--- _id: '4445' abstract: - lang: eng text: We present a type system for E code, which is an assembly language that manages the release, interaction, and termination of real-time tasks. E code specifies a deadline for each task, and the type system ensures that the deadlines are path-insensitive. We show that typed E programs allow, for given worst-case execution times of tasks, a simple schedulability analysis. Moreover, the real-time programming language Giotto can be compiled into typed E~code. This shows that typed E~code identifies an easily schedulable yet expressive class of real-time programs. We have extended the Giotto compiler to generate typed E code, and enabled the run-time system for E code to perform a type and schedulability check before executing the code. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and by the NSF grants CCR- 0208875 and CCR-0225610. author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch citation: ama: 'Henzinger TA, Kirsch C. A typed assembly language for real-time programs. In: ACM; 2004:104-113. doi:10.1145/1017753.1017774' apa: 'Henzinger, T. A., & Kirsch, C. (2004). A typed assembly language for real-time programs (pp. 104–113). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1017753.1017774' chicago: Henzinger, Thomas A, and Christoph Kirsch. “A Typed Assembly Language for Real-Time Programs,” 104–13. ACM, 2004. https://doi.org/10.1145/1017753.1017774. ieee: 'T. A. Henzinger and C. Kirsch, “A typed assembly language for real-time programs,” presented at the EMSOFT: Embedded Software , 2004, pp. 104–113.' ista: 'Henzinger TA, Kirsch C. 2004. A typed assembly language for real-time programs. EMSOFT: Embedded Software , 104–113.' mla: Henzinger, Thomas A., and Christoph Kirsch. A Typed Assembly Language for Real-Time Programs. ACM, 2004, pp. 104–13, doi:10.1145/1017753.1017774. short: T.A. Henzinger, C. Kirsch, in:, ACM, 2004, pp. 104–113. conference: name: 'EMSOFT: Embedded Software ' date_created: 2018-12-11T12:08:53Z date_published: 2004-09-01T00:00:00Z date_updated: 2021-01-12T07:57:01Z day: '01' doi: 10.1145/1017753.1017774 extern: 1 month: '09' page: 104 - 113 publication_status: published publisher: ACM publist_id: '285' quality_controlled: 0 status: public title: A typed assembly language for real-time programs type: conference year: '2004' ... --- _id: '4458' abstract: - lang: eng text: 'The success of model checking for large programs depends crucially on the ability to efficiently construct parsimonious abstractions. A predicate abstraction is parsimonious if at each control location, it specifies only relationships between current values of variables, and only those which are required for proving correctness. Previous methods for automatically refining predicate abstractions until sufficient precision is obtained do not systematically construct parsimonious abstractions: predicates usually contain symbolic variables, and are added heuristically and often uniformly to many or all control locations at once. We use Craig interpolation to efficiently construct, from a given abstract error trace which cannot be concretized, a parsominous abstraction that removes the trace. At each location of the trace, we infer the relevant predicates as an interpolant between the two formulas that define the past and the future segment of the trace. Each interpolant is a relationship between current values of program variables, and is relevant only at that particular program location. It can be found by a linear scan of the proof of infeasibility of the trace.We develop our method for programs with arithmetic and pointer expressions, and call-by-value function calls. For function calls, Craig interpolation offers a systematic way of generating relevant predicates that contain only the local variables of the function and the values of the formal parameters when the function was called. We have extended our model checker Blast with predicate discovery by Craig interpolation, and applied it successfully to C programs with more than 130,000 lines of code, which was not possible with approaches that build less parsimonious abstractions.' author: - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar - first_name: Kenneth full_name: McMillan, Kenneth L last_name: Mcmillan citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. Abstractions from proofs. In: ACM; 2004:232-244. doi:10.1145/964001.964021' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Mcmillan, K. (2004). Abstractions from proofs (pp. 232–244). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/964001.964021' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Kenneth Mcmillan. “Abstractions from Proofs,” 232–44. ACM, 2004. https://doi.org/10.1145/964001.964021. ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and K. Mcmillan, “Abstractions from proofs,” presented at the POPL: Principles of Programming Languages, 2004, pp. 232–244.' ista: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. 2004. Abstractions from proofs. POPL: Principles of Programming Languages, 232–244.' mla: Henzinger, Thomas A., et al. Abstractions from Proofs. ACM, 2004, pp. 232–44, doi:10.1145/964001.964021. short: T.A. Henzinger, R. Jhala, R. Majumdar, K. Mcmillan, in:, ACM, 2004, pp. 232–244. conference: name: 'POPL: Principles of Programming Languages' date_created: 2018-12-11T12:08:57Z date_published: 2004-04-01T00:00:00Z date_updated: 2021-01-12T07:57:06Z day: '01' doi: 10.1145/964001.964021 extern: 1 month: '04' page: 232 - 244 publication_status: published publisher: ACM publist_id: '270' quality_controlled: 0 status: public title: Abstractions from proofs type: conference year: '2004' ... --- _id: '4461' abstract: - lang: eng text: One of the central axioms of extreme programming is the disciplined use of regression testing during stepwise software development. Due to recent progress in software model checking, it has become possible to supplement this process with automatic checks for behavioral safety properties of programs, such as conformance with locking idioms and other programming protocols and patterns. For efficiency reasons, all checks must be incremental, i.e., they must reuse partial results from previous checks in order to avoid all unnecessary repetition of expensive verification tasks. We show that the lazy-abstraction algorithm, and its implementation in Blast, can be extended to support the fully automatic and incremental checking of temporal safety properties during software development. acknowledgement: 'This work was supported in part by the NSF grants CCR-9988172, CCR-0085949, and CCR-0234690, the ONR grant N00014-02-1-0671, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660. ' alternative_title: - LNCS author: - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar - first_name: Marco full_name: Sanvido, Marco A last_name: Sanvido citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. Extreme model checking. In: Verification: Theory and Practice. Vol 2772. Springer; 2004:332-358. doi:10.1007/978-3-540-39910-0_16' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sanvido, M. (2004). Extreme model checking. In Verification: Theory and Practice (Vol. 2772, pp. 332–358). Springer. https://doi.org/10.1007/978-3-540-39910-0_16' chicago: 'Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Marco Sanvido. “Extreme Model Checking.” In Verification: Theory and Practice, 2772:332–58. Springer, 2004. https://doi.org/10.1007/978-3-540-39910-0_16.' ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and M. Sanvido, “Extreme model checking,” in Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–358.' ista: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. 2004.Extreme model checking. In: Verification: Theory and Practice. LNCS, vol. 2772, 332–358.' mla: 'Henzinger, Thomas A., et al. “Extreme Model Checking.” Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–58, doi:10.1007/978-3-540-39910-0_16.' short: 'T.A. Henzinger, R. Jhala, R. Majumdar, M. Sanvido, in:, Verification: Theory and Practice, Springer, 2004, pp. 332–358.' date_created: 2018-12-11T12:08:58Z date_published: 2004-02-24T00:00:00Z date_updated: 2021-01-12T07:57:08Z day: '24' doi: 10.1007/978-3-540-39910-0_16 extern: 1 intvolume: ' 2772' month: '02' page: 332 - 358 publication: 'Verification: Theory and Practice' publication_status: published publisher: Springer publist_id: '269' quality_controlled: 0 status: public title: Extreme model checking type: book_chapter volume: 2772 year: '2004' ... --- _id: '4459' abstract: - lang: eng text: Software model checking has been successful for sequential programs, where predicate abstraction offers suitable models, and counterexample-guided abstraction refinement permits the automatic inference of models. When checking concurrent programs, we need to abstract threads as well as the contexts in which they execute. Stateless context models, such as predicates on global variables, prove insufficient for showing the absence of race conditions in many examples. We therefore use richer context models, which combine (1) predicates for abstracting data state, (2) control flow quotients for abstracting control state, and (3) counters for abstracting an unbounded number of threads. We infer suitable context models automatically by a combination of counterexample-guided abstraction refinement, bisimulation minimization, circular assume-guarantee reasoning, and parametric reasoning about an unbounded number of threads. This algorithm, called CIRC, has been implemented in BLAST and succeeds in checking many examples of NESC code for data races. In particular, BLAST proves the absence of races in several cases where previous race checkers give false positives. author: - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar citation: ama: 'Henzinger TA, Jhala R, Majumdar R. Race checking by context inference. In: ACM; 2004:1-13. doi:10.1145/996841.996844' apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Race checking by context inference (pp. 1–13). Presented at the PLDI: Programming Languages Design and Implementation, ACM. https://doi.org/10.1145/996841.996844' chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Race Checking by Context Inference,” 1–13. ACM, 2004. https://doi.org/10.1145/996841.996844. ieee: 'T. A. Henzinger, R. Jhala, and R. Majumdar, “Race checking by context inference,” presented at the PLDI: Programming Languages Design and Implementation, 2004, pp. 1–13.' ista: 'Henzinger TA, Jhala R, Majumdar R. 2004. Race checking by context inference. PLDI: Programming Languages Design and Implementation, 1–13.' mla: Henzinger, Thomas A., et al. Race Checking by Context Inference. ACM, 2004, pp. 1–13, doi:10.1145/996841.996844. short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, ACM, 2004, pp. 1–13. conference: name: 'PLDI: Programming Languages Design and Implementation' date_created: 2018-12-11T12:08:57Z date_published: 2004-06-01T00:00:00Z date_updated: 2021-01-12T07:57:07Z day: '01' doi: 10.1145/996841.996844 extern: 1 month: '06' page: 1 - 13 publication_status: published publisher: ACM publist_id: '271' quality_controlled: 0 status: public title: Race checking by context inference type: conference year: '2004' ... --- _id: '4525' abstract: - lang: eng text: 'We present a new high-level programming language, called xGiotto, for programming applications with hard real-time constraints. Like its predecessor, xGiotto is based on the LET (logical execution time) assumption: the programmer specifies when the outputs of a task become available, and the compiler checks if the specification can be implemented on a given platform. However, while the predecessor language xGiotto was purely time-triggered, xGiotto accommodates also asynchronous events. Indeed, through a mechanism called event scoping, events are the main structuring principle of the new language. The xGiotto compiler and run-time system implement event scoping through a tree-based event filter. The compiler also checks programs for determinism (absence of race conditions).' acknowledgement: This research is supported by the AFOSR MURI grant F49620-00-1-0327, the DARPA SEC grant F33615-C-98-3614, the MARCO GSRC grant 98-DT-660, and the NSF grants CCR-0208875 and CCR-0225610. alternative_title: - LNCS author: - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch - first_name: Marco full_name: Sanvido, Marco A last_name: Sanvido citation: ama: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. Event-driven programming with logical execution times. In: Vol 2993. Springer; 2004:167-170. doi:10.1007/978-3-540-24743-2_24' apa: 'Ghosal, A., Henzinger, T. A., Kirsch, C., & Sanvido, M. (2004). Event-driven programming with logical execution times (Vol. 2993, pp. 167–170). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-24743-2_24' chicago: Ghosal, Arkadeb, Thomas A Henzinger, Christoph Kirsch, and Marco Sanvido. “Event-Driven Programming with Logical Execution Times,” 2993:167–70. Springer, 2004. https://doi.org/10.1007/978-3-540-24743-2_24. ieee: 'A. Ghosal, T. A. Henzinger, C. Kirsch, and M. Sanvido, “Event-driven programming with logical execution times,” presented at the HSCC: Hybrid Systems - Computation and Control, 2004, vol. 2993, pp. 167–170.' ista: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. 2004. Event-driven programming with logical execution times. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 2993, 167–170.' mla: Ghosal, Arkadeb, et al. Event-Driven Programming with Logical Execution Times. Vol. 2993, Springer, 2004, pp. 167–70, doi:10.1007/978-3-540-24743-2_24. short: A. Ghosal, T.A. Henzinger, C. Kirsch, M. Sanvido, in:, Springer, 2004, pp. 167–170. conference: name: 'HSCC: Hybrid Systems - Computation and Control' date_created: 2018-12-11T12:09:18Z date_published: 2004-03-12T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '12' doi: 10.1007/978-3-540-24743-2_24 extern: 1 intvolume: ' 2993' month: '03' page: 167 - 170 publication_status: published publisher: Springer publist_id: '200' quality_controlled: 0 status: public title: Event-driven programming with logical execution times type: conference volume: 2993 year: '2004' ... --- _id: '4555' abstract: - lang: eng text: Strategies in repeated games can be classified as to whether or not they use memory and/or randomization. We consider Markov decision processes and 2-player graph games, both of the deterministic and probabilistic varieties. We characterize when memory and/or randomization are required for winning with respect to various classes of w-regular objectives, noting particularly when the use of memory can be traded for the use of randomization. In particular, we show that Markov decision processes allow randomized memoryless optimal strategies for all M?ller objectives. Furthermore, we show that 2-player probabilistic graph games allow randomized memoryless strategies for winning with probability 1 those M?ller objectives which are upward-closed. Upward-closure means that if a set α of infinitely repeating vertices is winning, then all supersets of α are also winning. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, De Alfaro L, Henzinger TA. Trading memory for randomness. In: IEEE; 2004:206-217. doi:10.1109/QEST.2004.10051' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2004). Trading memory for randomness (pp. 206–217). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2004.10051' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Trading Memory for Randomness,” 206–17. IEEE, 2004. https://doi.org/10.1109/QEST.2004.10051. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Trading memory for randomness,” presented at the QEST: Quantitative Evaluation of Systems, 2004, pp. 206–217.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2004. Trading memory for randomness. QEST: Quantitative Evaluation of Systems, 206–217.' mla: Chatterjee, Krishnendu, et al. Trading Memory for Randomness. IEEE, 2004, pp. 206–17, doi:10.1109/QEST.2004.10051. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2004, pp. 206–217. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:27Z date_published: 2004-09-30T00:00:00Z date_updated: 2021-01-12T07:59:40Z day: '30' doi: 10.1109/QEST.2004.10051 extern: 1 month: '09' page: 206 - 217 publication_status: published publisher: IEEE publist_id: '155' quality_controlled: 0 status: public title: Trading memory for randomness type: conference year: '2004' ... --- _id: '4558' abstract: - lang: eng text: We study perfect-information stochastic parity games. These are two-player nonterminating games which are played on a graph with turn-based probabilistic transitions. A play results in an infinite path and the conflicting goals of the two players are ω-regular path properties, formalized as parity winning conditions. The qualitative solution of such a game amounts to computing the set of vertices from which a player has a strategy to win with probability 1 (or with positive probability). The quantitative solution amounts to computing the value of the game in every vertex, i.e., the highest probability with which a player can guarantee satisfaction of his own objective in a play that starts from the vertex.For the important special case of one-player stochastic parity games (parity Markov decision processes) we give polynomial-time algorithms both for the qualitative and the quantitative solution. The running time of the qualitative solution is O(d · m3/2) for graphs with m edges and d priorities. The quantitative solution is based on a linear-programming formulation.For the two-player case, we establish the existence of optimal pure memoryless strategies. This has several important ramifications. First, it implies that the values of the games are rational. This is in contrast to the concurrent stochastic parity games of de Alfaro et al.; there, values are in general algebraic numbers, optimal strategies do not exist, and ε-optimal strategies have to be mixed and with infinite memory. Second, the existence of optimal pure memoryless strategies together with the polynomial-time solution forone-player case implies that the quantitative two-player stochastic parity game problem is in NP ∩ co-NP. This generalizes a result of Condon for stochastic games with reachability objectives. It also constitutes an exponential improvement over the best previous algorithm, which is based on a doubly exponential procedure of de Alfaro and Majumdar for concurrent stochastic parity games and provides only ε-approximations of the values. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Jurdziński M, Henzinger TA. Quantitative stochastic parity games. In: SIAM; 2004:121-130.' apa: 'Chatterjee, K., Jurdziński, M., & Henzinger, T. A. (2004). Quantitative stochastic parity games (pp. 121–130). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Quantitative Stochastic Parity Games,” 121–30. SIAM, 2004. ieee: 'K. Chatterjee, M. Jurdziński, and T. A. Henzinger, “Quantitative stochastic parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2004, pp. 121–130.' ista: 'Chatterjee K, Jurdziński M, Henzinger TA. 2004. Quantitative stochastic parity games. SODA: Symposium on Discrete Algorithms, 121–130.' mla: Chatterjee, Krishnendu, et al. Quantitative Stochastic Parity Games. SIAM, 2004, pp. 121–30. short: K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, SIAM, 2004, pp. 121–130. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:09:28Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:59:41Z day: '01' extern: 1 month: '01' page: 121 - 130 publication_status: published publisher: SIAM publist_id: '153' quality_controlled: 0 status: public title: Quantitative stochastic parity games type: conference year: '2004' ... --- _id: '4556' abstract: - lang: eng text: We study the problem of determining stack boundedness and the exact maximum stack size for three classes of interrupt-driven programs. Interrupt-driven programs are used in many real-time applications that require responsive interrupt handling. In order to ensure responsiveness, programmers often enable interrupt processing in the body of lower-priority interrupt handlers. In such programs a programming error can allow interrupt handlers to be interrupted in a cyclic fashion to lead to an unbounded stack, causing the system to crash. For a restricted class of interrupt-driven programs, we show that there is a polynomial-time procedure to check stack boundedness, while determining the exact maximum stack size is PSPACE-complete. For a larger class of programs, the two problems are both PSPACE-complete, and for the largest class of programs we consider, the two problems are PSPACE-hard and can be solved in exponential time. While the complexities are high, our algorithms are exponential only in the number of handlers, and polynomial in the size of the program. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Di full_name: Ma, Di last_name: Ma - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Tian full_name: Zhao, Tian last_name: Zhao - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jens full_name: Palsberg, Jens last_name: Palsberg citation: ama: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size analysis for interrupt-driven programs. Information and Computation. 2004;194(2):144-174. doi:10.1016/j.ic.2004.06.001 apa: Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., & Palsberg, J. (2004). Stack size analysis for interrupt-driven programs. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2004.06.001 chicago: Chatterjee, Krishnendu, Di Ma, Ritankar Majumdar, Tian Zhao, Thomas A Henzinger, and Jens Palsberg. “Stack Size Analysis for Interrupt-Driven Programs.” Information and Computation. Elsevier, 2004. https://doi.org/10.1016/j.ic.2004.06.001. ieee: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T. A. Henzinger, and J. Palsberg, “Stack size analysis for interrupt-driven programs,” Information and Computation, vol. 194, no. 2. Elsevier, pp. 144–174, 2004. ista: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. 2004. Stack size analysis for interrupt-driven programs. Information and Computation. 194(2), 144–174. mla: Chatterjee, Krishnendu, et al. “Stack Size Analysis for Interrupt-Driven Programs.” Information and Computation, vol. 194, no. 2, Elsevier, 2004, pp. 144–74, doi:10.1016/j.ic.2004.06.001. short: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg, Information and Computation 194 (2004) 144–174. date_created: 2018-12-11T12:09:28Z date_published: 2004-08-11T00:00:00Z date_updated: 2021-01-12T07:59:40Z day: '11' doi: 10.1016/j.ic.2004.06.001 extern: 1 intvolume: ' 194' issue: '2' month: '08' page: 144 - 174 publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '156' quality_controlled: 0 status: public title: Stack size analysis for interrupt-driven programs type: journal_article volume: 194 year: '2004' ... --- _id: '4578' abstract: - lang: eng text: 'BLAST is an automatic verification tool for checking temporal safety properties of C programs. Blast is based on lazy predicate abstraction driven by interpolation-based predicate discovery. In this paper, we present the Blast specification language. The language specifies program properties at two levels of precision. At the lower level, monitor automata are used to specify temporal safety properties of program executions (traces). At the higher level, relational reachability queries over program locations are used to combine lower-level trace properties. The two-level specification language can be used to break down a verification task into several independent calls of the model-checking engine. In this way, each call to the model checker may have to analyze only part of the program, or part of the specification, and may thus succeed in a reduction of the number of predicates needed for the analysis. In addition, the two-level specification language provides a means for structuring and maintaining specifications. ' acknowledgement: This research was supported in part by the NSF grants CCR-0085949, CCR-0234690, and ITR-0326577. alternative_title: - LNCS author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Adam full_name: Chlipala, Adam J last_name: Chlipala - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar citation: ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. The BLAST query language for software verification. In: Vol 3148. Springer; 2004:2-18. doi:10.1007/978-3-540-27864-1_2' apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). The BLAST query language for software verification (Vol. 3148, pp. 2–18). Presented at the SAS: Static Analysis Symposium, Springer. https://doi.org/10.1007/978-3-540-27864-1_2' chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “The BLAST Query Language for Software Verification,” 3148:2–18. Springer, 2004. https://doi.org/10.1007/978-3-540-27864-1_2. ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “The BLAST query language for software verification,” presented at the SAS: Static Analysis Symposium, 2004, vol. 3148, pp. 2–18.' ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. The BLAST query language for software verification. SAS: Static Analysis Symposium, LNCS, vol. 3148, 2–18.' mla: Beyer, Dirk, et al. The BLAST Query Language for Software Verification. Vol. 3148, Springer, 2004, pp. 2–18, doi:10.1007/978-3-540-27864-1_2. short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer, 2004, pp. 2–18. conference: name: 'SAS: Static Analysis Symposium' date_created: 2018-12-11T12:09:34Z date_published: 2004-08-17T00:00:00Z date_updated: 2021-01-12T07:59:50Z day: '17' doi: 10.1007/978-3-540-27864-1_2 extern: 1 intvolume: ' 3148' month: '08' page: 2 - 18 publication_status: published publisher: Springer publist_id: '130' quality_controlled: 0 status: public title: The BLAST query language for software verification type: conference volume: 3148 year: '2004' ... --- _id: '4577' abstract: - lang: eng text: While model checking has been successful in uncovering subtle bugs in code, its adoption in software engineering practice has been hampered by the absence of a simple interface to the programmer in an integrated development environment. We describe an integration of the software model checker BLAST into the Eclipse development environment. We provide a verification interface for practical solutions for some typical program analysis problems - assertion checking, reachability analysis, dead code analysis, and test generation - directly on the source code. The analysis is completely automatic, and assumes no knowledge of model checking or formal notation. Moreover, the interface supports incremental program verification to support incremental design and evolution of code. acknowledgement: This research was supported in part by the NSF grants CCR-0085949, CCR-0234690, and ITR-0326577. author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar citation: ama: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. An eclipse plug-in for model checking. In: IEEE; 2004:251-255. doi:10.1109/WPC.2004.1311069  ' apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). An eclipse plug-in for model checking (pp. 251–255). Presented at the IWPC: Program Comprehension, IEEE. https://doi.org/10.1109/WPC.2004.1311069  ' chicago: Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “An Eclipse Plug-in for Model Checking,” 251–55. IEEE, 2004. https://doi.org/10.1109/WPC.2004.1311069  . ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “An eclipse plug-in for model checking,” presented at the IWPC: Program Comprehension, 2004, pp. 251–255.' ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2004. An eclipse plug-in for model checking. IWPC: Program Comprehension, 251–255.' mla: Beyer, Dirk, et al. An Eclipse Plug-in for Model Checking. IEEE, 2004, pp. 251–55, doi:10.1109/WPC.2004.1311069  . short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 251–255. conference: name: 'IWPC: Program Comprehension' date_created: 2018-12-11T12:09:34Z date_published: 2004-07-12T00:00:00Z date_updated: 2021-01-12T07:59:50Z day: '12' doi: '10.1109/WPC.2004.1311069 ' extern: 1 month: '07' page: 251 - 255 publication_status: published publisher: IEEE publist_id: '129' quality_controlled: 0 status: public title: An eclipse plug-in for model checking type: conference year: '2004' ... --- _id: '4581' abstract: - lang: eng text: We have extended the software model checker BLAST to automatically generate test suites that guarantee full coverage with respect to a given predicate. More precisely, given a C program and a target predicate p, BLAST determines the set L of program locations which program execution can reach with p true, and automatically generates a set of test vectors that exhibit the truth of p at all locations in L. We have used BLAST to generate test suites and to detect dead code in C programs with up to 30 K lines of code. The analysis and test vector generation is fully automatic (no user intervention) and exact (no false positives). author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Adam full_name: Chlipala, Adam J last_name: Chlipala - first_name: Thomas A full_name: Thomas Henzinger 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 S last_name: Majumdar citation: ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. Generating tests from counterexamples. In: IEEE; 2004:326-335. doi:10.1109/ICSE.2004.1317455' apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Generating tests from counterexamples (pp. 326–335). Presented at the ICSE: Software Engineering, IEEE. https://doi.org/10.1109/ICSE.2004.1317455' chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Generating Tests from Counterexamples,” 326–35. IEEE, 2004. https://doi.org/10.1109/ICSE.2004.1317455. ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “Generating tests from counterexamples,” presented at the ICSE: Software Engineering, 2004, pp. 326–335.' ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. Generating tests from counterexamples. ICSE: Software Engineering, 326–335.' mla: Beyer, Dirk, et al. Generating Tests from Counterexamples. IEEE, 2004, pp. 326–35, doi:10.1109/ICSE.2004.1317455. short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 326–335. conference: name: 'ICSE: Software Engineering' date_created: 2018-12-11T12:09:35Z date_published: 2004-07-26T00:00:00Z date_updated: 2021-01-12T07:59:52Z day: '26' doi: 10.1109/ICSE.2004.1317455 extern: 1 month: '07' page: 326 - 335 publication_status: published publisher: IEEE publist_id: '128' quality_controlled: 0 status: public title: Generating tests from counterexamples type: conference year: '2004' ... --- _id: '4629' abstract: - lang: eng text: 'Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a generalization of the branching-time logic Ctl which achieves robustness with respect to model perturbations by giving a quantitative interpretation to predicates and logical operators, and by discounting the importance of events according to how late they occur. In every state, the value of a formula is a real number in the interval [0,1], where 1 corresponds to truth and 0 to falsehood. The boolean operators and and or are replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over all paths from a given state, and the temporal operators and □ specify sup and inf over a given path; a new operator averages all values along a path. Furthermore, all path operators are discounted by a parameter that can be chosen to give more weight to states that are closer to the beginning of the path. We interpret the resulting logic Dctl over transition systems, Markov chains, and Markov decision processes. We present two semantics for Dctl: a path semantics, inspired by the standard interpretation of state and path formulas in CTL, and a fixpoint semantics, inspired by the μ-calculus evaluation of CTL formulas. We show that, while these semantics coincide for CTL, they differ for Dctl, and we provide model-checking algorithms for both semantics.' acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the ONR grant N00014-02-1-0671, and the NSF grants CCR-0132780, CCR-9988172, CCR-0225610, and CCR-0234690. alternative_title: - LNCS author: - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Marco full_name: Faella, Marco last_name: Faella - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Mariëlle full_name: Stoelinga, Mariëlle last_name: Stoelinga citation: ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. In: Vol 2988. Springer; 2004:77-92. doi:10.1007/978-3-540-24730-2_6' apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2004). Model checking discounted temporal properties (Vol. 2988, pp. 77–92). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/978-3-540-24730-2_6' chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties,” 2988:77–92. Springer, 2004. https://doi.org/10.1007/978-3-540-24730-2_6. ieee: 'L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2004, vol. 2988, pp. 77–92.' ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2004. Model checking discounted temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 2988, 77–92.' mla: De Alfaro, Luca, et al. Model Checking Discounted Temporal Properties. Vol. 2988, Springer, 2004, pp. 77–92, doi:10.1007/978-3-540-24730-2_6. short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, Springer, 2004, pp. 77–92. conference: name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' date_created: 2018-12-11T12:09:50Z date_published: 2004-03-18T00:00:00Z date_updated: 2021-01-12T08:00:38Z day: '18' doi: 10.1007/978-3-540-24730-2_6 extern: 1 intvolume: ' 2988' month: '03' page: 77 - 92 publication_status: published publisher: Springer publist_id: '79' quality_controlled: 0 status: public title: Model checking discounted temporal properties type: conference volume: 2988 year: '2004' ... --- _id: '6155' abstract: - lang: eng text: 'The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.' author: - first_name: Benny H.H full_name: Cheung, Benny H.H last_name: Cheung - first_name: Fausto full_name: Arellano-Carbajal, Fausto last_name: Arellano-Carbajal - first_name: Irene full_name: Rybicki, Irene last_name: Rybicki - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027 apa: Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004). Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027 chicago: Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.027. ieee: B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp. 1105–1111, 2004. ista: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 14(12), 1105–1111. mla: Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology, vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027. short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology 14 (2004) 1105–1111. date_created: 2019-03-21T09:42:01Z date_published: 2004-06-22T00:00:00Z date_updated: 2021-01-12T08:06:25Z day: '22' doi: 10.1016/j.cub.2004.06.027 extern: '1' external_id: pmid: - '15203005' intvolume: ' 14' issue: '12' language: - iso: eng month: '06' oa_version: None page: 1105-1111 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2004' ... --- _id: '7334' abstract: - lang: eng text: 'Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. ' article_processing_charge: No article_type: original author: - first_name: John full_name: Mantzaras, John last_name: Mantzaras - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi - first_name: Markus full_name: Roos, Markus last_name: Roos - first_name: Wilhelm full_name: Brandstätter, Wilhelm last_name: Brandstätter - first_name: Michel full_name: Prestat, Michel last_name: Prestat - first_name: Ludwig J. full_name: Gauckler, Ludwig J. last_name: Gauckler - first_name: Bernhard full_name: Andreaus, Bernhard last_name: Andreaus - first_name: Faegheh full_name: Hajbolouri, Faegheh last_name: Hajbolouri - first_name: Stephan M. full_name: Senn, Stephan M. last_name: Senn - first_name: Dimos full_name: Poulikakos, Dimos last_name: Poulikakos - first_name: Andreas K. full_name: Chaniotis, Andreas K. last_name: Chaniotis - first_name: Diego full_name: Larrain, Diego last_name: Larrain - first_name: Nordahl full_name: Autissier, Nordahl last_name: Autissier - first_name: François full_name: Maréchal, François last_name: Maréchal citation: ama: Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029 apa: Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W., Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029 chicago: Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos, Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical Society, 2004. https://doi.org/10.2533/000942904777677029. ieee: J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society, pp. 857–868, 2004. ista: Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M, Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 58(12), 857–868. mla: Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp. 857–68, doi:10.2533/000942904777677029. short: J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M. Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos, A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal for Chemistry 58 (2004) 857–868. date_created: 2020-01-15T12:24:23Z date_published: 2004-12-01T00:00:00Z date_updated: 2021-01-12T08:13:09Z day: '01' doi: 10.2533/000942904777677029 extern: '1' intvolume: ' 58' issue: '12' language: - iso: eng month: '12' oa_version: None page: 857-868 publication: CHIMIA International Journal for Chemistry publication_identifier: issn: - 0009-4293 publication_status: published publisher: Swiss Chemical Society quality_controlled: '1' status: public title: Fuel cell modeling and simulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2004' ... --- _id: '7333' abstract: - lang: eng text: The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system. article_processing_charge: No article_type: original author: - first_name: M. full_name: Santis, M. last_name: Santis - first_name: D. full_name: Schmid, D. last_name: Schmid - first_name: M. full_name: Ruge, M. last_name: Ruge - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: F.N. full_name: Büchi, F.N. last_name: Büchi citation: ama: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218. doi:10.1002/fuce.200400028 apa: Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004). Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028 chicago: Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N. Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028. ieee: M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular stack-internal air humidification concept-verification in a 1 kW stack,” Fuel Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004. ista: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218. mla: Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028. short: M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4 (2004) 214–218. date_created: 2020-01-15T12:24:14Z date_published: 2004-08-01T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '01' doi: 10.1002/fuce.200400028 extern: '1' intvolume: ' 4' issue: '3' language: - iso: eng month: '08' oa_version: None page: 214-218 publication: Fuel Cells publication_identifier: issn: - 1615-6846 - 1615-6854 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Modular stack-internal air humidification concept-verification in a 1 kW stack type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2004' ... --- _id: '864' abstract: - lang: eng text: 'We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.' acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport. author: - first_name: Anna full_name: Panchenko, Anna R last_name: Panchenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephen full_name: Bryant, Stephen H last_name: Bryant citation: ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 2004;13(4):884-892. doi:10.1110/ps.03465504 apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. Wiley-Blackwell. https://doi.org/10.1110/ps.03465504 chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504. ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004. ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892. mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504. short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892. date_created: 2018-12-11T11:48:55Z date_published: 2004-04-01T00:00:00Z date_updated: 2021-01-12T08:20:22Z day: '01' doi: 10.1110/ps.03465504 extern: 1 intvolume: ' 13' issue: '4' month: '04' page: 884 - 892 publication: Protein Science publication_status: published publisher: Wiley-Blackwell publist_id: '6786' quality_controlled: 0 status: public title: Prediction of functional sites by analysis of sequence and structure conservation type: journal_article volume: 13 year: '2004' ... --- _id: '870' abstract: - lang: eng text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330 apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkh330 chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University Press, 2004. https://doi.org/10.1093/nar/gkh330. ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004. ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737. mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330. short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737. date_created: 2018-12-11T11:48:56Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T08:20:37Z day: '01' doi: 10.1093/nar/gkh330 extern: 1 intvolume: ' 32' issue: '5' month: '01' page: 1731 - 1737 publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '6780' quality_controlled: 0 status: public title: Bioinformatical assay of human gene morbidity type: journal_article volume: 32 year: '2004' ... --- _id: '875' abstract: - lang: eng text: The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001 apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001 chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001. ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004. ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291. mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001. short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291. date_created: 2018-12-11T11:48:58Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T08:20:54Z day: '01' doi: 10.1016/j.tig.2004.05.001 extern: 1 intvolume: ' 20' issue: '7' month: '07' page: 287 - 291 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6775' quality_controlled: 0 status: public title: A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications type: journal_article volume: 20 year: '2004' ... --- _id: '889' abstract: - lang: eng text: 'The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.' acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes author: - first_name: Andrew full_name: Kern, Andrew D last_name: Kern - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212. doi:10.1038/ng1451 apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng1451 chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing Group, 2004. https://doi.org/10.1038/ng1451. ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004. ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212. mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451. short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212. date_created: 2018-12-11T11:49:02Z date_published: 2004-11-01T00:00:00Z date_updated: 2021-01-12T08:21:17Z day: '01' doi: 10.1038/ng1451 extern: 1 intvolume: ' 36' issue: '11' month: '11' page: 1207 - 1212 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6759' quality_controlled: 0 status: public title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs type: journal_article volume: 36 year: '2004' ... --- _id: '9493' abstract: - lang: eng text: In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production. article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Xiaofeng full_name: Cao, Xiaofeng last_name: Cao - first_name: Lisa K. full_name: Johansen, Lisa K. last_name: Johansen - first_name: Zhixin full_name: Xie, Zhixin last_name: Xie - first_name: James C. full_name: Carrington, James C. last_name: Carrington - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen citation: ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055 apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., & Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055 chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.055. ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004. ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220. mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055. short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220. date_created: 2021-06-07T10:33:00Z date_published: 2004-07-13T00:00:00Z date_updated: 2021-12-14T08:52:00Z day: '13' department: - _id: DaZi doi: 10.1016/j.cub.2004.06.055 extern: '1' external_id: pmid: - '15242620 ' intvolume: ' 14' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2004.06.055 month: '07' oa: 1 oa_version: Published Version page: 1214-1220 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 14 year: '2004' ...