--- _id: '4468' abstract: - lang: eng text: Giotto is a high-level programming language for time-triggered control applications. The authors begin with a conceptual overview of its methodology, discuss the Giotto helicopter project, and summarize available Giotto implementations. acknowledgement: We thank Niklaus Wirth and Walter Schaufelberger for their advice and support of the reengineering effort of the ETH Zurich helicopter control system using Giotto. This research was supported in part by DARPA SEC grant F33615-C-98–3614, MARCO GSRC grant 98-DT-660, and AFOSR MURI grant F49620–00-1–0327. A preliminary version of this article appeared as [1]. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - first_name: Marco full_name: Sanvido, Marco last_name: Sanvido - first_name: Wolfgang full_name: Pree, Wolfgang last_name: Pree citation: ama: Henzinger TA, Kirsch C, Sanvido M, Pree W. From control models to real-time code using Giotto. IEEE Control Systems Magazine. 2003;23(1):50-64. doi:10.1109/MCS.2003.1172829 apa: Henzinger, T. A., Kirsch, C., Sanvido, M., & Pree, W. (2003). From control models to real-time code using Giotto. IEEE Control Systems Magazine. IEEE. https://doi.org/10.1109/MCS.2003.1172829 chicago: Henzinger, Thomas A, Christoph Kirsch, Marco Sanvido, and Wolfgang Pree. “From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems Magazine. IEEE, 2003. https://doi.org/10.1109/MCS.2003.1172829. ieee: T. A. Henzinger, C. Kirsch, M. Sanvido, and W. Pree, “From control models to real-time code using Giotto,” IEEE Control Systems Magazine, vol. 23, no. 1. IEEE, pp. 50–64, 2003. ista: Henzinger TA, Kirsch C, Sanvido M, Pree W. 2003. From control models to real-time code using Giotto. IEEE Control Systems Magazine. 23(1), 50–64. mla: Henzinger, Thomas A., et al. “From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems Magazine, vol. 23, no. 1, IEEE, 2003, pp. 50–64, doi:10.1109/MCS.2003.1172829. short: T.A. Henzinger, C. Kirsch, M. Sanvido, W. Pree, IEEE Control Systems Magazine 23 (2003) 50–64. date_created: 2018-12-11T12:09:00Z date_published: 2003-01-29T00:00:00Z date_updated: 2024-01-08T10:54:53Z day: '29' doi: 10.1109/MCS.2003.1172829 extern: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '01' oa_version: None page: 50 - 64 publication: IEEE Control Systems Magazine publication_identifier: issn: - '1066-033X ' publication_status: published publisher: IEEE publist_id: '260' quality_controlled: '1' scopus_import: '1' status: public title: From control models to real-time code using Giotto type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 23 year: '2003' ... --- _id: '4465' abstract: - lang: eng text: Giotto is a principled, tool-supported design methodology for implementing embedded control systems on platforms of possibly distributed sensors, actuators, CPUs, and networks. Giotto is based on the principle that time-triggered task invocations plus time-triggered mode switches can form the abstract essence of programming real-time control systems. Giotto consists of a programming language with a formal semantics, and a retargetable compiler and runtime library. Giotto supports the automation of control system design by strictly separating platform-independent functionality and timing concerns from platform-dependent scheduling and communication issues. The time-triggered predictability of Giotto makes it particularly suitable for safety-critical applications with hard real-time constraints. We illustrate the platform independence and time-triggered execution of Giotto by coordinating a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots. article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Benjamin full_name: Horowitz, Benjamin last_name: Horowitz - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch citation: ama: 'Henzinger TA, Horowitz B, Kirsch C. Embedded control systems development with Giotto. In: Software-Enabled Control: Information Technology for Dynamical Systems. Wiley-Blackwell; 2003:123-146. doi:10.1002/047172288X.ch8' apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Embedded control systems development with Giotto. In Software-Enabled Control: Information Technology for Dynamical Systems (pp. 123–146). Wiley-Blackwell. https://doi.org/10.1002/047172288X.ch8' chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Embedded Control Systems Development with Giotto.” In Software-Enabled Control: Information Technology for Dynamical Systems, 123–46. Wiley-Blackwell, 2003. https://doi.org/10.1002/047172288X.ch8.' ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Embedded control systems development with Giotto,” in Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.' ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003.Embedded control systems development with Giotto. In: Software-Enabled Control: Information Technology for Dynamical Systems. , 123–146.' mla: 'Henzinger, Thomas A., et al. “Embedded Control Systems Development with Giotto.” Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–46, doi:10.1002/047172288X.ch8.' short: 'T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.' date_created: 2018-12-11T12:08:59Z date_published: 2003-05-20T00:00:00Z date_updated: 2024-01-08T12:24:01Z day: '20' doi: 10.1002/047172288X.ch8 extern: '1' language: - iso: eng month: '05' oa_version: None page: 123 - 146 publication: 'Software-Enabled Control: Information Technology for Dynamical Systems' publication_identifier: isbn: - '9780471234364 ' publication_status: published publisher: Wiley-Blackwell publist_id: '262' quality_controlled: '1' status: public title: Embedded control systems development with Giotto type: book_chapter user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 year: '2003' ... --- _id: '4466' abstract: - lang: eng text: One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternationfree fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment. acknowledgement: This work was supported in part by NSF grant CCR-9988172, the AFOSR MURI grant F49620-00-1-0327, and a Microsoft Research Fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments of the mu-calculus. In: Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 2619. Springer; 2003:49-64. doi:10.1007/3-540-36577-X_5' apa: 'Henzinger, T. A., Kupferman, O., & Majumdar, R. (2003). On the universal and existential fragments of the mu-calculus. In Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 2619, pp. 49–64). Warsaw, Poland: Springer. https://doi.org/10.1007/3-540-36577-X_5' chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal and Existential Fragments of the Mu-Calculus.” In Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 2619:49–64. Springer, 2003. https://doi.org/10.1007/3-540-36577-X_5. ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential fragments of the mu-calculus,” in Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Warsaw, Poland, 2003, vol. 2619, pp. 49–64. ista: 'Henzinger TA, Kupferman O, Majumdar R. 2003. On the universal and existential fragments of the mu-calculus. Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 2619, 49–64.' mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of the Mu-Calculus.” Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 2619, Springer, 2003, pp. 49–64, doi:10.1007/3-540-36577-X_5. short: T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer, 2003, pp. 49–64. conference: end_date: 2003-04-11 location: Warsaw, Poland name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2003-04-07 date_created: 2018-12-11T12:08:59Z date_published: 2003-03-14T00:00:00Z date_updated: 2024-01-08T13:17:35Z day: '14' doi: 10.1007/3-540-36577-X_5 extern: '1' intvolume: ' 2619' language: - iso: eng month: '03' oa_version: None page: 49 - 64 publication: 'Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ' publication_identifier: isbn: - '9783540008989' publication_status: published publisher: Springer publist_id: '263' quality_controlled: '1' status: public title: On the universal and existential fragments of the mu-calculus type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2619 year: '2003' ... --- _id: '4467' abstract: - lang: eng text: 'BLAST (the Berkeley Lazy Abstraction Software verification Tool) is a verification system for checking safety properties of C programs using automatic property-driven construction and model checking of software abstractions. Blast implements an abstract-model check-refine loop to check for reachability of a specified label in the program. The abstract model is built on the fly using predicate abstraction. This model is then checked for reachability. If there is no (abstract) path to the specified error label, Blast reports that the system is safe and produces a succinct proof. Otherwise, it checks if the path is feasible using symbolic execution of the program. If the path is feasible, Blast outputs the path as an error trace, otherwise, it uses the infeasibility of the path to refine the abstract model. Blast short-circuits the loop from abstraction to verification to refinement, integrating the three steps tightly through “lazy abstraction” [5]. This integration can offer significant advantages in performance by avoiding the repetition of work from one iteration of the loop to the next. ' acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and CCR-9988172, the DARPA PCES grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660, and a Microsoft Research Fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Grégoire full_name: Sutre, Grégoire last_name: Sutre citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. Software verification with BLAST. In: Proceedings of the 10th International SPIN Workshop . Vol 2648. Springer; 2003:235-239. doi:10.1007/3-540-44829-2_17' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2003). Software verification with BLAST. In Proceedings of the 10th International SPIN Workshop (Vol. 2648, pp. 235–239). Portland, OR, USA: Springer. https://doi.org/10.1007/3-540-44829-2_17' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre. “Software Verification with BLAST.” In Proceedings of the 10th International SPIN Workshop , 2648:235–39. Springer, 2003. https://doi.org/10.1007/3-540-44829-2_17. ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Software verification with BLAST,” in Proceedings of the 10th International SPIN Workshop , Portland, OR, USA, 2003, vol. 2648, pp. 235–239. ista: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. 2003. Software verification with BLAST. Proceedings of the 10th International SPIN Workshop . SPIN: Model Checking Software, LNCS, vol. 2648, 235–239.' mla: Henzinger, Thomas A., et al. “Software Verification with BLAST.” Proceedings of the 10th International SPIN Workshop , vol. 2648, Springer, 2003, pp. 235–39, doi:10.1007/3-540-44829-2_17. short: T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the 10th International SPIN Workshop , Springer, 2003, pp. 235–239. conference: end_date: 2003-05-10 location: Portland, OR, USA name: 'SPIN: Model Checking Software' start_date: 2003-05-09 date_created: 2018-12-11T12:09:00Z date_published: 2003-04-28T00:00:00Z date_updated: 2024-01-08T14:05:29Z day: '28' doi: 10.1007/3-540-44829-2_17 extern: '1' intvolume: ' 2648' language: - iso: eng month: '04' oa_version: None page: 235 - 239 publication: 'Proceedings of the 10th International SPIN Workshop ' publication_identifier: isbn: - '9783540401179' publication_status: published publisher: Springer publist_id: '264' quality_controlled: '1' scopus_import: '1' status: public title: Software verification with BLAST type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2648 year: '2003' ... --- _id: '4463' abstract: - lang: eng text: We present an algorithm called TAR (“Thread-modular Abstraction Refinement”) for model checking safety properties of concurrent software. The TAR algorithm uses thread-modular assume-guarantee reasoning to overcome the exponential complexity in the control state of multithreaded programs. Thread modularity means that TAR explores the state space of one thread at a time, making assumptions about how the environment can interfere. The TAR algorithm uses counterexample-guided predicate-abstraction refinement to overcome the usually infinite complexity in the data state of C programs. A successive approximation scheme automatically infers the necessary precision on data variables as well as suitable environment assumptions. The scheme is novel in that transition relations are approximated from above, while at the same time environment assumptions are approximated from below. In our software verification tool BLAST we have implemented a fully automatic race checker for multithreaded C programs which is based on the TAR algorithm. This tool has verified a wide variety of commonly used locking idioms, including locking schemes that are not amenable to existing dynamic and static race checkers such as ERASER or WARLOCK. acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and CCR-0234690, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. Thread-modular abstraction refinement. In: Proceedings of the 15th International Conference on Computer Aided Verification. Vol 2725. Springer; 2003:262-274. doi:10.1007/978-3-540-45069-6_27' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Qadeer, S. (2003). Thread-modular abstraction refinement. In Proceedings of the 15th International Conference on Computer Aided Verification (Vol. 2725, pp. 262–274). Boulder, CO, USA: Springer. https://doi.org/10.1007/978-3-540-45069-6_27' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Shaz Qadeer. “Thread-Modular Abstraction Refinement.” In Proceedings of the 15th International Conference on Computer Aided Verification, 2725:262–74. Springer, 2003. https://doi.org/10.1007/978-3-540-45069-6_27. ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and S. Qadeer, “Thread-modular abstraction refinement,” in Proceedings of the 15th International Conference on Computer Aided Verification, Boulder, CO, USA, 2003, vol. 2725, pp. 262–274. ista: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. 2003. Thread-modular abstraction refinement. Proceedings of the 15th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 2725, 262–274.' mla: Henzinger, Thomas A., et al. “Thread-Modular Abstraction Refinement.” Proceedings of the 15th International Conference on Computer Aided Verification, vol. 2725, Springer, 2003, pp. 262–74, doi:10.1007/978-3-540-45069-6_27. short: T.A. Henzinger, R. Jhala, R. Majumdar, S. Qadeer, in:, Proceedings of the 15th International Conference on Computer Aided Verification, Springer, 2003, pp. 262–274. conference: end_date: 2003-07-12 location: Boulder, CO, USA name: 'CAV: Computer Aided Verification' start_date: 2003-07-08 date_created: 2018-12-11T12:08:59Z date_published: 2003-06-27T00:00:00Z date_updated: 2024-01-10T11:05:53Z day: '27' doi: 10.1007/978-3-540-45069-6_27 extern: '1' intvolume: ' 2725' language: - iso: eng month: '06' oa_version: None page: 262 - 274 publication: Proceedings of the 15th International Conference on Computer Aided Verification publication_identifier: isbn: - '9783540405245' publication_status: published publisher: Springer publist_id: '266' quality_controlled: '1' status: public title: Thread-modular abstraction refinement type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2725 year: '2003' ... --- _id: '4462' abstract: - lang: eng text: 'A major hurdle in the algorithmic verification and control of systems is the need to find suitable abstract models, which omit enough details to overcome the state-explosion problem, but retain enough details to exhibit satisfaction or controllability with respect to the specification. The paradigm of counterexample-guided abstraction refinement suggests a fully automatic way of finding suitable abstract models: one starts with a coarse abstraction, attempts to verify or control the abstract model, and if this attempt fails and the abstract counterexample does not correspond to a concrete counterexample, then one uses the spurious counterexample to guide the refinement of the abstract model. We present a counterexample-guided refinement algorithm for solving ω-regular control objectives. The main difficulty is that in control, unlike in verification, counterexamples are strategies in a game between system and controller. In the case that the controller has no choices, our scheme subsumes known counterexample-guided refinement algorithms for the verification of ω-regular specifications. Our algorithm is useful in all situations where ω-regular games need to be solved, such as supervisory control, sequential and program synthesis, and modular verification. The algorithm is fully symbolic, and therefore applicable also to infinite-state systems.' acknowledgement: This research was supported in part by the DARPA SEC grant F33615-C-98-3614, the ONR grant N00014-02-1-0671, and the NSF grants CCR-9988172, CCR-0085949, and CCR-0225610. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Henzinger TA, Jhala R, Majumdar R. Counterexample-guided control. In: Proceedings of the 30th International Colloquium on Automata, Languages and Programming. Vol 2719. Springer; 2003:886-902. doi:10.1007/3-540-45061-0_69' apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2003). Counterexample-guided control. In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (Vol. 2719, pp. 886–902). Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/3-540-45061-0_69' chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided Control.” In Proceedings of the 30th International Colloquium on Automata, Languages and Programming, 2719:886–902. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_69. ieee: T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided control,” in Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp. 886–902. ista: 'Henzinger TA, Jhala R, Majumdar R. 2003. Counterexample-guided control. Proceedings of the 30th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LNCS, vol. 2719, 886–902.' mla: Henzinger, Thomas A., et al. “Counterexample-Guided Control.” Proceedings of the 30th International Colloquium on Automata, Languages and Programming, vol. 2719, Springer, 2003, pp. 886–902, doi:10.1007/3-540-45061-0_69. short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 886–902. conference: end_date: 2003-07-04 location: Eindhoven, The Netherlands name: 'ICALP: Automata, Languages and Programming' start_date: 2003-06-30 date_created: 2018-12-11T12:08:58Z date_published: 2003-06-25T00:00:00Z date_updated: 2024-01-10T11:19:41Z day: '25' doi: 10.1007/3-540-45061-0_69 extern: '1' intvolume: ' 2719' language: - iso: eng month: '06' oa_version: None page: 886 - 902 publication: Proceedings of the 30th International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783540404934' publication_status: published publisher: Springer publist_id: '265' quality_controlled: '1' scopus_import: '1' status: public title: Counterexample-guided control type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2719 year: '2003' ... --- _id: '4464' abstract: - lang: eng text: We introduce the paradigm of schedule-carrying code (SCC). A hard real-time program can be executed on a given platform only if there exists a feasible schedule for the real-time tasks of the program. Traditionally, a scheduler determines the existence of a feasible schedule according to some scheduling strategy. With SCC, a compiler proves the existence of a feasible schedule by generating executable code that is attached to the program and represents its schedule. An SCC executable is a real-time program that carries its schedule as code, which is produced once and can be revalidated and executed with each use. We evaluate SCC both in theory and practice. In theory, we give two scenarios, of nonpreemptive and distributed scheduling for Giotto programs, where the generation of a feasible schedule is hard, while the validation of scheduling instructions that are attached to the programs is easy. In practice, we implement SCC and show that explicit scheduling instructions can reduce the scheduling overhead up to 35% and can provide an efficient, flexible, and verifiable means for compiling Giotto programs on complex architectures, such as the TTA. acknowledgement: This work was supported by the AFOSR MURI grant F49620-00-1-0327, the California MICRO grant 01-037, the DARPA grant F33615-C-98-3614, the MARCO grant 98-DT-660, and the NSF grants CCR-0208875, CCR-0085949, and CCR-0225610. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: 'Henzinger TA, Kirsch C, Matic S. Schedule-carrying code. In: Proceedings of the 3rd International Conference on Embedded Software. Vol 2855. ACM; 2003:241-256. doi:10.1007/978-3-540-45212-6_16' apa: 'Henzinger, T. A., Kirsch, C., & Matic, S. (2003). Schedule-carrying code. In Proceedings of the 3rd International Conference on Embedded Software (Vol. 2855, pp. 241–256). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_16' chicago: Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Schedule-Carrying Code.” In Proceedings of the 3rd International Conference on Embedded Software, 2855:241–56. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_16. ieee: T. A. Henzinger, C. Kirsch, and S. Matic, “Schedule-carrying code,” in Proceedings of the 3rd International Conference on Embedded Software, Philadelphia, PA, USA, 2003, vol. 2855, pp. 241–256. ista: 'Henzinger TA, Kirsch C, Matic S. 2003. Schedule-carrying code. Proceedings of the 3rd International Conference on Embedded Software. EMSOFT: Embedded Software , LNCS, vol. 2855, 241–256.' mla: Henzinger, Thomas A., et al. “Schedule-Carrying Code.” Proceedings of the 3rd International Conference on Embedded Software, vol. 2855, ACM, 2003, pp. 241–56, doi:10.1007/978-3-540-45212-6_16. short: T.A. Henzinger, C. Kirsch, S. Matic, in:, Proceedings of the 3rd International Conference on Embedded Software, ACM, 2003, pp. 241–256. conference: end_date: 2003-10-15 location: Philadelphia, PA, USA name: 'EMSOFT: Embedded Software ' start_date: 2003-10-13 date_created: 2018-12-11T12:08:59Z date_published: 2003-09-29T00:00:00Z date_updated: 2024-01-10T11:33:57Z day: '29' doi: 10.1007/978-3-540-45212-6_16 extern: '1' intvolume: ' 2855' language: - iso: eng month: '09' oa_version: None page: 241 - 256 publication: Proceedings of the 3rd International Conference on Embedded Software publication_identifier: isbn: - '9783540202233' publication_status: published publisher: ACM publist_id: '267' quality_controlled: '1' scopus_import: '1' status: public title: Schedule-carrying code type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2855 year: '2003' ... --- _id: '4460' abstract: - lang: eng text: "Symbolic model checking, which enables the automatic verification of large systems, proceeds by calculating expressions that represent state sets. Traditionally, symbolic model-checking tools are based on back- ward state traversal; their basic operation is the function pre, which, given a set of states, returns the set of all predecessor states. This is because specifiers usually employ formalisms with future-time modalities, which are naturally evaluated by iterating applications of pre. It has been shown experimentally that symbolic model checking can perform significantly better if it is based, instead, on forward state traversal; in this case, the basic operation is the function post, which, given a set of states, returns the set of all successor states. This is because forward state traversal can ensure that only parts of the state space that are reachable from an initial state and relevant for the satisfaction or violation of the specification are explored; that is, errors can be detected as soon as possible.\r\nIn this paper, we investigate which specifications can be checked by symbolic forward state traversal. We formulate the problems of symbolic backward and forward model checking by means of two μ-calculi. The pre-μ calculus is based on the pre operation, and the post-μ calculus is based on the post operation. These two μ-calculi induce query logics, which augment fixpoint expressions with a boolean emptiness query. Using query logics, we are able to relate and compare the symbolic backward and forward approaches. In particular, we prove that all ω-regular (linear-time) specifications can be expressed as post-μ queries, and therefore checked using symbolic forward state traversal. On the other hand, we show that there are simple branching-time specifications that cannot be checked in this way." acknowledgement: This research was supported in part by the SRC contract 99-TJ-683.003 and the NSF grant CCR-9988172. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: Henzinger TA, Kupferman O, Qadeer S. From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. 2003;23(3):303-327. doi:10.1023/A:1026228213080 apa: Henzinger, T. A., Kupferman, O., & Qadeer, S. (2003). From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. Springer. https://doi.org/10.1023/A:1026228213080 chicago: Henzinger, Thomas A, Orna Kupferman, and Shaz Qadeer. “From Pre-Historic to Post-Modern Symbolic Model Checking.” Formal Methods in System Design. Springer, 2003. https://doi.org/10.1023/A:1026228213080. ieee: T. A. Henzinger, O. Kupferman, and S. Qadeer, “From pre-historic to post-modern symbolic model checking,” Formal Methods in System Design, vol. 23, no. 3. Springer, pp. 303–327, 2003. ista: Henzinger TA, Kupferman O, Qadeer S. 2003. From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. 23(3), 303–327. mla: Henzinger, Thomas A., et al. “From Pre-Historic to Post-Modern Symbolic Model Checking.” Formal Methods in System Design, vol. 23, no. 3, Springer, 2003, pp. 303–27, doi:10.1023/A:1026228213080. short: T.A. Henzinger, O. Kupferman, S. Qadeer, Formal Methods in System Design 23 (2003) 303–327. date_created: 2018-12-11T12:08:58Z date_published: 2003-06-20T00:00:00Z date_updated: 2024-01-10T11:50:31Z day: '20' doi: 10.1023/A:1026228213080 extern: '1' intvolume: ' 23' issue: '3' language: - iso: eng month: '06' oa_version: None page: 303 - 327 publication: Formal Methods in System Design publication_identifier: issn: - 0925-9856 publication_status: published publisher: Springer publist_id: '268' quality_controlled: '1' scopus_import: '1' status: public title: From pre-historic to post-modern symbolic model checking type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 23 year: '2003' ... --- _id: '4469' abstract: - lang: eng text: Giotto provides an abstract programmer's model for the implementation of embedded control systems with hard real-time constraints. A typical control application consists of periodic software tasks together with a mode-switching logic for enabling and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations, actuator updates, and mode switches independent of any implementation platform. Giotto can be annotated with platform constraints such as task-to-host mappings, and task and communication schedules. The annotations are directives for the Giotto compiler, but they do not alter the functionality and timing of a Giotto program. By separating the platform-independent from the platform-dependent concerns, Giotto enables a great deal of flexibility in choosing control platforms as well as a great deal of automation in the validation and synthesis of control software. The time-triggered nature of Giotto achieves timing predictability, which makes Giotto particularly suitable for safety-critical applications. acknowledgement: The authors would like to thank R. Majumdar for implementing a prototype Giotto compiler for Lego Mindstorms robots. They would like to thank D. Derevyanko and W. Williams for building the Intel x86 robots; and E. Lee and X. Liu for help with implementing Giotto as a “model of computation” in Ptolemy II [26]. Finally, they would also like to thank M. Sanvido for his suggestions on the design of the Giotto drivers; and P. Griffiths for implementing the functionality code of the electronic throttle controller. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Benjamin full_name: Horowitz, Benjamin last_name: Horowitz - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch citation: ama: 'Henzinger TA, Horowitz B, Kirsch C. Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. 2003;91(1):84-99. doi:10.1109/JPROC.2002.805825' apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. IEEE. https://doi.org/10.1109/JPROC.2002.805825' chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Giotto: A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE. IEEE, 2003. https://doi.org/10.1109/JPROC.2002.805825.' ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Giotto: A time-triggered language for embedded programming,” Proceedings of the IEEE, vol. 91, no. 1. IEEE, pp. 84–99, 2003.' ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003. Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. 91(1), 84–99.' mla: 'Henzinger, Thomas A., et al. “Giotto: A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE, vol. 91, no. 1, IEEE, 2003, pp. 84–99, doi:10.1109/JPROC.2002.805825.' short: T.A. Henzinger, B. Horowitz, C. Kirsch, Proceedings of the IEEE 91 (2003) 84–99. date_created: 2018-12-11T12:09:00Z date_published: 2003-01-29T00:00:00Z date_updated: 2024-01-10T11:55:18Z day: '29' doi: 10.1109/JPROC.2002.805825 extern: '1' intvolume: ' 91' issue: '1' language: - iso: eng month: '01' oa_version: None page: 84 - 99 publication: Proceedings of the IEEE publication_identifier: issn: - '0018-9219 ' publication_status: published publisher: IEEE publist_id: '261' quality_controlled: '1' scopus_import: '1' status: public title: 'Giotto: A time-triggered language for embedded programming' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 91 year: '2003' ... --- _id: '4338' abstract: - lang: eng text: 'Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 × 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.' acknowledgement: "We thank G. Mara and T. Galbena for enthusiastic field\r\nassistance, A. Hofmann and R. Sieglstetter for access to their\r\nunpublished data, B. Fo¨rg-Brey and G. Praetzel for help in\r\nthe lab. Helpful comments on a previous version of the man-\r\nuscript were provided by R. Ennos, J. Szymura, F. Balloux,\r\nJ. Bridle, L. Kruuk, F. Bonhomme, M. Arnold, and two anon-\r\nymous reviewers. We also thank A. Pinggera for providing\r\nthe cover illustration. This work was supported by Natural\r\nEnvironment Research Council studentships to THV and TRS\r\nand Deutsche Forschungsgemeinschaft grant Nu 51/2-1 to BN." article_processing_charge: No article_type: original author: - first_name: Timothy full_name: Vines, Timothy last_name: Vines - first_name: S C full_name: Kohler, S C last_name: Kohler - first_name: M full_name: Thiel, M last_name: Thiel - first_name: Ioan full_name: Ghira, Ioan last_name: Ghira - first_name: T R full_name: Sands, T R last_name: Sands - first_name: Catriona full_name: Maccallum, Catriona last_name: Maccallum - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger citation: ama: Vines T, Kohler SC, Thiel M, et al. On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. 2003;57(8):1876-1888. doi:10.1111/j.0014-3820.2003.tb00595.x apa: Vines, T., Kohler, S. C., Thiel, M., Ghira, I., Sands, T. R., Maccallum, C., … Nürnberger, B. (2003). On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x chicago: Vines, Timothy, S C Kohler, M Thiel, Ioan Ghira, T R Sands, Catriona Maccallum, Nicholas H Barton, and Beate Nürnberger. “On the Maintenance of Reproductive Isolation in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution. Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x. ieee: T. Vines et al., “On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata,” Evolution, vol. 57, no. 8. Wiley-Blackwell, pp. 1876–1888, 2003. ista: Vines T, Kohler SC, Thiel M, Ghira I, Sands TR, Maccallum C, Barton NH, Nürnberger B. 2003. On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. 57(8), 1876–1888. mla: Vines, Timothy, et al. “On the Maintenance of Reproductive Isolation in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution, vol. 57, no. 8, Wiley-Blackwell, 2003, pp. 1876–88, doi:10.1111/j.0014-3820.2003.tb00595.x. short: T. Vines, S.C. Kohler, M. Thiel, I. Ghira, T.R. Sands, C. Maccallum, N.H. Barton, B. Nürnberger, Evolution 57 (2003) 1876–1888. date_created: 2018-12-11T12:08:20Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-01-23T09:16:43Z day: '01' doi: 10.1111/j.0014-3820.2003.tb00595.x extern: '1' intvolume: ' 57' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1876 - 1888 publication: Evolution publication_identifier: issn: - 0014-3820 publication_status: published publisher: Wiley-Blackwell publist_id: '1692' quality_controlled: '1' scopus_import: '1' status: public title: On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 57 year: '2003' ... --- _id: '4350' abstract: - lang: eng text: 'The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.' acknowledgement: "We thank Lou Densmore and Herb Dessauer for crocodylian tissue\r\nsamples. Dave Swofford, Jim Wilgenbusch, and Kevin de Queiroz gave\r\nus much helpful advice. Dave also allowed us to use an experimental\r\nversion of PAUP∗ with partitioned likelihood, and Jim also provided\r\nprograms to make possible partitioned model KH tests. Chris Brochu\r\nand Lou Densmore sent us preprints of their papers in press, and Chris\r\nprovided an unpublished version of his morphological data set. Allan\r\nBaker, Lou Densmore, and an anonymous reviewer provided useful\r\ncomments on the manuscript. We especially wish to acknowledge Chris\r\nBrochu’s help; although we remain in disagreement on many points,\r\nhis comments on several previous drafts have greatly improved this\r\npaper." article_processing_charge: No article_type: original author: - first_name: John full_name: Harshman, John last_name: Harshman - first_name: Christopher full_name: Huddleston, Christopher last_name: Huddleston - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Thomas full_name: Parsons, Thomas last_name: Parsons - first_name: Michael full_name: Braun, Michael last_name: Braun citation: ama: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402. doi:10.1080/10635150390197028' apa: 'Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M. (2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150390197028' chicago: 'Harshman, John, Christopher Huddleston, Jonathan P Bollback, Thomas Parsons, and Michael Braun. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390197028.' ieee: 'J. Harshman, C. Huddleston, J. P. Bollback, T. Parsons, and M. Braun, “True and false gharials: A nuclear gene phylogeny of crocodylia,” Systematic Biology, vol. 52, no. 3. Oxford University Press, pp. 386–402, 2003.' ista: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. 2003. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 52(3), 386–402.' mla: 'Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press, 2003, pp. 386–402, doi:10.1080/10635150390197028.' short: J. Harshman, C. Huddleston, J.P. Bollback, T. Parsons, M. Braun, Systematic Biology 52 (2003) 386–402. date_created: 2018-12-11T12:08:24Z date_published: 2003-06-01T00:00:00Z date_updated: 2024-01-23T08:53:58Z day: '01' doi: 10.1080/10635150390197028 extern: '1' external_id: pmid: - ' 12775527' intvolume: ' 52' issue: '3' language: - iso: eng month: '06' oa_version: None page: 386 - 402 pmid: 1 publication: Systematic Biology publication_identifier: issn: - '0039-7989 ' publication_status: published publisher: Oxford University Press publist_id: '1110' quality_controlled: '1' scopus_import: '1' status: public title: 'True and false gharials: A nuclear gene phylogeny of crocodylia' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 52 year: '2003' ... --- _id: '4348' abstract: - lang: eng text: Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation. acknowledgement: "We thank J. Kohn, D. Stern, and M. Hart for sending the alignments\r\nused in this study. J.P.H. was supported by NSF grants DEB-0075406\r\nand MCB-0075404. R.N. was supported by NSF grant DEB-0089487." article_processing_charge: No article_type: original author: - first_name: John full_name: Huelsenbeck, John last_name: Huelsenbeck - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780 apa: Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping of morphological characters. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150390192780 chicago: Huelsenbeck, John, Rasmus Nielsen, and Jonathan P Bollback. “Stochastic Mapping of Morphological Characters.” Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390192780. ieee: J. Huelsenbeck, R. Nielsen, and J. P. Bollback, “Stochastic mapping of morphological characters,” Systematic Biology, vol. 52, no. 2. Oxford University Press, pp. 131–158, 2003. ista: Huelsenbeck J, Nielsen R, Bollback JP. 2003. Stochastic mapping of morphological characters. Systematic Biology. 52(2), 131–158. mla: Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.” Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp. 131–58, doi:10.1080/10635150390192780. short: J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158. date_created: 2018-12-11T12:08:24Z date_published: 2003-04-01T00:00:00Z date_updated: 2024-01-23T09:10:59Z day: '01' doi: 10.1080/10635150390192780 extern: '1' external_id: pmid: - '12746144 ' intvolume: ' 52' issue: '2' language: - iso: eng month: '04' oa_version: None page: 131 - 158 pmid: 1 publication: Systematic Biology publication_identifier: issn: - '0039-7989 ' publication_status: published publisher: Oxford University Press publist_id: '1111' quality_controlled: '1' scopus_import: '1' status: public title: Stochastic mapping of morphological characters type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 52 year: '2003' ... --- _id: '4254' abstract: - lang: eng text: Chromosomal rearrangements can promote reproductive isolation by reducing recombination along a large section of the genome. We model the effects of the genetic barrier to gene flow caused by a chromosomal rearrangement on the rate of accumulation of postzygotic isolation genes in parapatry. We find that, if reproductive isolation is produced by the accumulation in parapatry of sets of alleles compatible within but incompatible across species, chromosomal rearrangements are far more likely to favor it than classical genetic barriers without chromosomal changes. New evidence of the role of chromosomal rearrangements in parapatric speciation suggests that postzygotic isolation is often due to the accumulation of such incompatibilities. The model makes testable qualitative predictions about the genetic signature of speciation. acknowledgement: "We thank A. Andrés, C. Bartolomé, J. Bertranpetit, F. Calafell, B. Charlesworth, D. Charlesworth, F. Depaulis, S. Gavrilets, T. Johnson, P. Keightley, M. Kirkpatrik, A. Kondrashov, H. Laayouni, X. Maside, M. Noor, D. Ortiz-Barrientos,\r\nL. Rieseberg, and T. Vines for valuable discussion and criticism. The detailed comments of B. Charlesworth, D. Charlesworth, and F. Depaulis greatly improved the original manuscript. AN is particularly grateful to X. Maside, who was a patient guide through the jungle of speciation. This work was supported by the NERC grant GR3/11635 (United Kingdom). AN is funded by the Ramón y Cajal Program (Spain)." article_processing_charge: No article_type: original author: - first_name: Arcadio full_name: Navarro, Arcadio last_name: Navarro - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Navarro A, Barton NH. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. 2003;57(3):447-459. doi:10.1111/j.0014-3820.2003.tb01537.x' apa: 'Navarro, A., & Barton, N. H. (2003). Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x' chicago: 'Navarro, Arcadio, and Nicholas H Barton. “Accumulating Postzygotic Isolation Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x.' ieee: 'A. Navarro and N. H. Barton, “Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation,” Evolution; International Journal of Organic Evolution, vol. 57, no. 3. Wiley-Blackwell, pp. 447–459, 2003.' ista: 'Navarro A, Barton NH. 2003. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. 57(3), 447–459.' mla: 'Navarro, Arcadio, and Nicholas H. Barton. “Accumulating Postzygotic Isolation Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International Journal of Organic Evolution, vol. 57, no. 3, Wiley-Blackwell, 2003, pp. 447–59, doi:10.1111/j.0014-3820.2003.tb01537.x.' short: A. Navarro, N.H. Barton, Evolution; International Journal of Organic Evolution 57 (2003) 447–459. date_created: 2018-12-11T12:07:52Z date_published: 2003-03-01T00:00:00Z date_updated: 2024-01-23T10:21:57Z day: '01' doi: 10.1111/j.0014-3820.2003.tb01537.x extern: '1' external_id: pmid: - '12703935 ' intvolume: ' 57' issue: '3' language: - iso: eng month: '03' oa_version: None page: 447 - 459 pmid: 1 publication: Evolution; International Journal of Organic Evolution publication_identifier: issn: - 0014-3820 publication_status: published publisher: Wiley-Blackwell publist_id: '1840' quality_controlled: '1' scopus_import: '1' status: public title: 'Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 57 year: '2003' ... --- _id: '4257' abstract: - lang: eng text: Variation within a species may be structured both geographically and by genetic background. We review the effects of such structuring on neutral variants, using a framework based on the coalescent process. Short-term effects of sex differences and age structure can be averaged out using fast timescale approximations, allowing a simple general treatment of effective population size and migration. We consider the effects of geographic structure on variation within and between local populations, first in general terms, and then for specific migration models. We discuss the close parallels between geographic structure and stable types of genetic structure caused by selection, including balancing selection and background selection. The effects of departures from stability, such as selective sweeps and population bottlenecks, are also described. Methods for distinguishing population history from the effects of ongoing gene flow are discussed. We relate the theoretical results to observed patterns of variation in natural populations. article_processing_charge: No article_type: original author: - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - first_name: Deborah full_name: Charlesworth, Deborah last_name: Charlesworth - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Charlesworth B, Charlesworth D, Barton NH. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. 2003;34:99-125. doi:10.1146/annurev.ecolsys.34.011802.132359 apa: Charlesworth, B., Charlesworth, D., & Barton, N. H. (2003). The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. Annual Reviews. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359 chicago: Charlesworth, Brian, Deborah Charlesworth, and Nicholas H Barton. “The Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review of Ecology and Systematics. Annual Reviews, 2003. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359. ieee: B. Charlesworth, D. Charlesworth, and N. H. Barton, “The effects of genetic and geographic structure on neutral variation,” Annual Review of Ecology and Systematics, vol. 34. Annual Reviews, pp. 99–125, 2003. ista: Charlesworth B, Charlesworth D, Barton NH. 2003. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. 34, 99–125. mla: Charlesworth, Brian, et al. “The Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review of Ecology and Systematics, vol. 34, Annual Reviews, 2003, pp. 99–125, doi:10.1146/annurev.ecolsys.34.011802.132359. short: B. Charlesworth, D. Charlesworth, N.H. Barton, Annual Review of Ecology and Systematics 34 (2003) 99–125. date_created: 2018-12-11T12:07:53Z date_published: 2003-11-01T00:00:00Z date_updated: 2024-01-23T10:15:44Z day: '01' doi: 10.1146/annurev.ecolsys.34.011802.132359 extern: '1' intvolume: ' 34' language: - iso: eng month: '11' oa_version: None page: 99 - 125 publication: Annual Review of Ecology and Systematics publication_identifier: issn: - 1543-592X publication_status: published publisher: Annual Reviews publist_id: '1839' quality_controlled: '1' status: public title: The effects of genetic and geographic structure on neutral variation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 34 year: '2003' ... --- _id: '4256' abstract: - lang: eng text: Artificial Life models may shed new light on the long-standing challenge for evolutionary biology of explaining the origins of complex organs. Real progress on this issue, however, requires Artificial Life researchers to take seriously the tools and insights from population genetics. article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Willem full_name: Zuidema, Willem last_name: Zuidema citation: ama: Barton NH, Zuidema W. The erratic path towards complexity. Current Biology. 2003;13(16):R649-R651. doi:10.1016/S0960-9822(03)00573-6 apa: Barton, N. H., & Zuidema, W. (2003). The erratic path towards complexity. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00573-6 chicago: Barton, Nicholas H, and Willem Zuidema. “The Erratic Path towards Complexity.” Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00573-6. ieee: N. H. Barton and W. Zuidema, “The erratic path towards complexity,” Current Biology, vol. 13, no. 16. Cell Press, pp. R649–R651, 2003. ista: Barton NH, Zuidema W. 2003. The erratic path towards complexity. Current Biology. 13(16), R649–R651. mla: Barton, Nicholas H., and Willem Zuidema. “The Erratic Path towards Complexity.” Current Biology, vol. 13, no. 16, Cell Press, 2003, pp. R649–51, doi:10.1016/S0960-9822(03)00573-6. short: N.H. Barton, W. Zuidema, Current Biology 13 (2003) R649–R651. date_created: 2018-12-11T12:07:53Z date_published: 2003-08-19T00:00:00Z date_updated: 2024-01-23T09:41:33Z day: '19' doi: 10.1016/S0960-9822(03)00573-6 extern: '1' intvolume: ' 13' issue: '16' language: - iso: eng month: '08' oa_version: Published Version page: R649 - R651 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1838' quality_controlled: '1' scopus_import: '1' status: public title: The erratic path towards complexity type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2003' ... --- _id: '4255' abstract: - lang: eng text: 'Humans and their closest evolutionary relatives, the chimpanzees, differ in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages. ' article_processing_charge: No article_type: original author: - first_name: Arcadio full_name: Navarro, Arcadio last_name: Navarro - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Navarro A, Barton NH. Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. 2003;300(5617):321-324. doi:10.1126/science.1080600 apa: Navarro, A., & Barton, N. H. (2003). Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1080600 chicago: Navarro, Arcadio, and Nicholas H Barton. “Chromosomal Speciation and Molecular Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science. American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1080600 . ieee: A. Navarro and N. H. Barton, “Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes,” Science, vol. 300, no. 5617. American Association for the Advancement of Science, pp. 321–324, 2003. ista: Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. 300(5617), 321–324. mla: Navarro, Arcadio, and Nicholas H. Barton. “Chromosomal Speciation and Molecular Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science, vol. 300, no. 5617, American Association for the Advancement of Science, 2003, pp. 321–24, doi:10.1126/science.1080600 . short: A. Navarro, N.H. Barton, Science 300 (2003) 321–324. date_created: 2018-12-11T12:07:53Z date_published: 2003-04-11T00:00:00Z date_updated: 2024-02-26T13:37:51Z day: '11' doi: '10.1126/science.1080600 ' extern: '1' external_id: pmid: - ' 12690198' intvolume: ' 300' issue: '5617' language: - iso: eng month: '04' oa_version: None page: 321 - 324 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science publist_id: '1841' quality_controlled: '1' scopus_import: '1' status: public title: Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 300 year: '2003' ... --- _id: '4146' abstract: - lang: eng text: During vertebrate gastrulation, highly coordinated cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. In zebrafish, silberblick (slb)/wnt11 regulates normal gastrulation movements by activating a signalling pathway similar to the Frizzled-signalling pathway, which establishes epithelial planar cell polarity (PCP) in Drosophila. However, the cellular mechanisms by which slb/wnt11 functions during zebrafish gastrulation are still unclear. Using high-resolution two-photon confocal imaging followed by computer-assisted reconstruction and motion analysis, we have analysed the movement and morphology of individual cells in three dimensions during the course of gastrulation. We show that in slb-mutant embryos, hypoblast cells within the forming germ ring have slower, less directed migratory movements at the onset of gastrulation. These aberrant cell movements are accompanied by defects in the orientation of cellular processes along the individual movement directions of these cells. We conclude that slb/wnt11-mediated orientation of cellular processes plays a role in facilitating and stabilising movements of hypoblast cells in the germ ring, thereby pointing at a novel function of the slb/wnt11 signalling pathway for the regulation of migratory cell movements at early stages of gastrulation. acknowledgement: 'We thank Jennifer Geiger, Mathias Köppen, Christian Dahmann and Marcos Gonzalez-Gaitan for helpful comments on earlier versions of this manuscript,Beate Kilian for technical assistance, Ugur Yalcin, Katrin Anczok and Viktor Schnabel for help with the image analysis, Vinzenz Link for programming Excel Macros and Harald Brush-Janovjak for extensive reviews of the statistics part of this work. We are grateful to Kurt Anderson and Jan Peychl for help with the confocal microscopy. P.J.H., E.V. and D.R.S. are supported by NIH grant HD-18577, The W.M Keck Foundation and the Developmental Studies Hybridoma Bank(DSHB), P.J.H. by The American Cancer Society (grant # PF-01-110-01-CSM),M.L.C. and S.W.W. by the Wellcome Trust, M.T. by an MRC Career Development Award, and F.U. and C.P.H. by an Emmy-Noether-Fellowship from the DFG.' article_processing_charge: No article_type: original author: - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Miguel full_name: Concha, Miguel last_name: Concha - first_name: Paul full_name: Heid, Paul last_name: Heid - first_name: Ed full_name: Voss, Ed last_name: Voss - first_name: Sabine full_name: Witzel, Sabine last_name: Witzel - first_name: Henry full_name: Roehl, Henry last_name: Roehl - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson - first_name: Richard full_name: Adams, Richard last_name: Adams - first_name: David full_name: Soll, David last_name: Soll - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Ulrich F, Concha M, Heid P, et al. Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. 2003;130(22):5375-5384. doi:10.1242/dev.00758 apa: Ulrich, F., Concha, M., Heid, P., Voss, E., Witzel, S., Roehl, H., … Heisenberg, C.-P. J. (2003). Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.00758 chicago: Ulrich, Florian, Miguel Concha, Paul Heid, Ed Voss, Sabine Witzel, Henry Roehl, Masazumi Tada, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and Morphogenesis at the Onset of Zebrafish Gastrulation.” Development. Company of Biologists, 2003. https://doi.org/10.1242/dev.00758. ieee: F. Ulrich et al., “Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation,” Development, vol. 130, no. 22. Company of Biologists, pp. 5375–5384, 2003. ista: Ulrich F, Concha M, Heid P, Voss E, Witzel S, Roehl H, Tada M, Wilson S, Adams R, Soll D, Heisenberg C-PJ. 2003. Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. 130(22), 5375–5384. mla: Ulrich, Florian, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and Morphogenesis at the Onset of Zebrafish Gastrulation.” Development, vol. 130, no. 22, Company of Biologists, 2003, pp. 5375–84, doi:10.1242/dev.00758. short: F. Ulrich, M. Concha, P. Heid, E. Voss, S. Witzel, H. Roehl, M. Tada, S. Wilson, R. Adams, D. Soll, C.-P.J. Heisenberg, Development 130 (2003) 5375–5384. date_created: 2018-12-11T12:07:13Z date_published: 2003-11-15T00:00:00Z date_updated: 2024-02-27T10:14:21Z day: '15' doi: 10.1242/dev.00758 extern: '1' external_id: pmid: - ' PMC1414802' intvolume: ' 130' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1414802/ month: '11' oa: 1 oa_version: None page: 5375 - 5384 pmid: 1 publication: Development publication_identifier: issn: - 1011-6370 publication_status: published publisher: Company of Biologists publist_id: '1975' quality_controlled: '1' scopus_import: '1' status: public title: Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 130 year: '2003' ... --- _id: '4169' abstract: - lang: eng text: 'Background: During vertebrate gastrulation, cell polarization and migration are core components in the cellular rearrangements that lead to the formation of the three germ layers, ectoderm, mesoderm, and endoderm. Previous studies have implicated the Wnt/planar cell polarity (PCP) signaling pathway in controlling cell morphology and movement during gastrulation. However, cell polarization and directed cell migration are reduced but not completely abolished in the absence of Wnt/PCP signals; this observation indicates that other signaling pathways must be involved. Results: We show that Phosphoinositide 3-Kinases (PI3Ks) are required at the onset of zebrafish gastrulation in mesendodermal cells for process formation and cell polarization. Platelet Derived Growth Factor (PDGF) functions upstream of PI3K, while Protein Kinase B (PKB), a downstream effector of PI3K activity, localizes to the leading edge of migrating mesendodermal cells. In the absence of PI3K activity, PKB localization and cell polarization are strongly reduced in mesendodermal cells and are followed by slower but still highly coordinated and directed movements of these cells. Conclusions: We have identified a novel role of a signaling pathway comprised of PDGF, PI3K, and PKB in the control of morphogenetic cell movements during gastrulation. Furthermore, our findings provide insight into the relationship between cell polarization and directed cell migration at the onset of zebrafish gastrulation.' acknowledgement: 'We would like to thank Jennifer Geiger, Juan Hurl& Hannu Mansu-koski, Florian Raible, Marino Zerial, Steve Wilson, and Kurt Anderson for critical reading of earlier versions of this manuscript. We thank Erez Raz, Bart Vanhaesebroeck, and Lukas Roth for sending us the pCS2-PH-GFP-nos, the p1IOCAAX, and the pCS2-actin-GFP constructs, respectively. We are grateful to Marino Zerial and his lab for encouraging us to start this work and providing us with the dnP13K construct and to Florian Ulrich and Franziska Friedrich for help with the confocal microscope and artwork, respectively. We thank Gunter Junghanns and Evelyn Lehmann for excellent fish care. C.-P.H. is supported by an Emmy-Noother-Fellowship from the Deutsche Forschungsgemeinschaft. ' article_processing_charge: No article_type: original author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Beate full_name: Kilian, Beate last_name: Kilian - first_name: Joanne full_name: Chan, Joanne last_name: Chan - first_name: Peter full_name: Bayliss, Peter last_name: Bayliss - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. 2003;13(15):1279-1289. doi:10.1016/S0960-9822(03)00505-0 apa: Montero, J., Kilian, B., Chan, J., Bayliss, P., & Heisenberg, C.-P. J. (2003). Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00505-0 chicago: Montero, Juan, Beate Kilian, Joanne Chan, Peter Bayliss, and Carl-Philipp J Heisenberg. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth and Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00505-0. ieee: J. Montero, B. Kilian, J. Chan, P. Bayliss, and C.-P. J. Heisenberg, “Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells,” Current Biology, vol. 13, no. 15. Cell Press, pp. 1279–1289, 2003. ista: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. 2003. Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. 13(15), 1279–1289. mla: Montero, Juan, et al. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth and Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology, vol. 13, no. 15, Cell Press, 2003, pp. 1279–89, doi:10.1016/S0960-9822(03)00505-0. short: J. Montero, B. Kilian, J. Chan, P. Bayliss, C.-P.J. Heisenberg, Current Biology 13 (2003) 1279–1289. date_created: 2018-12-11T12:07:22Z date_published: 2003-08-05T00:00:00Z date_updated: 2024-02-27T10:03:37Z day: '05' doi: 10.1016/S0960-9822(03)00505-0 extern: '1' external_id: pmid: - ' 12906787' intvolume: ' 13' issue: '15' language: - iso: eng month: '08' oa_version: None page: 1279 - 1289 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1950' quality_controlled: '1' scopus_import: '1' status: public title: Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2003' ... --- _id: '4185' abstract: - lang: eng text: Wnt genes play important roles in regulating patterning and morphogenesis during vertebrate gastrulation. In zebrafish, slb/wnt11 is required for convergence and extension movements, but not cell fate specification during gastrulation. To determine if other Wnt genes functionally interact with slb/wnt11, we analysed the role of ppt/wnt5 during zebrafish gastrulation. ppt/wnt5 is maternally provided and zygotically expressed at all stages during gastrulation. The analysis of ppt mutant embryos reveals that Ppt/Wnt5 regulates cell elongation and convergent extension movements in posterior regions of the gastrula, while its function in more anterior regions is largely redundant to that of Slb/Wnt11. Frizzled-2 functions downstream of ppt/wnt5, indicating that it might act as a receptor for Ppt/Wnt5 in this process. The characterisation of the role of Ppt/Wnt5 provides insight into the functional diversity of Wnt genes in regulating vertebrate gastrulation movements. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved. acknowledgement: We thank Michael Brand, Florian Raible, Gerlinde Reim, Tobias Langenberg, Jennifer Geiger and Kate Poole for helpful comments on earlier versions of this manuscript. We are grateful to Henry Roehl and Christiane Nüsslein Volhard for sending us the ppt mutant stock. M.T. was supported by a Career Development Fellowship from the MRC. B.K., H.M. and C.P.H. are supported by an Emmy Noether-Fellowship from the DFG. article_processing_charge: No article_type: original author: - first_name: Beate full_name: Kilian, Beate last_name: Kilian - first_name: Hannu full_name: Mansukoski, Hannu last_name: Mansukoski - first_name: Filipa full_name: Barbosa, Filipa last_name: Barbosa - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. 2003;120(4):467-476. doi:10.1016/S0925-4773(03)00004-2 apa: Kilian, B., Mansukoski, H., Barbosa, F., Ulrich, F., Tada, M., & Heisenberg, C.-P. J. (2003). The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. Elsevier. https://doi.org/10.1016/S0925-4773(03)00004-2 chicago: Kilian, Beate, Hannu Mansukoski, Filipa Barbosa, Florian Ulrich, Masazumi Tada, and Carl-Philipp J Heisenberg. “The Role of Ppt/Wnt5 in Regulating Cell Shape and Movement during Zebrafish Gastrulation.” Mechanisms of Development. Elsevier, 2003. https://doi.org/10.1016/S0925-4773(03)00004-2. ieee: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, and C.-P. J. Heisenberg, “The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation,” Mechanisms of Development, vol. 120, no. 4. Elsevier, pp. 467–476, 2003. ista: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. 2003. The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. 120(4), 467–476. mla: Kilian, Beate, et al. “The Role of Ppt/Wnt5 in Regulating Cell Shape and Movement during Zebrafish Gastrulation.” Mechanisms of Development, vol. 120, no. 4, Elsevier, 2003, pp. 467–76, doi:10.1016/S0925-4773(03)00004-2. short: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, C.-P.J. Heisenberg, Mechanisms of Development 120 (2003) 467–476. date_created: 2018-12-11T12:07:27Z date_published: 2003-04-01T00:00:00Z date_updated: 2024-02-27T09:46:39Z day: '01' doi: 10.1016/S0925-4773(03)00004-2 extern: '1' external_id: pmid: - '12676324 ' intvolume: ' 120' issue: '4' language: - iso: eng month: '04' oa_version: None page: 467 - 476 pmid: 1 publication: Mechanisms of Development publication_identifier: issn: - 0925-4773 publication_status: published publisher: Elsevier publist_id: '1934' quality_controlled: '1' scopus_import: '1' status: public title: The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 120 year: '2003' ... --- _id: '3992' abstract: - lang: eng text: Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl citation: ama: Edelsbrunner H, Koehl P. The weighted-volume derivative of a space-filling diagram. PNAS. 2003;100(5):2203-2208. doi:10.1073/pnas.0537830100 apa: Edelsbrunner, H., & Koehl, P. (2003). The weighted-volume derivative of a space-filling diagram. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0537830100 chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative of a Space-Filling Diagram.” PNAS. National Academy of Sciences, 2003. https://doi.org/10.1073/pnas.0537830100. ieee: H. Edelsbrunner and P. Koehl, “The weighted-volume derivative of a space-filling diagram,” PNAS, vol. 100, no. 5. National Academy of Sciences, pp. 2203–2208, 2003. ista: Edelsbrunner H, Koehl P. 2003. The weighted-volume derivative of a space-filling diagram. PNAS. 100(5), 2203–2208. mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative of a Space-Filling Diagram.” PNAS, vol. 100, no. 5, National Academy of Sciences, 2003, pp. 2203–08, doi:10.1073/pnas.0537830100. short: H. Edelsbrunner, P. Koehl, PNAS 100 (2003) 2203–2208. date_created: 2018-12-11T12:06:19Z date_published: 2003-03-04T00:00:00Z date_updated: 2024-02-27T12:31:59Z day: '04' doi: 10.1073/pnas.0537830100 extern: '1' external_id: pmid: - '12601153' intvolume: ' 100' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151318/ month: '03' oa: 1 oa_version: Published Version page: 2203 - 2208 pmid: 1 publication: PNAS publication_identifier: issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences publist_id: '2133' quality_controlled: '1' scopus_import: '1' status: public title: The weighted-volume derivative of a space-filling diagram type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 100 year: '2003' ... --- _id: '3999' abstract: - lang: eng text: We introduce relaxed scheduling as a paradigm for mesh maintenance and demonstrate its applicability to triangulating a skin surface in R-3. acknowledgement: NSF under grant CCR-00- 86013. alternative_title: - LNCS article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alper full_name: Üngör, Alper last_name: Üngör citation: ama: 'Edelsbrunner H, Üngör A. Relaxed scheduling in dynamic skin triangulation. In: Proceedings of the Japanese Conference on Discrete and Computational Geometry . Vol 2866. Springer; 2003:135-151. doi:10.1007/978-3-540-44400-8_14' apa: 'Edelsbrunner, H., & Üngör, A. (2003). Relaxed scheduling in dynamic skin triangulation. In Proceedings of the Japanese Conference on Discrete and Computational Geometry (Vol. 2866, pp. 135–151). Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-540-44400-8_14' chicago: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic Skin Triangulation.” In Proceedings of the Japanese Conference on Discrete and Computational Geometry , 2866:135–51. Springer, 2003. https://doi.org/10.1007/978-3-540-44400-8_14. ieee: H. Edelsbrunner and A. Üngör, “Relaxed scheduling in dynamic skin triangulation,” in Proceedings of the Japanese Conference on Discrete and Computational Geometry , Tokyo, Japan, 2003, vol. 2866, pp. 135–151. ista: 'Edelsbrunner H, Üngör A. 2003. Relaxed scheduling in dynamic skin triangulation. Proceedings of the Japanese Conference on Discrete and Computational Geometry . JCDCG: Japanese Conference on Discrete and Computational Geometry, LNCS, vol. 2866, 135–151.' mla: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic Skin Triangulation.” Proceedings of the Japanese Conference on Discrete and Computational Geometry , vol. 2866, Springer, 2003, pp. 135–51, doi:10.1007/978-3-540-44400-8_14. short: H. Edelsbrunner, A. Üngör, in:, Proceedings of the Japanese Conference on Discrete and Computational Geometry , Springer, 2003, pp. 135–151. conference: end_date: 2002-12-09 location: Tokyo, Japan name: 'JCDCG: Japanese Conference on Discrete and Computational Geometry' start_date: 2002-12-06 date_created: 2018-12-11T12:06:21Z date_published: 2003-12-16T00:00:00Z date_updated: 2024-02-27T11:07:15Z day: '16' doi: 10.1007/978-3-540-44400-8_14 extern: '1' intvolume: ' 2866' language: - iso: eng month: '12' oa_version: None page: 135 - 151 publication: 'Proceedings of the Japanese Conference on Discrete and Computational Geometry ' publication_identifier: isbn: - '9783540207764' publication_status: published publisher: Springer publist_id: '2127' quality_controlled: '1' scopus_import: '1' status: public title: Relaxed scheduling in dynamic skin triangulation type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2866 year: '2003' ... --- _id: '3997' abstract: - lang: eng text: We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex, we construct a topological hierarchy by progressively canceling critical points in pairs. Concurrently, we create a geometric hierarchy by adapting the geometry to the changes in topology. The data structure supports mesh traversal operations similarly to traditional multi-resolution representations. acknowledgement: This work was performed under the auspices of the U. S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48. H. Edelsbrunner is partially supported by the National Science Foundation (NFS) under grants EIA-99-72879 and CCR-00-86013. B. Hamann is supported by the NSF under contract ACI 9624034, through the LSSDSV program under contract ACI 9982251, and through the NPACI; the National Institute of Mental Health and the NSF under contract NIMH 2 P20 MH60975-06A2; the Lawrence Livermore National Laboratory under ASCI ASAP Level-2 Memorandum Agreement B347878 and under Memorandum Agreement B503159. article_processing_charge: No author: - first_name: Peer full_name: Bremer, Peer last_name: Bremer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernd full_name: Hamann, Bernd last_name: Hamann - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A multi-resolution data structure for two-dimensional Morse-Smale functions. In: Proceedings of the 14th IEEE Conference on Visualization . IEEE; 2003:139-146. doi:10.1109/VISUAL.2003.1250365' apa: 'Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2003). A multi-resolution data structure for two-dimensional Morse-Smale functions. In Proceedings of the 14th IEEE Conference on Visualization (pp. 139–146). Seattle, WA, USA : IEEE. https://doi.org/10.1109/VISUAL.2003.1250365' chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci. “A Multi-Resolution Data Structure for Two-Dimensional Morse-Smale Functions.” In Proceedings of the 14th IEEE Conference on Visualization , 139–46. IEEE, 2003. https://doi.org/10.1109/VISUAL.2003.1250365. ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A multi-resolution data structure for two-dimensional Morse-Smale functions,” in Proceedings of the 14th IEEE Conference on Visualization , Seattle, WA, USA , 2003, pp. 139–146. ista: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2003. A multi-resolution data structure for two-dimensional Morse-Smale functions. Proceedings of the 14th IEEE Conference on Visualization . VIS: IEEE Visualization, 139–146.' mla: Bremer, Peer, et al. “A Multi-Resolution Data Structure for Two-Dimensional Morse-Smale Functions.” Proceedings of the 14th IEEE Conference on Visualization , IEEE, 2003, pp. 139–46, doi:10.1109/VISUAL.2003.1250365. short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, in:, Proceedings of the 14th IEEE Conference on Visualization , IEEE, 2003, pp. 139–146. conference: end_date: 2003-10-24 location: 'Seattle, WA, USA ' name: 'VIS: IEEE Visualization' start_date: 2003-10-19 date_created: 2018-12-11T12:06:21Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-02-27T11:12:50Z day: '01' doi: 10.1109/VISUAL.2003.1250365 extern: '1' language: - iso: eng month: '08' oa_version: None page: 139 - 146 publication: 'Proceedings of the 14th IEEE Conference on Visualization ' publication_identifier: isbn: - '0780381203' publication_status: published publisher: IEEE publist_id: '2131' quality_controlled: '1' scopus_import: '1' status: public title: A multi-resolution data structure for two-dimensional Morse-Smale functions type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 year: '2003' ... --- _id: '4168' abstract: - lang: eng text: Recent studies show that signaling through integrin receptors is required for normal cell movements during Xenopus gastrulation. Integrins function in this process by modulating the activity of cadherin adhesion molecules within tissues undergoing convergence and extension movements. article_processing_charge: No article_type: original author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Montero J, Heisenberg C-PJ. Adhesive crosstalk in gastrulation. Developmental Cell. 2003;5(2):190-191. doi:10.1016/S1534-5807(03)00235-1 apa: Montero, J., & Heisenberg, C.-P. J. (2003). Adhesive crosstalk in gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/S1534-5807(03)00235-1 chicago: Montero, Juan, and Carl-Philipp J Heisenberg. “Adhesive Crosstalk in Gastrulation.” Developmental Cell. Cell Press, 2003. https://doi.org/10.1016/S1534-5807(03)00235-1. ieee: J. Montero and C.-P. J. Heisenberg, “Adhesive crosstalk in gastrulation,” Developmental Cell, vol. 5, no. 2. Cell Press, pp. 190–191, 2003. ista: Montero J, Heisenberg C-PJ. 2003. Adhesive crosstalk in gastrulation. Developmental Cell. 5(2), 190–191. mla: Montero, Juan, and Carl-Philipp J. Heisenberg. “Adhesive Crosstalk in Gastrulation.” Developmental Cell, vol. 5, no. 2, Cell Press, 2003, pp. 190–91, doi:10.1016/S1534-5807(03)00235-1. short: J. Montero, C.-P.J. Heisenberg, Developmental Cell 5 (2003) 190–191. date_created: 2018-12-11T12:07:21Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-02-27T09:54:53Z day: '01' doi: 10.1016/S1534-5807(03)00235-1 extern: '1' external_id: pmid: - '12919669 ' intvolume: ' 5' issue: '2' language: - iso: eng month: '08' oa_version: None page: 190 - 191 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Cell Press publist_id: '1949' quality_controlled: '1' scopus_import: '1' status: public title: Adhesive crosstalk in gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 5 year: '2003' ... --- _id: '3991' abstract: - lang: eng text: We give analytic inclusion-exclusion formulas for the area and perimeter derivatives of a union of finitely many disks in the plane. acknowledgement: Partially supported by NSF under grant DMS-98-73945 and CCR-00-86013. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ho full_name: Cheng, Ho last_name: Cheng - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Cheng H, Edelsbrunner H. Area and perimeter derivatives of a union of disks. In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann. Vol 2598. Springer; 2003:88-97. doi:10.1007/3-540-36477-3_7' apa: 'Cheng, H., & Edelsbrunner, H. (2003). Area and perimeter derivatives of a union of disks. In Computer Science in Perspective: Essays Dedicated to Thomas Ottmann (Vol. 2598, pp. 88–97). Springer. https://doi.org/10.1007/3-540-36477-3_7' chicago: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of a Union of Disks.” In Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, 2598:88–97. Springer, 2003. https://doi.org/10.1007/3-540-36477-3_7.' ieee: 'H. Cheng and H. Edelsbrunner, “Area and perimeter derivatives of a union of disks,” in Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, vol. 2598, Springer, 2003, pp. 88–97.' ista: 'Cheng H, Edelsbrunner H. 2003.Area and perimeter derivatives of a union of disks. In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann. LNCS, vol. 2598, 88–97.' mla: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of a Union of Disks.” Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, vol. 2598, Springer, 2003, pp. 88–97, doi:10.1007/3-540-36477-3_7.' short: 'H. Cheng, H. Edelsbrunner, in:, Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, Springer, 2003, pp. 88–97.' date_created: 2018-12-11T12:06:18Z date_published: 2003-02-17T00:00:00Z date_updated: 2024-02-27T12:15:02Z day: '17' doi: 10.1007/3-540-36477-3_7 extern: '1' intvolume: ' 2598' language: - iso: eng month: '02' oa_version: None page: 88 - 97 publication: 'Computer Science in Perspective: Essays Dedicated to Thomas Ottmann' publication_identifier: isbn: - '9783540005797' publication_status: published publisher: Springer publist_id: '2132' quality_controlled: '1' scopus_import: '1' status: public title: Area and perimeter derivatives of a union of disks type: book_chapter user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2598 year: '2003' ...