--- _id: '3728' abstract: - lang: eng text: Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins. author: - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Sławomir full_name: Filipek, Sławomir last_name: Filipek - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Krystiana full_name: Krzysko, Krystiana A last_name: Krzysko citation: ama: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2006;1758(4):537-544. doi:10.1016/j.bbamem.2006.03.028' apa: 'Cieplak, M., Filipek, S., Janovjak, H. L., & Krzysko, K. (2006). Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2006.03.028' chicago: 'Cieplak, Marek, Sławomir Filipek, Harald L Janovjak, and Krystiana Krzysko. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2006. https://doi.org/10.1016/j.bbamem.2006.03.028.' ieee: 'M. Cieplak, S. Filipek, H. L. Janovjak, and K. Krzysko, “Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4. Elsevier, pp. 537–544, 2006.' ista: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. 2006. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1758(4), 537–544.' mla: 'Cieplak, Marek, et al. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4, Elsevier, 2006, pp. 537–44, doi:10.1016/j.bbamem.2006.03.028.' short: M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica Acta (BBA) - Biomembranes 1758 (2006) 537–544. date_created: 2018-12-11T12:04:50Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:51:46Z day: '01' doi: 10.1016/j.bbamem.2006.03.028 extern: 1 intvolume: ' 1758' issue: '4' month: '04' page: 537 - 544 publication: Biochimica et Biophysica Acta (BBA) - Biomembranes publication_status: published publisher: Elsevier publist_id: '2502' quality_controlled: 0 status: public title: 'Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment' type: journal_article volume: 1758 year: '2006' ... --- _id: '3722' author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum Akademischer Verlag; 2006.' apa: Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik. Spektrum Akademischer Verlag. chicago: Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik. Spektrum Akademischer Verlag, 2006. ieee: H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik, Spektrum Akademischer Verlag, 2006. ista: 'Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .' mla: Janovjak, Harald L., and Daniel Mueller. “Rastersondenmikroskopie.” Bioanalytik, Spektrum Akademischer Verlag, 2006. short: H.L. Janovjak, D. Mueller, in:, Bioanalytik, Spektrum Akademischer Verlag, 2006. date_created: 2018-12-11T12:04:48Z date_published: 2006-06-16T00:00:00Z date_updated: 2021-01-12T07:51:44Z day: '16' extern: 1 month: '06' publication: Bioanalytik publication_status: published publisher: Spektrum Akademischer Verlag publist_id: '2508' quality_controlled: 0 status: public title: Rastersondenmikroskopie type: book_chapter year: '2006' ... --- _id: '3755' abstract: - lang: eng text: A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems. author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Thierry full_name: Emonet,Thierry last_name: Emonet - first_name: Sébastien full_name: Harlepp, Sébastien last_name: Harlepp - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321. doi:10.1529/biophysj.105.073353 apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353 chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353. ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants of drug-inducible gene expression in a single bacterium,” Biophysical Journal, vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006. ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 90(9), 3315–3321. mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353. short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 3315–3321. date_created: 2018-12-11T12:04:59Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:51:58Z day: '01' doi: 10.1529/biophysj.105.073353 extern: 1 intvolume: ' 90' issue: '9' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/ month: '01' oa: 1 page: 3315 - 3321 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2472' quality_controlled: 0 status: public title: Dynamical determinants of drug-inducible gene expression in a single bacterium type: journal_article volume: 90 year: '2006' ... --- _id: '3758' abstract: - lang: eng text: Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations. article_processing_charge: No author: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Peter full_name: Mucha, Peter last_name: Mucha - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: 'Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using the adjoint method. In: ACM; 2006:15-23.' apa: 'Wojtan, C., Mucha, P., & Turk, G. (2006). Keyframe control of complex particle systems using the adjoint method (pp. 15–23). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, ACM.' chicago: Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006. ieee: 'C. Wojtan, P. Mucha, and G. Turk, “Keyframe control of complex particle systems using the adjoint method,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 2006, pp. 15–23.' ista: 'Wojtan C, Mucha P, Turk G. 2006. Keyframe control of complex particle systems using the adjoint method. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 15–23.' mla: Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using the Adjoint Method. ACM, 2006, pp. 15–23. short: C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23. conference: name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation' date_created: 2018-12-11T12:05:00Z date_published: 2006-09-01T00:00:00Z date_updated: 2023-02-23T11:41:22Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf month: '09' oa_version: None page: 15 - 23 publication_status: published publisher: ACM publist_id: '2469' status: public title: Keyframe control of complex particle systems using the adjoint method type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '3818' abstract: - lang: eng text: Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein. author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Liyi full_name: Li, Liyi last_name: Li - first_name: Jörg full_name: Geiger, Jörg R last_name: Geiger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081. doi:10.1038/nprot.2006.312 apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006). Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312 chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 . ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp recording from mossy fiber terminals in hippocampal slices,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006. ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81. mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 . short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols 1 (2006) 2075–81. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:25Z day: '01' doi: '10.1038/nprot.2006.312 ' extern: 1 intvolume: ' 1' issue: '4' month: '01' page: 2075 - 81 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '2392' quality_controlled: 0 status: public title: Patch-clamp recording from mossy fiber terminals in hippocampal slices type: journal_article volume: 1 year: '2006' ... --- _id: '3890' abstract: - lang: eng text: We consider two-player infinite games played on graphs. The games are concurrent, in that at each state the players choose their moves simultaneously and independently, and stochastic, in that the moves determine a probability distribution for the successor state. The value of a game is the maximal probability with which a player can guarantee the satisfaction of her objective. We show that the values of concurrent games with w-regular objectives expressed as parity conditions can be decided in NP boolean AND coNP. This result substantially improves the best known previous bound of 3EXPTIME. It also shows that the full class of concurrent parity games is no harder than the special case of turn-based stochastic reachability games, for which NP boolean AND coNP is the best known bound. While the previous, more restricted NP boolean AND coNP results for graph games relied on the existence of particularly simple (pure memoryless) optimal strategies, in concurrent games with parity objectives optimal strategies may not exist, and epsilon-optimal strategies (which achieve the value of the game within a parameter epsilon > 0) require in general both randomization and infinite memory. Hence our proof must rely on a more detailed analysis of strategies and, in addition to the main result, yields two results that are interesting on their own. First, we show that there exist epsilon-optimal strategies that in the limit coincide with memoryless strategies; this parallels the celebrated result of Mertens-Neyman for concurrent games with limit-average objectives. Second, we complete the characterization of the memory requirements for epsilon-optimal strategies for concurrent games with parity conditions, by showing that memoryless strategies suffice for epsilon-optimality for coBachi conditions. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. 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. The complexity of quantitative concurrent parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity of quantitative concurrent parity games (pp. 678–687). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2006, pp. 678–687.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.' mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:05:43Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '01' doi: 10.1145/1109557.1109631 extern: 1 month: '01' page: 678 - 687 publication_status: published publisher: SIAM publist_id: '2273' quality_controlled: 0 status: public title: The complexity of quantitative concurrent parity games type: conference year: '2006' ... --- _id: '3889' abstract: - lang: eng text: We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant 2.4530.02. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19' apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19' chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302. Springer, 2006. https://doi.org/10.1007/11874683_19. ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for omega-regular games with imperfect information,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 287–302.' ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207, 287–302.' mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19. short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 287–302. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:43Z date_published: 2006-11-13T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '13' doi: 10.1007/11874683_19 extern: 1 intvolume: ' 4207' month: '11' page: 287 - 302 publication_status: published publisher: Springer publist_id: '2276' quality_controlled: 0 status: public title: Algorithms for omega-regular games with imperfect information type: conference volume: 4207 year: '2006' ... --- _id: '3891' abstract: - lang: eng text: 'We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).' alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Concurrent games with tail objectives. In: Vol 4207. Springer; 2006:256-270. doi:10.1007/11874683_17' apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp. 256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17' chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70. Springer, 2006. https://doi.org/10.1007/11874683_17. ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.' ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 256–270.' mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol. 4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17. short: K. Chatterjee, in:, Springer, 2006, pp. 256–270. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:44Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '28' doi: 10.1007/11874683_17 extern: 1 intvolume: ' 4207' month: '09' page: 256 - 270 publication_status: published publisher: Springer publist_id: '2272' quality_controlled: 0 status: public title: Concurrent games with tail objectives type: conference volume: 4207 year: '2006' ... --- _id: '3888' abstract: - lang: eng text: A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with omega-regular winning conditions specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete, respectively. The value of the game for a player at a state s given an objective Phi is the maximal probability with which the player can guarantee the satisfaction of Phi from s. We present a strategy-improvement algorithm to compute values in stochastic Rabin games, where an improvement step involves solving Markov decision processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values for stochastic Streett games but does not directly yield an optimal strategy for Streett objectives. We then show how to obtain an optimal strategy for Streett objectives by solving certain nonstochastic Streett games. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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, Henzinger TA. Strategy improvement for stochastic Rabin and Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2006:375-389. doi:10.1007/11817949_25' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006. https://doi.org/10.1007/11817949_25. ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137, pp. 375–389.' ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25. short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–389. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:43Z date_published: 2006-08-10T00:00:00Z date_updated: 2021-01-12T07:52:58Z day: '10' doi: 10.1007/11817949_25 extern: 1 intvolume: ' 4137' month: '08' page: 375 - 389 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2278' quality_controlled: 0 status: public title: Strategy improvement for stochastic Rabin and Streett games type: conference volume: 4137 year: '2006' ... --- _id: '3908' abstract: - lang: eng text: 'It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.' author: - first_name: Jana full_name: Ustinova, Jana last_name: Ustinova - first_name: Roland full_name: Achmann, Roland last_name: Achmann - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Frieder full_name: Mayer, Frieder last_name: Mayer citation: ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 2006;62(2):158-167. doi:10.1007/s00239-005-0022-6' apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6' chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.' ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.' ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 62(2), 158–167.' mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution, vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.' short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution 62 (2006) 158–167. date_created: 2018-12-11T12:05:49Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '01' doi: 10.1007/s00239-005-0022-6 extern: '1' intvolume: ' 62' issue: '2' language: - iso: eng month: '02' oa_version: None page: 158 - 167 publication: Journal of Molecular Evolution publication_status: published publisher: Springer publist_id: '2242' status: public title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2006' ... --- _id: '3934' abstract: - lang: eng text: T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla. author: - first_name: Mihaela full_name: Drumea-Mirancea, Mihaela last_name: Drumea Mirancea - first_name: Johannes full_name: Wessels, Johannes T last_name: Wessels - first_name: Claudia full_name: Müller, Claudia A last_name: Müller - first_name: Mike full_name: Essl, Mike last_name: Essl - first_name: Johannes full_name: Eble, Johannes A last_name: Eble - first_name: Eva full_name: Tolosa, Eva last_name: Tolosa - first_name: Manuel full_name: Koch, Manuel last_name: Koch - first_name: Dieter full_name: Reinhardt, Dieter P last_name: Reinhardt - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin - first_name: York full_name: Stierhof, York-Dieter last_name: Stierhof - first_name: Heinz full_name: Schwarz, Heinz last_name: Schwarz - first_name: Gerd full_name: Klein, Gerd last_name: Klein citation: ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405. doi:10.1242/​jcs.02840' apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa, E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.02840' chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl, Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/​jcs.02840.' ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules,” Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp. 1396–1405, 2006.' ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M, Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.' mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006, pp. 1396–405, doi:10.1242/​jcs.02840.' short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M. Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein, Journal of Cell Science 119 (2006) 1396–1405. date_created: 2018-12-11T12:05:58Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1242/​jcs.02840 extern: 1 intvolume: ' 119' issue: Pt 7 month: '04' page: 1396 - 1405 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '2192' quality_controlled: 0 status: public title: 'Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules' type: journal_article volume: 119 year: '2006' ... --- _id: '3935' abstract: - lang: eng text: Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis. author: - first_name: Haiyan full_name: Chu, Haiyan last_name: Chu - first_name: Ingo full_name: Thievessen, Ingo last_name: Thievessen - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Ari full_name: Waisman, Ari last_name: Waisman - first_name: Attila full_name: Braun, Attila last_name: Braun - first_name: Angelika full_name: Noegel, Angelika A last_name: Noegel - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006 apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A., … Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006 chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman, Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology. American Society for Microbiology, 2006. https://doi.org/10.1128/MCB.26.5.1817-1825.2006. ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response,” Molecular and Cellular Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825, 2006. ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A, Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5), 1817–1825. mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology, vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006. short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A. Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825. date_created: 2018-12-11T12:05:58Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1128/MCB.26.5.1817-1825.2006 extern: 1 intvolume: ' 26' issue: '5' month: '03' page: 1817 - 1825 publication: Molecular and Cellular Biology publication_status: published publisher: American Society for Microbiology publist_id: '2193' quality_controlled: 0 status: public title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response type: journal_article volume: 26 year: '2006' ... --- _id: '3936' abstract: - lang: eng text: At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials. author: - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Martina full_name: Bauer, Martina last_name: Bauer - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490. doi:10.1016/j.ceb.2006.08.007' apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007' chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.' ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes and signaling relay for blood cells,” Current Opinion in Cell Biology, vol. 18, no. 5. Elsevier, pp. 482–490, 2006.' ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.' mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier, 2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.' short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology 18 (2006) 482–490. date_created: 2018-12-11T12:05:59Z date_published: 2006-10-01T00:00:00Z date_updated: 2021-01-12T07:53:19Z day: '01' doi: 10.1016/j.ceb.2006.08.007 extern: 1 intvolume: ' 18' issue: '5' month: '10' page: 482 - 490 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '2191' quality_controlled: 0 status: public title: 'β1 integrins: zip codes and signaling relay for blood cells' type: journal_article volume: 18 year: '2006' ... --- _id: '4140' abstract: - lang: eng text: Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation. article_processing_charge: No author: - first_name: Sabine full_name: Witzel, Sabine last_name: Witzel - first_name: Vitaly full_name: Zimyanin, Vitaly last_name: Zimyanin - first_name: Filipa full_name: Carreira Barbosa, Filipa last_name: Carreira Barbosa - 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: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017 apa: Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg, C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200606017 chicago: Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada, and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology. Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017. ieee: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg, “Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller University Press, pp. 791–802, 2006. ista: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 175(5), 791–802. mla: Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175, no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017. short: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 791–802. date_created: 2018-12-11T12:07:11Z date_published: 2006-12-04T00:00:00Z date_updated: 2021-01-12T07:54:48Z day: '04' doi: 10.1083/jcb.200606017 extern: '1' intvolume: ' 175' issue: '5' language: - iso: eng month: '12' oa_version: None page: 791 - 802 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '1980' status: public title: Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 175 year: '2006' ... --- _id: '4145' abstract: - lang: eng text: The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development. article_processing_charge: No author: - first_name: Davide full_name: Tonelli, Davide last_name: Tonelli - first_name: Frederico full_name: Calegari, Frederico last_name: Calegari - first_name: Ji full_name: Fei, Ji last_name: Fei - first_name: Tadashi full_name: Nomura, Tadashi last_name: Nomura - first_name: Noriko full_name: Osumi, Noriko last_name: Osumi - 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 - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner citation: ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296 apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296 chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296. ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006. ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732. mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296. short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732. date_created: 2018-12-11T12:07:12Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:54:50Z day: '01' doi: 10.2144/000112296 extern: '1' intvolume: ' 41' issue: '6' language: - iso: eng month: '12' oa_version: None page: 727 - 732 publication: Biotechniques publication_status: published publisher: Informa Healthcare publist_id: '1974' status: public title: Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2006' ... --- _id: '4176' abstract: - lang: eng text: 'During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Petra full_name: Stockinger, Petra last_name: Stockinger - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - 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: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928 apa: Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02928 chicago: Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928. ieee: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P. J. Heisenberg, “Identification of regulators of germ layer morphogenesis using proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company of Biologists, pp. 2073–2083, 2006. ista: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. 2006. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 119(10), 2073–2083. mla: Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no. 10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928. short: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J. Heisenberg, Journal of Cell Science 119 (2006) 2073–2083. date_created: 2018-12-11T12:07:24Z date_published: 2006-05-15T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '15' doi: 10.1242/jcs.02928 extern: '1' intvolume: ' 119' issue: '10' language: - iso: eng month: '05' oa_version: None page: 2073 - 2083 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '1944' status: public title: Identification of regulators of germ layer morphogenesis using proteomics in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2006' ... --- _id: '4173' abstract: - lang: eng text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - 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: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1 apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1 chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central, 2006. https://doi.org/10.1186/1471-213X-6-1. ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006. ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9. mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1. short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9. date_created: 2018-12-11T12:07:23Z date_published: 2006-01-13T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '13' doi: 10.1186/1471-213X-6-1 extern: '1' intvolume: ' 6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.biomedcentral.com/1471-213X/6/1 month: '01' oa: 1 oa_version: None page: 1 - 9 publication: BMC Developmental Biology publication_status: published publisher: BioMed Central publist_id: '1945' status: public title: Proteomics of early zebrafish embryos tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2006' ... --- _id: '4178' abstract: - lang: eng text: Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools. article_processing_charge: No author: - first_name: Tobias full_name: Langenberg, Tobias last_name: Langenberg - first_name: Tadeusz full_name: Dracz, Tadeusz last_name: Dracz - first_name: Andrew full_name: Oates, Andrew last_name: Oates - 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 - first_name: Michael full_name: Brand, Michael last_name: Brand citation: ama: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 2006;235(4):928-933. doi:10.1002/dvdy.20692 apa: Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M. (2006). Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692 chicago: Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg, and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692. ieee: T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis and visualization of cell movement in the developing zebrafish brain,” Developmental Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006. ista: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 235(4), 928–933. mla: Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no. 4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692. short: T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental Dynamics 235 (2006) 928–933. date_created: 2018-12-11T12:07:25Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '01' doi: 10.1002/dvdy.20692 extern: '1' intvolume: ' 235' issue: '4' language: - iso: eng month: '04' oa_version: None page: 928 - 933 publication: Developmental Dynamics publication_status: published publisher: Wiley-Blackwell publist_id: '1940' status: public title: Analysis and visualization of cell movement in the developing zebrafish brain type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2006' ... --- _id: '4184' abstract: - lang: eng text: Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis. article_processing_charge: No author: - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Beatriz full_name: Fernández, Beatriz last_name: Fernández - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: António full_name: Jacinto, António last_name: Jacinto - 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: 'Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 2006;133(14):2671-2681. doi:doi: 10.1242/dev.02439' apa: 'Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P. J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439' chicago: 'Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development. Company of Biologists, 2006. https://doi.org/doi: 10.1242/dev.02439.' ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,” Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006. ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 133(14), 2671–2681. mla: 'Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company of Biologists, 2006, pp. 2671–81, doi:doi: 10.1242/dev.02439.' short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development 133 (2006) 2671–2681. date_created: 2018-12-11T12:07:27Z date_published: 2006-07-15T00:00:00Z date_updated: 2021-01-12T07:55:08Z day: '15' doi: 'doi: 10.1242/dev.02439' extern: '1' intvolume: ' 133' issue: '14' language: - iso: eng month: '07' oa_version: None page: 2671 - 2681 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1935' status: public title: Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 133 year: '2006' ... --- _id: '4218' abstract: - lang: eng text: The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration. article_processing_charge: No author: - first_name: Heiko full_name: Blaser, Heiko last_name: Blaser - first_name: Michal full_name: Reichman Fried, Michal last_name: Reichman Fried - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Karin full_name: Dumstrei, Karin last_name: Dumstrei - first_name: Florence full_name: Marlow, Florence last_name: Marlow - first_name: Koichi full_name: Kawakami, Koichi last_name: Kawakami - first_name: Lilianna full_name: Solnica Krezel, Lilianna last_name: Solnica Krezel - 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 - first_name: Erez full_name: Raz, Erez last_name: Raz citation: ama: 'Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023' apa: 'Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami, K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2006.09.023' chicago: 'Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei, Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2006.09.023.' ieee: 'H. Blaser et al., “Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow,” Developmental Cell, vol. 11, no. 5. Cell Press, pp. 613–627, 2006.' ista: 'Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K, Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 11(5), 613–627.' mla: 'Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol. 11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.' short: H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami, L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627. date_created: 2018-12-11T12:07:39Z date_published: 2006-11-06T00:00:00Z date_updated: 2021-01-12T07:55:23Z day: '06' doi: 10.1016/j.devcel.2006.09.023 extern: '1' intvolume: ' 11' issue: '5' language: - iso: eng month: '11' oa_version: None page: 613 - 627 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '1898' status: public title: 'Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2006' ... --- _id: '4237' abstract: - lang: eng text: The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved. article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802 apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. Elsevier. https://doi.org/3802 chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802. ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,” Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256, 2006. ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 238(2), 245–256. mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56, doi:3802. short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256. date_created: 2018-12-11T12:07:46Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:31Z day: '01' doi: '3802' extern: '1' intvolume: ' 238' issue: '2' language: - iso: eng month: '01' oa_version: None page: 245 - 256 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1878' status: public title: Density-dependence as a size-independent regulatory mechanism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 238 year: '2006' ... --- _id: '4235' author: - first_name: Harold full_name: Harold Vladar id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: J. full_name: González,J. A last_name: González citation: ama: de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109. apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier. chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2006. ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology. Elsevier, pp. 91–109, 2006. ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology., 91–109. mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, Elsevier, 2006, pp. 91–109. short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109. date_created: 2018-12-11T12:07:45Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:30Z day: '01' extern: 1 month: '01' page: 91 - 109 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1879' quality_controlled: 0 status: public title: Dynamic response of cancer under the influence of immunological activity and therapy type: journal_article year: '2006' ... --- _id: '4248' abstract: - lang: eng text: 'In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.' author: - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination. Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586 apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586 chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.106.058586 . ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of recombination,” Genetics, vol. 173, no. 3. Genetics Society of America, pp. 1793–1811, 2006. ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination. Genetics. 173(3), 1793–1811. mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America, 2006, pp. 1793–811, doi:10.1534/genetics.106.058586 . short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811. date_created: 2018-12-11T12:07:50Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T07:55:36Z day: '01' doi: '10.1534/genetics.106.058586 ' extern: 1 intvolume: ' 173' issue: '3' month: '07' page: 1793 - 1811 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '1854' quality_controlled: 0 status: public title: The Hill-Robertson effect and the evolution of recombination type: journal_article volume: 173 year: '2006' ... --- _id: '4250' abstract: - lang: eng text: A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032' apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032' chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.' ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.' ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current Biology. 16(16), 647–650.' mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.' short: N.H. Barton, Current Biology 16 (2006) 647–650. date_created: 2018-12-11T12:07:51Z date_published: 2006-08-22T00:00:00Z date_updated: 2019-04-26T07:22:41Z day: '22' doi: 10.1016/j.cub.2006.07.032 extern: 1 intvolume: ' 16' issue: '16' month: '08' page: 647 - 650 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '1850' quality_controlled: 0 status: public title: 'Evolutionary Biology: How did the human species form?' type: review volume: 16 year: '2006' ... --- _id: '4359' alternative_title: - LNCS 3855 author: - first_name: Thomas full_name: Thomas Wies id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Viktor full_name: Kuncak, Viktor last_name: Kuncak - first_name: Patrick full_name: Lam,Patrick last_name: Lam - first_name: Andreas full_name: Podelski,Andreas last_name: Podelski - first_name: Martin full_name: Rinard,Martin last_name: Rinard citation: ama: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis. In: Springer; 2006:157-173. doi:1551' apa: 'Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Springer. https://doi.org/1551' chicago: Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551. ieee: 'T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, 2006, pp. 157–173.' ista: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, , 157–173.' mla: Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp. 157–73, doi:1551. short: T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006, pp. 157–173. conference: name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' date_created: 2018-12-11T12:08:27Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:23Z day: '01' doi: '1551' extern: 1 month: '01' page: 157 - 173 publication_status: published publisher: Springer publist_id: '1097' quality_controlled: 0 status: public title: Field Constraint Analysis type: conference year: '2006' ... --- _id: '4373' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future. In: Springer; 2006:2-16. doi:1571' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic: Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1571' chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic: Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.' ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present, Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 2–16.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present, Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.' mla: 'Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future. Springer, 2006, pp. 2–16, doi:1571.' short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-01-23T00:00:00Z date_updated: 2021-01-12T07:56:29Z day: '23' doi: '1571' extern: 1 month: '01' page: 2 - 16 publication_status: published publisher: Springer publist_id: '1084' quality_controlled: 0 status: public title: 'Real Time Temporal Logic: Past, Present, Future' type: conference year: '2006' ... --- _id: '4374' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer; 2006:274-289. doi:1570' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata (pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1570' chicago: Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,” 274–89. Springer, 2006. https://doi.org/1570. ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.' mla: Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp. 274–89, doi:1570. short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-10-19T00:00:00Z date_updated: 2021-01-12T07:56:30Z day: '19' doi: '1570' extern: 1 month: '10' page: 274 - 289 publication_status: published publisher: Springer publist_id: '1085' quality_controlled: 0 status: public title: From MITL to Timed Automata type: conference year: '2006' ... --- _id: '4406' abstract: - lang: eng text: We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata. acknowledgement: This research was supported in part by the NSF grants CCR-0234690 and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre Fédéré en Vérification.” alternative_title: - LNCS author: - first_name: Martin full_name: De Wulf, Martin last_name: De Wulf - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30. doi:10.1007/11817963_5' apa: 'De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains: A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5' chicago: 'De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains: A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer, 2006. https://doi.org/10.1007/11817963_5.' ieee: 'M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new algorithm for checking universality of finite automata,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 17–30.' ista: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm for checking universality of finite automata. CAV: Computer Aided Verification, LNCS, vol. 4144, 17–30.' mla: 'De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.' short: M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 17–30. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:41Z date_published: 2006-08-08T00:00:00Z date_updated: 2021-01-12T07:56:45Z day: '08' doi: 10.1007/11817963_5 extern: 1 intvolume: ' 4144' month: '08' page: 17 - 30 publication_status: published publisher: Springer publist_id: '326' quality_controlled: 0 status: public title: 'Antichains: A new algorithm for checking universality of finite automata' type: conference volume: 4144 year: '2006' ... --- _id: '4401' alternative_title: - LNCS author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Steve full_name: Zdancewic,Steve last_name: Zdancewic citation: ama: 'Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer; 2006:107-118. doi:1543' apa: 'Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/1543' chicago: Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under Refinement,” 107–18. Springer, 2006. https://doi.org/1543. ieee: 'R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,” presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.' ista: 'Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement. ICALP: Automata, Languages and Programming, LNCS, , 107–118.' mla: Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer, 2006, pp. 107–18, doi:1543. short: R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:08:40Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:42Z day: '01' doi: '1543' extern: 1 month: '01' page: 107 - 118 publication_status: published publisher: Springer publist_id: '1054' quality_controlled: 0 status: public title: Preserving Secrecy Under Refinement type: conference year: '2006' ... --- _id: '4437' abstract: - lang: eng text: The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies. acknowledgement: This research was supported in part by the Swiss National Science Foundation. 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: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207. Springer; 2006:395-410. doi:10.1007/11874683_26' apa: 'Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization (Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_26' chicago: Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,” 4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26. ieee: 'T. A. Henzinger and N. Piterman, “Solving games without determinization,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.' ista: 'Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL: Computer Science Logic, LNCS, vol. 4207, 395–410.' mla: Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization. Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26. short: T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:08:51Z date_published: 2006-09-20T00:00:00Z date_updated: 2021-01-12T07:56:58Z day: '20' doi: 10.1007/11874683_26 extern: 1 intvolume: ' 4207' month: '09' page: 395 - 410 publication_status: published publisher: Springer publist_id: '295' quality_controlled: 0 status: public title: Solving games without determinization type: conference volume: 4207 year: '2006' ... --- _id: '4436' abstract: - lang: eng text: We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments. 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: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: 'Henzinger TA, Matic S. An interface algebra for real-time components. In: IEEE; 2006:253-266. doi:10.1109/RTAS.2006.11' apa: 'Henzinger, T. A., & Matic, S. (2006). An interface algebra for real-time components (pp. 253–266). Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, IEEE. https://doi.org/10.1109/RTAS.2006.11' chicago: Henzinger, Thomas A, and Slobodan Matic. “An Interface Algebra for Real-Time Components,” 253–66. IEEE, 2006. https://doi.org/10.1109/RTAS.2006.11. ieee: 'T. A. Henzinger and S. Matic, “An interface algebra for real-time components,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, 2006, pp. 253–266.' ista: 'Henzinger TA, Matic S. 2006. An interface algebra for real-time components. RTAS: Real-time and Embedded Technology and Applications Symposium, 253–266.' mla: Henzinger, Thomas A., and Slobodan Matic. An Interface Algebra for Real-Time Components. IEEE, 2006, pp. 253–66, doi:10.1109/RTAS.2006.11. short: T.A. Henzinger, S. Matic, in:, IEEE, 2006, pp. 253–266. conference: name: 'RTAS: Real-time and Embedded Technology and Applications Symposium' date_created: 2018-12-11T12:08:50Z date_published: 2006-04-24T00:00:00Z date_updated: 2021-01-12T07:56:57Z day: '24' doi: 10.1109/RTAS.2006.11 extern: 1 month: '04' page: 253 - 266 publication_status: published publisher: IEEE publist_id: '294' quality_controlled: 0 status: public title: An interface algebra for real-time components type: conference year: '2006' ... --- _id: '4432' abstract: - lang: eng text: We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision. acknowledgement: This research was supported in part by the NSF grants CCR-0208875, CCR-0225610, and CCR-0234690. 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: Vinayak full_name: Prabhu, Vinayak S last_name: Prabhu citation: ama: 'Henzinger TA, Prabhu V. Timed alternating-time temporal logic. In: Vol 4202. Springer; 2006:1-17. doi:10.1007/11867340_1' apa: 'Henzinger, T. A., & Prabhu, V. (2006). Timed alternating-time temporal logic (Vol. 4202, pp. 1–17). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/11867340_1' chicago: Henzinger, Thomas A, and Vinayak Prabhu. “Timed Alternating-Time Temporal Logic,” 4202:1–17. Springer, 2006. https://doi.org/10.1007/11867340_1. ieee: 'T. A. Henzinger and V. Prabhu, “Timed alternating-time temporal logic,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, vol. 4202, pp. 1–17.' ista: 'Henzinger TA, Prabhu V. 2006. Timed alternating-time temporal logic. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 4202, 1–17.' mla: Henzinger, Thomas A., and Vinayak Prabhu. Timed Alternating-Time Temporal Logic. Vol. 4202, Springer, 2006, pp. 1–17, doi:10.1007/11867340_1. short: T.A. Henzinger, V. Prabhu, in:, Springer, 2006, pp. 1–17. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:49Z date_published: 2006-09-19T00:00:00Z date_updated: 2021-01-12T07:56:56Z day: '19' doi: 10.1007/11867340_1 extern: 1 intvolume: ' 4202' month: '09' page: 1 - 17 publication_status: published publisher: Springer publist_id: '296' quality_controlled: 0 status: public title: Timed alternating-time temporal logic type: conference volume: 4202 year: '2006' ... --- _id: '4431' abstract: - lang: eng text: 'We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science.' acknowledgement: Supported in part by the ARTIST2 European Network of Excellence on Embedded Systems Design, by the NSF ITR Center on Hybrid and Embedded Software Systems (CHESS), and by the SNSF NCCR on Mobile Information and Communication Systems (MICS). 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: Joseph full_name: Sifakis, Joseph last_name: Sifakis citation: ama: 'Henzinger TA, Sifakis J. The embedded systems design challenge. In: Vol 4085. Springer; 2006:1-15. doi:10.1007/11813040_1' apa: 'Henzinger, T. A., & Sifakis, J. (2006). The embedded systems design challenge (Vol. 4085, pp. 1–15). Presented at the FM: Formal Methods, Springer. https://doi.org/10.1007/11813040_1' chicago: Henzinger, Thomas A, and Joseph Sifakis. “The Embedded Systems Design Challenge,” 4085:1–15. Springer, 2006. https://doi.org/10.1007/11813040_1. ieee: 'T. A. Henzinger and J. Sifakis, “The embedded systems design challenge,” presented at the FM: Formal Methods, 2006, vol. 4085, pp. 1–15.' ista: 'Henzinger TA, Sifakis J. 2006. The embedded systems design challenge. FM: Formal Methods, LNCS, vol. 4085, 1–15.' mla: Henzinger, Thomas A., and Joseph Sifakis. The Embedded Systems Design Challenge. Vol. 4085, Springer, 2006, pp. 1–15, doi:10.1007/11813040_1. short: T.A. Henzinger, J. Sifakis, in:, Springer, 2006, pp. 1–15. conference: name: 'FM: Formal Methods' date_created: 2018-12-11T12:08:49Z date_published: 2006-08-10T00:00:00Z date_updated: 2021-01-12T07:56:55Z day: '10' doi: 10.1007/11813040_1 extern: 1 intvolume: ' 4085' month: '08' page: 1 - 15 publication_status: published publisher: Springer publist_id: '301' quality_controlled: 0 status: public title: The embedded systems design challenge type: conference volume: 4085 year: '2006' ... --- _id: '4451' 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 alternation-free 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. 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: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 2006;354(2):173-186. doi:10.1016/j.tcs.2005.11.015 apa: Henzinger, T. A., Kupferman, O., & Majumdar, R. (2006). On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2005.11.015 chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2005.11.015. ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential fragments of the mu-calculus,” Theoretical Computer Science, vol. 354, no. 2. Elsevier, pp. 173–186, 2006. ista: Henzinger TA, Kupferman O, Majumdar R. 2006. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 354(2), 173–186. mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science, vol. 354, no. 2, Elsevier, 2006, pp. 173–86, doi:10.1016/j.tcs.2005.11.015. short: T.A. Henzinger, O. Kupferman, R. Majumdar, Theoretical Computer Science 354 (2006) 173–186. date_created: 2018-12-11T12:08:55Z date_published: 2006-03-28T00:00:00Z date_updated: 2021-01-12T07:57:04Z day: '28' doi: 10.1016/j.tcs.2005.11.015 extern: 1 intvolume: ' 354' issue: '2' month: '03' page: 173 - 186 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '276' quality_controlled: 0 status: public title: On the universal and existential fragments of the mu-calculus type: journal_article volume: 354 year: '2006' ... --- _id: '4523' abstract: - lang: eng text: We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi. author: - first_name: Bhargav full_name: Gulavani, Bhargav S last_name: Gulavani - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Yamini full_name: Kannan, Yamini last_name: Kannan - first_name: Aditya full_name: Nori, Aditya V last_name: Nori - first_name: Sriram full_name: Rajamani, Sriram K last_name: Rajamani citation: ama: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. Synergy: A new algorithm for property checking. In: ACM; 2006:117-127. doi:10.1145/1181775.1181790' apa: 'Gulavani, B., Henzinger, T. A., Kannan, Y., Nori, A., & Rajamani, S. (2006). Synergy: A new algorithm for property checking (pp. 117–127). Presented at the FSE: Foundations of Software Engineering, ACM. https://doi.org/10.1145/1181775.1181790' chicago: 'Gulavani, Bhargav, Thomas A Henzinger, Yamini Kannan, Aditya Nori, and Sriram Rajamani. “Synergy: A New Algorithm for Property Checking,” 117–27. ACM, 2006. https://doi.org/10.1145/1181775.1181790.' ieee: 'B. Gulavani, T. A. Henzinger, Y. Kannan, A. Nori, and S. Rajamani, “Synergy: A new algorithm for property checking,” presented at the FSE: Foundations of Software Engineering, 2006, pp. 117–127.' ista: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. 2006. Synergy: A new algorithm for property checking. FSE: Foundations of Software Engineering, 117–127.' mla: 'Gulavani, Bhargav, et al. Synergy: A New Algorithm for Property Checking. ACM, 2006, pp. 117–27, doi:10.1145/1181775.1181790.' short: B. Gulavani, T.A. Henzinger, Y. Kannan, A. Nori, S. Rajamani, in:, ACM, 2006, pp. 117–127. conference: name: 'FSE: Foundations of Software Engineering' date_created: 2018-12-11T12:09:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '01' doi: 10.1145/1181775.1181790 extern: 1 month: '01' page: 117 - 127 publication_status: published publisher: ACM publist_id: '206' quality_controlled: 0 status: public title: 'Synergy: A new algorithm for property checking' type: conference year: '2006' ... --- _id: '4526' abstract: - lang: eng text: 'We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller.' 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: Daniel full_name: Iercan, Daniel last_name: Iercan - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch - first_name: Alberto full_name: Sangiovanni-Vincentelli, Alberto last_name: Sangiovanni Vincentelli citation: ama: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. A hierarchical coordination language for interacting real-time tasks. In: ACM; 2006:132-141. doi:10.1145/1176887.1176907' apa: 'Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., & Sangiovanni Vincentelli, A. (2006). A hierarchical coordination language for interacting real-time tasks (pp. 132–141). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1176887.1176907' chicago: Ghosal, Arkadeb, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, and Alberto Sangiovanni Vincentelli. “A Hierarchical Coordination Language for Interacting Real-Time Tasks,” 132–41. ACM, 2006. https://doi.org/10.1145/1176887.1176907. ieee: 'A. Ghosal, T. A. Henzinger, D. Iercan, C. Kirsch, and A. Sangiovanni Vincentelli, “A hierarchical coordination language for interacting real-time tasks,” presented at the EMSOFT: Embedded Software , 2006, pp. 132–141.' ista: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. 2006. A hierarchical coordination language for interacting real-time tasks. EMSOFT: Embedded Software , 132–141.' mla: Ghosal, Arkadeb, et al. A Hierarchical Coordination Language for Interacting Real-Time Tasks. ACM, 2006, pp. 132–41, doi:10.1145/1176887.1176907. short: A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, A. Sangiovanni Vincentelli, in:, ACM, 2006, pp. 132–141. conference: name: 'EMSOFT: Embedded Software ' date_created: 2018-12-11T12:09:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:27Z day: '01' doi: 10.1145/1176887.1176907 extern: 1 month: '01' page: 132 - 141 publication_status: published publisher: ACM publist_id: '201' quality_controlled: 0 status: public title: A hierarchical coordination language for interacting real-time tasks type: conference year: '2006' ... --- _id: '4528' abstract: - lang: eng text: Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models mathematical and computational - according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems executable biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline. author: - first_name: Jasmin full_name: Fisher, Jasmin last_name: Fisher - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Fisher J, Henzinger TA. Executable biology. In: IEEE; 2006:1675-1682. doi:10.1109/WSC.2006.322942' apa: 'Fisher, J., & Henzinger, T. A. (2006). Executable biology (pp. 1675–1682). Presented at the WSC: Winter Simulation Conference, IEEE. https://doi.org/10.1109/WSC.2006.322942' chicago: Fisher, Jasmin, and Thomas A Henzinger. “Executable Biology,” 1675–82. IEEE, 2006. https://doi.org/10.1109/WSC.2006.322942. ieee: 'J. Fisher and T. A. Henzinger, “Executable biology,” presented at the WSC: Winter Simulation Conference, 2006, pp. 1675–1682.' ista: 'Fisher J, Henzinger TA. 2006. Executable biology. WSC: Winter Simulation Conference, 1675–1682.' mla: Fisher, Jasmin, and Thomas A. Henzinger. Executable Biology. IEEE, 2006, pp. 1675–82, doi:10.1109/WSC.2006.322942. short: J. Fisher, T.A. Henzinger, in:, IEEE, 2006, pp. 1675–1682. conference: name: 'WSC: Winter Simulation Conference' date_created: 2018-12-11T12:09:19Z date_published: 2006-12-03T00:00:00Z date_updated: 2021-01-12T07:59:28Z day: '03' doi: 10.1109/WSC.2006.322942 extern: 1 month: '12' page: 1675 - 1682 publication_status: published publisher: IEEE publist_id: '197' quality_controlled: 0 status: public title: Executable biology type: conference year: '2006' ... --- _id: '4539' abstract: - lang: eng text: Games on graphs with ω-regular objectives provide a model for the control and synthesis of reactive systems. Every ω-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Büchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett (fairness) objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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, Henzinger TA. Finitary winning in omega-regular games. In: Vol 3920. Springer; 2006:257-271. doi:10.1007/11691372_17' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Finitary winning in omega-regular games (Vol. 3920, pp. 257–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/11691372_17' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Finitary Winning in Omega-Regular Games,” 3920:257–71. Springer, 2006. https://doi.org/10.1007/11691372_17. ieee: 'K. Chatterjee and T. A. Henzinger, “Finitary winning in omega-regular games,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2006, vol. 3920, pp. 257–271.' ista: 'Chatterjee K, Henzinger TA. 2006. Finitary winning in omega-regular games. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 3920, 257–271.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Finitary Winning in Omega-Regular Games. Vol. 3920, Springer, 2006, pp. 257–71, doi:10.1007/11691372_17. short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 257–271. conference: name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' date_created: 2018-12-11T12:09:22Z date_published: 2006-03-15T00:00:00Z date_updated: 2021-01-12T07:59:32Z day: '15' doi: 10.1007/11691372_17 extern: 1 intvolume: ' 3920' month: '03' page: 257 - 271 publication_status: published publisher: Springer publist_id: '183' quality_controlled: 0 status: public title: Finitary winning in omega-regular games type: conference volume: 3920 year: '2006' ... --- _id: '4538' abstract: - lang: eng text: A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives. These games lie in NP ∩ coNP. We present a strategy improvement algorithm for stochastic parity games; this is the first non-brute-force algorithm for solving these games. From the strategy improvement algorithm we obtain a randomized subexponential-time algorithm to solve such games. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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, Henzinger TA. Strategy improvement and randomized subexponential algorithms for stochastic parity games. In: Vol 3884. Springer; 2006:512-523. doi:10.1007/11672142_42' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement and randomized subexponential algorithms for stochastic parity games (Vol. 3884, pp. 512–523). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_42' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games,” 3884:512–23. Springer, 2006. https://doi.org/10.1007/11672142_42. ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement and randomized subexponential algorithms for stochastic parity games,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 512–523.' ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement and randomized subexponential algorithms for stochastic parity games. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 512–523.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games. Vol. 3884, Springer, 2006, pp. 512–23, doi:10.1007/11672142_42. short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 512–523. conference: name: 'STACS: Theoretical Aspects of Computer Science' date_created: 2018-12-11T12:09:22Z date_published: 2006-02-14T00:00:00Z date_updated: 2021-01-12T07:59:32Z day: '14' doi: 10.1007/11672142_42 extern: 1 intvolume: ' 3884' month: '02' page: 512 - 523 publication_status: published publisher: Springer publist_id: '184' quality_controlled: 0 status: public title: Strategy improvement and randomized subexponential algorithms for stochastic parity games type: conference volume: 3884 year: '2006' ... --- _id: '4551' abstract: - lang: eng text: "We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.\nThis research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. " acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - 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, Majumdar R, Henzinger TA. Markov decision processes with multiple objectives. In: Vol 3884. Springer; 2006:325-336. doi:10.1007/11672142_26' apa: 'Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2006). Markov decision processes with multiple objectives (Vol. 3884, pp. 325–336). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_26' chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Markov Decision Processes with Multiple Objectives,” 3884:325–36. Springer, 2006. https://doi.org/10.1007/11672142_26. ieee: 'K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Markov decision processes with multiple objectives,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 325–336.' ista: 'Chatterjee K, Majumdar R, Henzinger TA. 2006. Markov decision processes with multiple objectives. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 325–336.' mla: Chatterjee, Krishnendu, et al. Markov Decision Processes with Multiple Objectives. Vol. 3884, Springer, 2006, pp. 325–36, doi:10.1007/11672142_26. short: K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2006, pp. 325–336. conference: name: 'STACS: Theoretical Aspects of Computer Science' date_created: 2018-12-11T12:09:26Z date_published: 2006-02-14T00:00:00Z date_updated: 2021-01-12T07:59:38Z day: '14' doi: 10.1007/11672142_26 extern: 1 intvolume: ' 3884' month: '02' page: 325 - 336 publication_status: published publisher: Springer publist_id: '161' quality_controlled: 0 status: public title: Markov decision processes with multiple objectives type: conference volume: 3884 year: '2006' ... --- _id: '4550' abstract: - lang: eng text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent''s payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński citation: ama: Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. Theoretical Computer Science. 2006;365(1-2):67-82. doi:10.1016/j.tcs.2006.07.032 apa: Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2006). Games with secure equilibria. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2006.07.032 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2006.07.032. ieee: K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” Theoretical Computer Science, vol. 365, no. 1–2. Elsevier, pp. 67–82, 2006. ista: Chatterjee K, Henzinger TA, Jurdziński M. 2006. Games with secure equilibria. Theoretical Computer Science. 365(1–2), 67–82. mla: Chatterjee, Krishnendu, et al. “Games with Secure Equilibria.” Theoretical Computer Science, vol. 365, no. 1–2, Elsevier, 2006, pp. 67–82, doi:10.1016/j.tcs.2006.07.032. short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, Theoretical Computer Science 365 (2006) 67–82. date_created: 2018-12-11T12:09:26Z date_published: 2006-08-07T00:00:00Z date_updated: 2021-01-12T07:59:38Z day: '07' doi: 10.1016/j.tcs.2006.07.032 extern: 1 intvolume: ' 365' issue: 1-2 month: '08' page: 67 - 82 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '164' quality_controlled: 0 status: public title: Games with secure equilibria type: journal_article volume: 365 year: '2006' ... --- _id: '4549' abstract: - lang: eng text: We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time. acknowledgement: Supported in part by the NSF grants CCR-0234690, CCR-0208875, and CCR-0225610; by the NSF grant CCR-0132780 and ARP grant SC20051123. 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: 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: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Compositional quantitative reasoning. In: IEEE; 2006:179-188. doi:10.1109/QEST.2006.11' apa: 'Chatterjee, K., De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2006). Compositional quantitative reasoning (pp. 179–188). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.11' chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Compositional Quantitative Reasoning,” 179–88. IEEE, 2006. https://doi.org/10.1109/QEST.2006.11. ieee: 'K. Chatterjee, L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Compositional quantitative reasoning,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 179–188.' ista: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2006. Compositional quantitative reasoning. QEST: Quantitative Evaluation of Systems, 179–188.' mla: Chatterjee, Krishnendu, et al. Compositional Quantitative Reasoning. IEEE, 2006, pp. 179–88, doi:10.1109/QEST.2006.11. short: K. Chatterjee, L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, IEEE, 2006, pp. 179–188. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:26Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:59:37Z day: '01' doi: 10.1109/QEST.2006.11 extern: 1 month: '09' page: 179 - 188 publication_status: published publisher: IEEE publist_id: '163' quality_controlled: 0 status: public title: Compositional quantitative reasoning type: conference year: '2006' ... --- _id: '4552' abstract: - lang: eng text: 'A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.' 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. Strategy improvement for concurrent reachability games. In: IEEE; 2006:291-300. doi:10.1109/QEST.2006.48' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). Strategy improvement for concurrent reachability games (pp. 291–300). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.48' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability Games,” 291–300. IEEE, 2006. https://doi.org/10.1109/QEST.2006.48. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability games,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 291–300.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. Strategy improvement for concurrent reachability games. QEST: Quantitative Evaluation of Systems, 291–300.' mla: Chatterjee, Krishnendu, et al. Strategy Improvement for Concurrent Reachability Games. IEEE, 2006, pp. 291–300, doi:10.1109/QEST.2006.48. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2006, pp. 291–300. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:26Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:39Z day: '01' doi: 10.1109/QEST.2006.48 extern: 1 month: '01' page: 291 - 300 publication_status: published publisher: IEEE publist_id: '162' quality_controlled: 0 status: public title: Strategy improvement for concurrent reachability games type: conference year: '2006' ... --- _id: '4574' abstract: - lang: eng text: Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla. alternative_title: - LNCS 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: Grégory full_name: Théoduloz, Grégory last_name: Théoduloz citation: ama: 'Beyer D, Henzinger TA, Théoduloz G. Lazy shape analysis. In: Vol 4144. Springer; 2006:532-546. doi:10.1007/11817963_48' apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2006). Lazy shape analysis (Vol. 4144, pp. 532–546). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_48' chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Lazy Shape Analysis,” 4144:532–46. Springer, 2006. https://doi.org/10.1007/11817963_48. ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Lazy shape analysis,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 532–546.' ista: 'Beyer D, Henzinger TA, Théoduloz G. 2006. Lazy shape analysis. CAV: Computer Aided Verification, LNCS, vol. 4144, 532–546.' mla: Beyer, Dirk, et al. Lazy Shape Analysis. Vol. 4144, Springer, 2006, pp. 532–46, doi:10.1007/11817963_48. short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, Springer, 2006, pp. 532–546. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:09:33Z date_published: 2006-08-08T00:00:00Z date_updated: 2021-01-12T07:59:49Z day: '08' doi: 10.1007/11817963_48 extern: 1 intvolume: ' 4144' month: '08' page: 532 - 546 publication_status: published publisher: Springer publist_id: '133' quality_controlled: 0 status: public title: Lazy shape analysis type: conference volume: 4144 year: '2006' ... --- _id: '573' abstract: - lang: eng text: 'Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol. ' article_processing_charge: No author: - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Matthew full_name: Rakher, Matthew last_name: Rakher - first_name: Julio full_name: Barreiro, Julio last_name: Barreiro - first_name: Nicholas full_name: Peters, Nicholas last_name: Peters - first_name: Paul full_name: Kwiat, Paul last_name: Kwiat citation: ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual computation revisited. 2006. apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual computation revisited. ArXiv. chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Computation Revisited.” ArXiv, 2006. ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual computation revisited.” ArXiv, 2006. ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual computation revisited. mla: Hosten, Onur, et al. Counterfactual Computation Revisited. ArXiv, 2006. short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, (2006). date_created: 2018-12-11T11:47:16Z date_published: 2006-08-06T00:00:00Z date_updated: 2020-05-12T08:23:52Z day: '06' extern: '1' external_id: arxiv: - '0607101' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/quant-ph/0607101 month: '08' oa: 1 oa_version: Preprint page: '12' publication_status: published publisher: ArXiv publist_id: '7241' status: public title: Counterfactual computation revisited type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '574' abstract: - lang: eng text: 'Vaidman, in a recent article adopts the method of ''quantum weak measurements in pre- and postselected ensembles'' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. ' article_processing_charge: No author: - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul last_name: Kwiat citation: ama: Hosten O, Kwiat P. Weak measurements and counterfactual computation. 2006. apa: Hosten, O., & Kwiat, P. (2006). Weak measurements and counterfactual computation. ArXiv. chicago: Hosten, Onur, and Paul Kwiat. “Weak Measurements and Counterfactual Computation.” ArXiv, 2006. ieee: O. Hosten and P. Kwiat, “Weak measurements and counterfactual computation.” ArXiv, 2006. ista: Hosten O, Kwiat P. 2006. Weak measurements and counterfactual computation. mla: Hosten, Onur, and Paul Kwiat. Weak Measurements and Counterfactual Computation. ArXiv, 2006. short: O. Hosten, P. Kwiat, (2006). date_created: 2018-12-11T11:47:16Z date_published: 2006-12-19T00:00:00Z date_updated: 2020-05-12T08:18:01Z day: '19' extern: '1' external_id: arxiv: - '0612159' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/quant-ph/0612159 month: '12' oa: 1 oa_version: Preprint page: '2' publication_status: published publisher: ArXiv publist_id: '7240' status: public title: Weak measurements and counterfactual computation type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '578' abstract: - lang: eng text: A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control. alternative_title: - Proc. SPIE author: - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Keith full_name: Arnold, Keith J last_name: Arnold - first_name: Aaron full_name: VanDevender, Aaron P last_name: Vandevender - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Julio full_name: Barreiro, Julio T last_name: Barreiro - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Peters N, Arnold K, Vandevender A, et al. Towards a quasi-deterministic single-photon source. In: Vol 6305. SPIE; 2006. doi:10.1117/12.684702' apa: Peters, N., Arnold, K., Vandevender, A., Jeffrey, E., Rangarajan, R., Hosten, O., … Kwiat, P. (2006). Towards a quasi-deterministic single-photon source (Vol. 6305). Presented at the Quantum Communications and Quantum Imaging, SPIE. https://doi.org/10.1117/12.684702 chicago: Peters, Nicholas, Keith Arnold, Aaron Vandevender, Evan Jeffrey, Radhika Rangarajan, Onur Hosten, Julio Barreiro, Joseph Altepeter, and Paul Kwiat. “Towards a Quasi-Deterministic Single-Photon Source,” Vol. 6305. SPIE, 2006. https://doi.org/10.1117/12.684702. ieee: N. Peters et al., “Towards a quasi-deterministic single-photon source,” presented at the Quantum Communications and Quantum Imaging, 2006, vol. 6305. ista: Peters N, Arnold K, Vandevender A, Jeffrey E, Rangarajan R, Hosten O, Barreiro J, Altepeter J, Kwiat P. 2006. Towards a quasi-deterministic single-photon source. Quantum Communications and Quantum Imaging, Proc. SPIE, vol. 6305. mla: Peters, Nicholas, et al. Towards a Quasi-Deterministic Single-Photon Source. Vol. 6305, SPIE, 2006, doi:10.1117/12.684702. short: N. Peters, K. Arnold, A. Vandevender, E. Jeffrey, R. Rangarajan, O. Hosten, J. Barreiro, J. Altepeter, P. Kwiat, in:, SPIE, 2006. conference: name: Quantum Communications and Quantum Imaging date_created: 2018-12-11T11:47:17Z date_published: 2006-01-01T00:00:00Z date_updated: 2020-07-14T12:47:11Z day: '01' doi: 10.1117/12.684702 extern: 1 intvolume: ' 6305' month: '01' publication_status: published publisher: SPIE publist_id: '7234' quality_controlled: 0 status: public title: Towards a quasi-deterministic single-photon source type: conference volume: 6305 year: '2006' ... --- _id: '577' abstract: - lang: eng text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio. alternative_title: - Proceedings of SPIE author: - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Micah full_name: Stoutimore, Micah J last_name: Stoutimore - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Rangarajan R, Altepeter J, Jeffrey E, et al. High-efficiency single-photon detectors. In: Vol 6372. SPIE; 2006. doi:10.1117/12.686117' apa: Rangarajan, R., Altepeter, J., Jeffrey, E., Stoutimore, M., Peters, N., Hosten, O., & Kwiat, P. (2006). High-efficiency single-photon detectors (Vol. 6372). Presented at the Unknown (978-081946470-5), SPIE. https://doi.org/10.1117/12.686117 chicago: Rangarajan, Radhika, Joseph Altepeter, Evan Jeffrey, Micah Stoutimore, Nicholas Peters, Onur Hosten, and Paul Kwiat. “High-Efficiency Single-Photon Detectors,” Vol. 6372. SPIE, 2006. https://doi.org/10.1117/12.686117. ieee: R. Rangarajan et al., “High-efficiency single-photon detectors,” presented at the Unknown (978-081946470-5), 2006, vol. 6372. ista: Rangarajan R, Altepeter J, Jeffrey E, Stoutimore M, Peters N, Hosten O, Kwiat P. 2006. High-efficiency single-photon detectors. Unknown (978-081946470-5), Proceedings of SPIE, vol. 6372. mla: Rangarajan, Radhika, et al. High-Efficiency Single-Photon Detectors. Vol. 6372, SPIE, 2006, doi:10.1117/12.686117. short: R. Rangarajan, J. Altepeter, E. Jeffrey, M. Stoutimore, N. Peters, O. Hosten, P. Kwiat, in:, SPIE, 2006. conference: name: Unknown (978-081946470-5) date_created: 2018-12-11T11:47:17Z date_published: 2006-01-01T00:00:00Z date_updated: 2020-07-14T12:47:11Z day: '01' doi: 10.1117/12.686117 extern: 1 intvolume: ' 6372' month: '01' publication_status: published publisher: SPIE publist_id: '7233' quality_controlled: 0 status: public title: High-efficiency single-photon detectors type: conference volume: 6372 year: '2006' ... --- _id: '579' abstract: - lang: eng text: 'The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of ''running'' and ''not running'' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover''s search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel ''chained'' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. ' author: - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Matthew full_name: Rakher, Matthew T last_name: Rakher - first_name: Julio full_name: Barreiro, Julio T last_name: Barreiro - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation through quantum interrogation. Nature. 2006;439(7079):949-952. doi:10.1038/nature04523 apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual quantum computation through quantum interrogation. Nature. Nature Publishing Group. https://doi.org/10.1038/nature04523 chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature. Nature Publishing Group, 2006. https://doi.org/10.1038/nature04523. ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation through quantum interrogation,” Nature, vol. 439, no. 7079. Nature Publishing Group, pp. 949–952, 2006. ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual quantum computation through quantum interrogation. Nature. 439(7079), 949–952. mla: Hosten, Onur, et al. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature, vol. 439, no. 7079, Nature Publishing Group, 2006, pp. 949–52, doi:10.1038/nature04523. short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, Nature 439 (2006) 949–952. date_created: 2018-12-11T11:47:18Z date_published: 2006-02-23T00:00:00Z date_updated: 2021-01-12T08:03:29Z day: '23' doi: 10.1038/nature04523 extern: 1 intvolume: ' 439' issue: '7079' month: '02' page: 949 - 952 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '7235' quality_controlled: 0 status: public title: Counterfactual quantum computation through quantum interrogation type: journal_article volume: 439 year: '2006' ... --- _id: '583' abstract: - lang: eng text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics. author: - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. Improved single-photon detection. In: IEEE; 2006. doi:10.1109/CLEO.2006.4628641' apa: 'Rangarajan, R., Peters, N., Hosten, O., Altepeter, J., Jeffrey, E., & Kwiat, P. (2006). Improved single-photon detection. Presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, IEEE. https://doi.org/10.1109/CLEO.2006.4628641' chicago: Rangarajan, Radhika, Nicholas Peters, Onur Hosten, Joseph Altepeter, Evan Jeffrey, and Paul Kwiat. “Improved Single-Photon Detection.” IEEE, 2006. https://doi.org/10.1109/CLEO.2006.4628641. ieee: 'R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, and P. Kwiat, “Improved single-photon detection,” presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, 2006.' ista: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. 2006. Improved single-photon detection. CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference.' mla: Rangarajan, Radhika, et al. Improved Single-Photon Detection. IEEE, 2006, doi:10.1109/CLEO.2006.4628641. short: R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, P. Kwiat, in:, IEEE, 2006. conference: name: 'CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference' date_created: 2018-12-11T11:47:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T08:03:43Z day: '01' doi: 10.1109/CLEO.2006.4628641 extern: 1 month: '01' publication_status: published publisher: IEEE publist_id: '7232' quality_controlled: 0 status: public title: Improved single-photon detection type: conference year: '2006' ...