--- _id: '1838' abstract: - lang: eng text: Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples. acknowledgement: 'This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).' alternative_title: - LNCS author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Swen full_name: Jacobs, Swen last_name: Jacobs - first_name: Robert full_name: Könighofer, Robert last_name: Könighofer citation: ama: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50' apa: 'Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50' chicago: Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50. ieee: 'R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.' ista: 'Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.' mla: Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50. short: R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:17Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:32Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_50 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1411.4604 month: '01' oa: 1 oa_version: Preprint page: 517 - 532 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5264' scopus_import: 1 status: public title: Assume-guarantee synthesis for concurrent reactive programs with partial information type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1839' abstract: - lang: eng text: We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12' apa: 'Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12' chicago: 'Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.' ieee: 'T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.' ista: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.' mla: 'Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12.' short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2020-01-21T13:18:52Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_12 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.03093 month: '01' oa: 1 oa_version: Preprint page: 181 - 187 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5263' quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: 'Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1837' abstract: - lang: eng text: 'Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.' article_number: R3 article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: P full_name: Braunshier, P last_name: Braunshier - first_name: M full_name: Schwegel, M last_name: Schwegel - first_name: Hendrik full_name: Kuhlmann, Hendrik last_name: Kuhlmann - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184 apa: Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184 chicago: Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184. ieee: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015. ista: Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3. mla: Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184. short: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015). date_created: 2018-12-11T11:54:17Z date_published: 2015-04-08T00:00:00Z date_updated: 2021-01-12T06:53:31Z day: '08' department: - _id: BjHo doi: 10.1017/jfm.2015.184 ec_funded: 1 external_id: arxiv: - '1508.06559' intvolume: ' 770' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.06559 month: '04' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '5265' quality_controlled: '1' scopus_import: 1 status: public title: Subcritical versus supercritical transition to turbulence in curved pipes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 770 year: '2015' ... --- _id: '1848' abstract: - lang: eng text: The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis. article_processing_charge: No article_type: original author: - first_name: Bettina full_name: Schwamb, Bettina last_name: Schwamb - first_name: Robert full_name: Pick, Robert last_name: Pick - first_name: Sara full_name: Fernández, Sara last_name: Fernández - first_name: Kirsten full_name: Völp, Kirsten last_name: Völp - first_name: Jan full_name: Heering, Jan last_name: Heering - first_name: Volker full_name: Dötsch, Volker last_name: Dötsch - first_name: Susanne full_name: Bösser, Susanne last_name: Bösser - first_name: Jennifer full_name: Jung, Jennifer last_name: Jung - first_name: Rasa full_name: Beinoravičiute Kellner, Rasa last_name: Beinoravičiute Kellner - first_name: Josephine full_name: Wesely, Josephine last_name: Wesely - first_name: Inka full_name: Zörnig, Inka last_name: Zörnig - first_name: Matthias full_name: Hammerschmidt, Matthias last_name: Hammerschmidt - first_name: Matthias full_name: Nowak, Matthias id: 30845DAA-F248-11E8-B48F-1D18A9856A87 last_name: Nowak - first_name: Roland full_name: Penzel, Roland last_name: Penzel - first_name: Kurt full_name: Zatloukal, Kurt last_name: Zatloukal - first_name: Stefan full_name: Joos, Stefan last_name: Joos - first_name: Ralf full_name: Rieker, Ralf last_name: Rieker - first_name: Abbas full_name: Agaimy, Abbas last_name: Agaimy - first_name: Stephan full_name: Söder, Stephan last_name: Söder - first_name: Kmarie full_name: Reid Lombardo, Kmarie last_name: Reid Lombardo - first_name: Michael full_name: Kendrick, Michael last_name: Kendrick - first_name: Michael full_name: Bardsley, Michael last_name: Bardsley - first_name: Yujiro full_name: Hayashi, Yujiro last_name: Hayashi - first_name: David full_name: Asuzu, David last_name: Asuzu - first_name: Sabriya full_name: Syed, Sabriya last_name: Syed - first_name: Tamás full_name: Ördög, Tamás last_name: Ördög - first_name: Martin full_name: Zörnig, Martin last_name: Zörnig citation: ama: Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498 apa: Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498 chicago: Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498. ieee: B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015. ista: Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329. mla: Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498. short: B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329. date_created: 2018-12-11T11:54:20Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' department: - _id: LifeSc doi: 10.1002/ijc.29498 external_id: pmid: - '25716227' intvolume: ' 137' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/ month: '09' oa: 1 oa_version: Submitted Version page: 1318 - 1329 pmid: 1 publication: International Journal of Cancer publication_status: published publisher: Wiley publist_id: '5253' quality_controlled: '1' scopus_import: 1 status: public title: FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2015' ... --- _id: '1846' abstract: - lang: eng text: Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS. article_processing_charge: No article_type: original author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Kim full_name: Larsen, Kim last_name: Larsen - first_name: Mikael full_name: Möller, Mikael last_name: Möller - first_name: Salomon full_name: Sickert, Salomon last_name: Sickert - first_name: Jiří full_name: Srba, Jiří last_name: Srba citation: ama: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4 apa: Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4 chicago: Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4. ieee: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015. ista: Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297. mla: Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4. short: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297. date_created: 2018-12-11T11:54:20Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/s00236-015-0215-4 ec_funded: 1 file: - access_level: open_access checksum: fb4037ddc4fc05f33080dd3547ede350 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:57:44Z date_updated: 2020-07-14T12:45:19Z file_id: '7854' file_name: 2015_ActaInfo_Benes.pdf file_size: 488482 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 52' issue: 2-3 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 269 - 297 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Acta Informatica publication_status: published publisher: Springer publist_id: '5255' quality_controlled: '1' scopus_import: 1 status: public title: Refinement checking on parametric modal transition systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2015' ... --- _id: '1845' abstract: - lang: eng text: Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. article_processing_charge: No author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006 apa: Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006 chicago: Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006. ieee: D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015. ista: Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151. mla: Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006. short: D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151. date_created: 2018-12-11T11:54:19Z date_published: 2015-03-18T00:00:00Z date_updated: 2021-10-08T09:07:34Z day: '18' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2015.03.006 file: - access_level: open_access checksum: d1808550e376a0eca2a950fda017cfa6 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5192' file_name: IST-2017-822-v1+1_Perspective_Fig__Final.pdf file_size: 411832 relation: main_file - access_level: open_access checksum: a279f4ae61e6c8f33d68f69a0d02097d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5193' file_name: IST-2017-822-v1+2_Perspective_Final2.pdf file_size: 100769 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 85' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '03' oa: 1 oa_version: Published Version page: 1149 - 1151 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5256' pubrep_id: '822' quality_controlled: '1' scopus_import: '1' status: public title: Excitement about inhibitory presynaptic terminals tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 85 year: '2015' ... --- _id: '1840' abstract: - lang: eng text: In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions. acknowledgement: "This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n" author: - first_name: Bernhard full_name: Geiger, Bernhard last_name: Geiger - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Gernot full_name: Kubin, Gernot last_name: Kubin - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl citation: ama: Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971 apa: Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971 chicago: Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971. ieee: B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015. ista: Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022. mla: Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971. short: B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022. date_created: 2018-12-11T11:54:18Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: CaGu - _id: ToHe doi: 10.1109/TAC.2014.2364971 intvolume: ' 60' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.6603 month: '04' oa: 1 oa_version: Preprint page: 1010 - 1022 publication: IEEE Transactions on Automatic Control publication_identifier: issn: - 0018-9286 publication_status: published publisher: IEEE publist_id: '5262' quality_controlled: '1' scopus_import: 1 status: public title: Optimal Kullback-Leibler aggregation via information bottleneck type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2015' ... --- _id: '1841' abstract: - lang: eng text: We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465 apa: Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465 chicago: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465. ieee: V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015. ista: Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930. mla: Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465. short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930. date_created: 2018-12-11T11:54:18Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2014.2363465 ec_funded: 1 intvolume: ' 37' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5655 month: '05' oa: 1 oa_version: Preprint page: 919 - 930 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '5261' quality_controlled: '1' scopus_import: 1 status: public title: A new look at reweighted message passing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2015' ... --- _id: '1849' abstract: - lang: eng text: 'Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.' acknowledgement: The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.). author: - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017 apa: Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017 chicago: Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017. ieee: E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015. ista: Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172. mla: Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017. short: E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172. date_created: 2018-12-11T11:54:21Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' department: - _id: JiFr doi: 10.1016/j.bbamcr.2015.02.017 intvolume: ' 1853' issue: '9' language: - iso: eng month: '09' oa_version: None page: 2168 - 2172 publication: Biochimica et Biophysica Acta - Molecular Cell Research publication_status: published publisher: Elsevier publist_id: '5252' quality_controlled: '1' scopus_import: 1 status: public title: Calcium is an organizer of cell polarity in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1853 year: '2015' ... --- _id: '1847' acknowledgement: This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637S). author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013' apa: 'Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013' chicago: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.' ieee: 'P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.' ista: 'Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.' mla: 'Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.' short: P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358. date_created: 2018-12-11T11:54:20Z date_published: 2015-03-02T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '02' department: - _id: JiFr doi: 10.1016/j.molp.2014.12.013 intvolume: ' 8' issue: '3' language: - iso: eng month: '03' oa_version: None page: 356 - 358 publication: Molecular Plant publication_status: published publisher: Elsevier publist_id: '5254' quality_controlled: '1' scopus_import: 1 status: public title: 'ABP1: Finally docking' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ...