018-12-11T11:56:53Z","year":"2013","page":"43 - 50","oa_version":"None","author":[{"last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"}],"publist_id":"4623","status":"public","department":[{"_id":"HeEd"}],"title":"Van der Corput sequences and linear permutations","date_updated":"2021-01-12T06:56:39Z","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","citation":{"short":"F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50.","ama":"Pausinger F. Van der Corput sequences and linear permutations. <i>Electronic Notes in Discrete Mathematics</i>. 2013;43:43-50. doi:<a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">10.1016/j.endm.2013.07.008</a>","chicago":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">https://doi.org/10.1016/j.endm.2013.07.008</a>.","apa":"Pausinger, F. (2013). Van der Corput sequences and linear permutations. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">https://doi.org/10.1016/j.endm.2013.07.008</a>","ista":"Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50.","mla":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 43, Elsevier, 2013, pp. 43–50, doi:<a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">10.1016/j.endm.2013.07.008</a>.","ieee":"F. Pausinger, “Van der Corput sequences and linear permutations,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 43. Elsevier, pp. 43–50, 2013."},"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter."}],"date_published":"2013-09-05T00:00:00Z","doi":"10.1016/j.endm.2013.07.008","_id":"2304","month":"09","scopus_import":1,"quality_controlled":"1","publication_status":"published","intvolume":"        43","publication":"Electronic Notes in Discrete Mathematics"},{"related_material":{"record":[{"relation":"later_version","id":"1294","status":"public"}]},"scopus_import":1,"abstract":[{"text":"We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time.","lang":"eng"}],"day":"01","citation":{"ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” in <i>28th Annual ACM/IEEE Symposium</i>, New Orleans, LA, United States, 2013, pp. 331–340.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>28th Annual ACM/IEEE Symposium</i>, IEEE, 2013, pp. 331–40, doi:<a href=\"https://doi.org/10.1109/LICS.2013.39\">10.1109/LICS.2013.39</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” In <i>28th Annual ACM/IEEE Symposium</i>, 331–40. 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Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013.","chicago":"Danowski, Patrick, and Adrian Pohl. <i>(Open) Linked Data in Bibliotheken</i>. Vol. 50. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/9783110278736\">https://doi.org/10.1515/9783110278736</a>.","ama":"Danowski P, Pohl A. <i>(Open) Linked Data in Bibliotheken</i>. Vol 50. De Gruyter; 2013. doi:<a href=\"https://doi.org/10.1515/9783110278736\">10.1515/9783110278736</a>","ista":"Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p.","apa":"Danowski, P., &#38; Pohl, A. (2013). <i>(Open) Linked Data in Bibliotheken</i> (Vol. 50). De Gruyter. <a href=\"https://doi.org/10.1515/9783110278736\">https://doi.org/10.1515/9783110278736</a>","mla":"Danowski, Patrick, and Adrian Pohl. <i>(Open) Linked Data in Bibliotheken</i>. Vol. 50, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/9783110278736\">10.1515/9783110278736</a>.","ieee":"P. Danowski and A. Pohl, <i>(Open) Linked Data in Bibliotheken</i>, vol. 50. De Gruyter, 2013."},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"ger","text":"Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut 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The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.","lang":"eng"}],"citation":{"mla":"Henzinger, Thomas A., and Jan Otop. <i>From Model Checking to Model Measuring</i>. Vol. 8052, Springer, 2013, pp. 273–87, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>.","ieee":"T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013.","short":"T.A. Henzinger, J. Otop, 8052 (2013) 273–287.","ama":"Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>","apa":"Henzinger, T. A., &#38; Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>","chicago":"Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>.","ista":"Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287."},"day":"01","pubrep_id":"129","publisher":"Springer","date_updated":"2023-02-23T12:25:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["005","000"],"title":"From model checking to model measuring","status":"public","page":"273 - 287","date_created":"2018-12-11T11:57:00Z","year":"2013","volume":8052},{"title":"Aspect-oriented linearizability proofs","ddc":["000","004"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2023-02-23T10:16:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"197","volume":8052,"year":"2013","date_created":"2018-12-11T11:57:01Z","page":"242 - 256","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"status":"public","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"1832","relation":"later_version"}]},"scopus_import":1,"day":"01","citation":{"ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","mla":"Henzinger, Thomas A., et al. <i>Aspect-Oriented Linearizability Proofs</i>. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>.","ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256.","ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>","apa":"Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>.","short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256."},"abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof.","lang":"eng"}],"file":[{"file_size":337059,"creator":"system","relation":"main_file","file_id":"4721","date_created":"2018-12-12T10:08:58Z","access_level":"open_access","checksum":"bdbb520de91751fe0136309ad4ef67e4","content_type":"application/pdf","file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","date_updated":"2020-07-14T12:45:39Z"}],"ec_funded":1,"department":[{"_id":"ToHe"}],"series_title":"Lecture Notes in Computer Science","publist_id":"4598","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"full_name":"Vafeiadis, Viktor","last_name":"Vafeiadis","first_name":"Viktor"}],"oa_version":"Submitted Version","_id":"2328","doi":"10.1007/978-3-642-40184-8_18","date_published":"2013-08-01T00:00:00Z","conference":{"end_date":"2013-08-30","location":"Buenos Aires, Argentina","name":"CONCUR: Concurrency Theory","start_date":"2013-08-27"},"month":"08","publication_status":"published","quality_controlled":"1","oa":1,"intvolume":"      8052","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:39Z","type":"conference"},{"volume":8052,"date_created":"2018-12-11T11:57:01Z","year":"2013","page":"500 - 515","main_file_link":[{"url":"http://arxiv.org/abs/1210.3141","open_access":"1"}],"status":"public","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"title":"Hyperplane separation technique for multidimensional mean-payoff games","date_updated":"2023-02-23T13:00:42Z","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"short":"K. Chatterjee, Y. Velner, 8052 (2013) 500–515.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>.","apa":"Chatterjee, K., &#38; Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>","ista":"Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515.","mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Hyperplane Separation Technique for Multidimensional Mean-Payoff Games</i>. Vol. 8052, Springer, 2013, pp. 500–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013."},"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 both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. 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. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.","lang":"eng"}],"related_material":{"record":[{"id":"717","relation":"later_version","status":"public"}]},"scopus_import":1,"series_title":"Lecture Notes in Computer Science","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"oa_version":"Preprint","publist_id":"4597","department":[{"_id":"KrCh"}],"ec_funded":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"type":"conference","date_published":"2013-08-01T00:00:00Z","doi":"10.1007/978-3-642-40184-8_35","_id":"2329","month":"08","arxiv":1,"conference":{"location":"Buenos Aires, Argentinia","end_date":"2013-08-30","start_date":"2013-08-27","name":"CONCUR: Concurrency Theory"},"external_id":{"arxiv":["1210.3141"]},"quality_controlled":"1","publication_status":"published","oa":1,"intvolume":"      8052"},{"intvolume":"         1","oa":1,"publication":"Genome Announcements","publication_status":"published","quality_controlled":"1","month":"06","_id":"2410","doi":"10.1128/genomeA.00216-13","date_published":"2013-06-13T00:00:00Z","issue":"3","type":"journal_article","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:40Z","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"file":[{"date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","content_type":"application/pdf","checksum":"0751ec74b695567e0cdf02aaf9c26829","access_level":"open_access","relation":"main_file","file_id":"5291","date_created":"2018-12-12T10:17:36Z","creator":"system","file_size":130026}],"publist_id":"4516","oa_version":"Published Version","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793"},{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stift","full_name":"Stift, Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","first_name":"Gertraud"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. "}],"citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>, vol. 1, no. 3, American Society for Microbiology, 2013, doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>.","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” <i>Genome Announcements</i>, vol. 1, no. 3. American Society for Microbiology, 2013.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3).","chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>. American Society for Microbiology, 2013. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>.","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. 2013;1(3). doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., &#38; Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>"},"day":"13","date_updated":"2021-01-12T06:57:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Microbiology","pubrep_id":"398","ddc":["576"],"title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","status":"public","year":"2013","date_created":"2018-12-11T11:57:30Z","volume":1},{"type":"journal_article","issue":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:40Z","publication":"BMC Evolutionary Biology","oa":1,"intvolume":"        13","quality_controlled":"1","publication_status":"published","month":"02","date_published":"2013-02-26T00:00:00Z","doi":"10.1186/1471-2148-13-54","_id":"2412","author":[{"first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne","last_name":"Kupczok"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","publist_id":"4514","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"JoBo"}],"file":[{"file_size":518729,"creator":"system","relation":"main_file","file_id":"5268","date_created":"2018-12-12T10:17:15Z","checksum":"029c7e0b198c19312b66ecce3cabb22f","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf"}],"abstract":[{"text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.","lang":"eng"}],"citation":{"ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. 2013;13(1):54-54. doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>.","apa":"Kupczok, A., &#38; Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>."},"day":"26","scopus_import":1,"has_accepted_license":"1","status":"public","page":"54 - 54","date_created":"2018-12-11T11:57:31Z","year":"2013","volume":13,"pubrep_id":"397","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:57:20Z","publisher":"BioMed Central","ddc":["576"],"title":"Probabilistic models for CRISPR spacer content evolution "},{"_id":"2413","doi":"10.1002/9783527671632.ch08","date_published":"2013-08-01T00:00:00Z","scopus_import":1,"month":"08","publication_status":"published","quality_controlled":"1","publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","day":"01","alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"citation":{"ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013.","mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>.","chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>.","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley-VCH; 2013. doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>","apa":"Valderrama, M., Botella Soler, V., &#38; Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer &#38; Z. Pesenson (Eds.), <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley-VCH. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013."},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783527671632"],"isbn":["9783527411986 "]},"abstract":[{"text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.","lang":"eng"}],"type":"book_chapter","title":"Neuronal oscillations scale up and scale down the brain dynamics ","department":[{"_id":"GaTk"}],"publisher":"Wiley-VCH","date_updated":"2021-01-12T06:57:20Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","editor":[{"first_name":"Misha","last_name":"Meyer","full_name":"Meyer, Misha"},{"first_name":"Z.","last_name":"Pesenson","full_name":"Pesenson, Z."}],"year":"2013","date_created":"2018-12-11T11:57:31Z","publist_id":"4513","status":"public","author":[{"first_name":"Mario","last_name":"Valderrama","full_name":"Valderrama, Mario"},{"first_name":"Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","orcid":"0000-0002-8790-1914","last_name":"Botella Soler"},{"full_name":"Le Van Quyen, Michel","last_name":"Le Van Quyen","first_name":"Michel"}],"oa_version":"None"},{"type":"conference","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:40Z","alternative_title":["LNCS"],"oa":1,"intvolume":"      8044","publication_status":"published","quality_controlled":"1","conference":{"start_date":"2013-07-13","name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","end_date":"2013-07-19"},"month":"07","_id":"2445","doi":"10.1007/978-3-642-39799-8_68","date_published":"2013-07-01T00:00:00Z","publist_id":"4458","author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach"}],"oa_version":"Submitted Version","ec_funded":1,"department":[{"_id":"ToHe"}],"file":[{"file_id":"5158","date_created":"2018-12-12T10:15:37Z","relation":"main_file","file_size":365548,"creator":"system","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","date_updated":"2020-07-14T12:45:40Z","checksum":"70c70ca5487faba82262c63e1b678a27","content_type":"application/pdf","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers."}],"citation":{"mla":"Cerny, Pavol, et al. <i>Efficient Synthesis for Concurrency by Semantics-Preserving Transformations</i>. Vol. 8044, Springer, 2013, pp. 951–67, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>.","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., &#38; Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>"},"day":"01","scopus_import":1,"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"1130","relation":"dissertation_contains"}]},"status":"public","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"page":"951 - 967","year":"2013","date_created":"2018-12-11T11:57:42Z","volume":8044,"publisher":"Springer","date_updated":"2023-09-07T11:57:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"199","ddc":["000","004"],"title":"Efficient synthesis for concurrency by semantics-preserving transformations"},{"ec_funded":1,"department":[{"_id":"KrCh"}],"series_title":"Lecture Notes in Computer Science","publist_id":"4457","oa_version":"Preprint","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Gaiser","full_name":"Gaiser, Andreas","first_name":"Andreas"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1304.5281"]},"arxiv":1,"conference":{"name":"CAV: Computer Aided Verification","start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19"},"month":"07","_id":"2446","date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-39799-8_37","oa":1,"intvolume":"      8044","publication_status":"published","quality_controlled":"1","alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2020-08-11T10:09:47Z","year":"2013","date_created":"2018-12-11T11:57:42Z","volume":8044,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"page":"559 - 575","scopus_import":1,"citation":{"short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","apa":"Chatterjee, K., Gaiser, A., &#38; Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>.","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>","mla":"Chatterjee, Krishnendu, et al. <i>Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis</i>. Vol. 8044, Springer, 2013, pp. 559–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>.","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013."},"day":"01","abstract":[{"text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements.","lang":"eng"}]},{"file":[{"file_name":"2013_CAV_Piskac.pdf","date_updated":"2020-07-14T12:45:41Z","checksum":"2e866932ab688f47ecd504acb4d5c7d4","access_level":"open_access","content_type":"application/pdf","file_id":"7859","date_created":"2020-05-15T11:13:01Z","relation":"main_file","creator":"dernst","file_size":309182}],"department":[{"_id":"ToHe"}],"series_title":"Lecture Notes in Computer Science","publist_id":"4456","author":[{"last_name":"Piskac","full_name":"Piskac, Ruzica","first_name":"Ruzica"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"},{"first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","last_name":"Zufferey"}],"oa_version":"Submitted Version","_id":"2447","date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-39799-8_54","conference":{"end_date":"2013-07-19","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","start_date":"2013-07-13"},"month":"07","publication_status":"published","quality_controlled":"1","oa":1,"intvolume":"      8044","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:41Z","type":"conference","article_processing_charge":"No","title":"Automating separation logic using SMT","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","date_updated":"2020-08-11T10:09:47Z","volume":8044,"year":"2013","date_created":"2018-12-11T11:57:43Z","page":"773 - 789","status":"public","has_accepted_license":"1","scopus_import":1,"day":"01","citation":{"mla":"Piskac, Ruzica, et al. <i>Automating Separation Logic Using SMT</i>. Vol. 8044, Springer, 2013, pp. 773–89, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>.","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","apa":"Piskac, R., Wies, T., &#38; Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>.","ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>"},"abstract":[{"text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n","lang":"eng"}]},{"publist_id":"4455","author":[{"first_name":"Estelle","last_name":"Remy","full_name":"Remy, Estelle"},{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Duque","full_name":"Duque, Paula","first_name":"Paula"}],"oa_version":"Submitted Version","ec_funded":1,"department":[{"_id":"JiFr"}],"issue":"10","type":"journal_article","language":[{"iso":"eng"}],"publication":"Plant Signaling & Behavior","oa":1,"intvolume":"         8","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["23857365"]},"month":"07","_id":"2448","date_published":"2013-07-10T00:00:00Z","doi":"10.4161/psb.25688","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"status":"public","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/","open_access":"1"}],"article_type":"original","year":"2013","date_created":"2018-12-11T11:57:43Z","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Taylor & Francis","date_updated":"2025-05-07T11:12:32Z","article_processing_charge":"No","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","pmid":1,"article_number":"e25688","abstract":[{"text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.","lang":"eng"}],"citation":{"short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013).","apa":"Remy, E., Baster, P., Friml, J., &#38; Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>","ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. 2013;8(10). doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>","chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>.","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling &#38; Behavior. 8(10), e25688.","mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10, e25688, Taylor &#38; Francis, 2013, doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>.","ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10. Taylor &#38; Francis, 2013."},"day":"10","scopus_import":"1"},{"page":"1849 - 1862","publist_id":"4454","status":"public","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Murguel","full_name":"Feraru, Murguel","last_name":"Feraru"},{"first_name":"Sibylle","full_name":"Hirsch, Sibylle","last_name":"Hirsch"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"full_name":"Nicuales, Claudiu","last_name":"Nicuales","first_name":"Claudiu"},{"first_name":"Jelle","full_name":"Van Leene, Jelle","last_name":"Van Leene"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":6,"year":"2013","date_created":"2018-12-11T11:57:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:57:33Z","publisher":"Cell Press","title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"issue":"6","abstract":[{"lang":"eng","text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. "}],"type":"journal_article","day":"01","citation":{"apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>","chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>.","ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. 2013;6(6):1849-1862. doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.","ieee":"T. Nodzyński <i>et al.</i>, “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” <i>Molecular Plant</i>, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013.","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>."},"publication_status":"published","quality_controlled":"1","publication":"Molecular Plant","intvolume":"         6","_id":"2449","doi":"10.1093/mp/sst044","date_published":"2013-11-01T00:00:00Z","scopus_import":1,"month":"11"},{"type":"journal_article","issue":"4","file_date_updated":"2020-07-14T12:45:41Z","language":[{"iso":"eng"}],"month":"07","date_published":"2013-07-01T00:00:00Z","doi":"10.1145/2461912.2461982","_id":"2466","intvolume":"        32","oa":1,"publication":"ACM Transactions on Graphics","quality_controlled":"1","publication_status":"published","author":[{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","publist_id":"4436","department":[{"_id":"ChWo"}],"file":[{"creator":"system","file_size":8601561,"file_id":"5279","date_created":"2018-12-12T10:17:25Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","date_updated":"2020-07-14T12:45:41Z"}],"day":"01","abstract":[{"text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.","lang":"eng"}],"scopus_import":"1","has_accepted_license":"1","date_created":"2018-12-11T11:57:50Z","year":"2013","volume":32,"status":"public","title":"Highly adaptive liquid simulations on tetrahedral meshes","article_processing_charge":"No","article_number":"103","pubrep_id":"605","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-11-19T11:56:45Z","ddc":["000"]}]