[{"title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","type":"journal_article","abstract":[{"lang":"eng","text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n"}],"quality_controlled":"1","author":[{"full_name":"Castanon, Irinka","last_name":"Castanon","first_name":"Irinka"},{"last_name":"Abrami","first_name":"Laurence","full_name":"Abrami, Laurence"},{"full_name":"Holtzer, Laurent","first_name":"Laurent","last_name":"Holtzer"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Françoise","last_name":"Van Der Goot","full_name":"Van Der Goot, Françoise"},{"full_name":"González Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"}],"department":[{"_id":"CaHe"}],"publist_id":"3819","isi":1,"publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        15","_id":"2918","page":"28 - 39","date_published":"2013-01-01T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","date_created":"2018-12-11T12:00:20Z","issue":"1","scopus_import":"1","status":"public","publication_status":"published","doi":"10.1038/ncb2632","date_updated":"2025-09-30T08:16:16Z","volume":15,"article_processing_charge":"No","day":"01","oa_version":"None","year":"2013","citation":{"apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., &#38; González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. 2013;15(1):28-39. doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>","ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39.","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>.","short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>.","ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” <i>Nature Cell Biology</i>, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013."},"external_id":{"isi":["000312841300007"]},"publication":"Nature Cell Biology","month":"01"},{"publication":"EMBO Journal","month":"01","external_id":{"pmid":["23211744"],"isi":["000316464500009"]},"year":"2013","citation":{"ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>.","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>"},"day":"23","article_processing_charge":"No","volume":32,"oa_version":"Submitted Version","oa":1,"doi":"10.1038/emboj.2012.310","publication_status":"published","status":"public","date_updated":"2025-09-29T13:28:19Z","page":"260 - 274","_id":"2919","intvolume":"        32","date_published":"2013-01-23T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"scopus_import":"1","issue":"2","date_created":"2018-12-11T12:00:20Z","publist_id":"3818","publisher":"Wiley-Blackwell","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","abstract":[{"text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.","lang":"eng"}],"author":[{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Kania, Urszula","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","corr_author":"1","type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/","open_access":"1"}]},{"type":"journal_article","corr_author":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/"}],"title":"Neurulation coordinating cell polarisation and lumen formation","author":[{"full_name":"Compagnon, Julien","first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","last_name":"Compagnon"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"}],"quality_controlled":"1","abstract":[{"text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.","lang":"eng"}],"publisher":"Wiley-Blackwell","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3817","language":[{"iso":"eng"}],"scopus_import":"1","issue":"1","date_created":"2018-12-11T12:00:20Z","page":"1 - 3","intvolume":"        32","_id":"2920","date_published":"2013-01-09T00:00:00Z","pmid":1,"date_updated":"2025-09-29T13:27:27Z","doi":"10.1038/emboj.2012.325","status":"public","publication_status":"published","oa_version":"Submitted Version","oa":1,"day":"09","article_processing_charge":"No","volume":32,"external_id":{"isi":["000314141900001"],"pmid":["23211745"]},"year":"2013","citation":{"ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. 2013;32(1):1-3. doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>","apa":"Compagnon, J., &#38; Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>","chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>.","mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013."},"publication":"EMBO Journal","month":"01"},{"citation":{"chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, Current Biology 23 (2013) 76–82.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 23(1), 76–82.","mla":"Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>, vol. 23, no. 1, Cell Press, 2013, pp. 76–82, doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>.","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. 2013;23(1):76-82. doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” <i>Current Biology</i>, vol. 23, no. 1. Cell Press, pp. 76–82, 2013."},"year":"2013","external_id":{"isi":["000313383700026"]},"ec_funded":1,"month":"01","publication":"Current Biology","publication_status":"published","status":"public","doi":"10.1016/j.cub.2012.11.034","date_updated":"2026-04-08T14:22:39Z","project":[{"grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution"},{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"volume":23,"day":"07","article_processing_charge":"No","oa_version":"None","publist_id":"3811","isi":1,"publisher":"Cell Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2926","intvolume":"        23","page":"76 - 82","date_published":"2013-01-07T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"Funding for this project was obtained by the German Research Foundation (DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal strain and its characterization; Volker Witte for chemical information; Eva Sixt for ant drawings; and Robert Hauschild for help with image analysis. We further thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript. \r\n","date_created":"2018-12-11T12:00:23Z","issue":"1","scopus_import":"1","title":"Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","related_material":{"record":[{"id":"9757","status":"public","relation":"research_data"},{"id":"961","relation":"dissertation_contains","status":"public"}]},"type":"journal_article","corr_author":"1","abstract":[{"text":"To fight infectious diseases, host immune defenses are employed at multiple levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first line of defense to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care toward pathogen-exposed group members [2]. One of the most common behaviors is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores; it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behavior extends the current understanding of grooming and the establishment of social immunity in insect societies.","lang":"eng"}],"quality_controlled":"1","author":[{"last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon"},{"full_name":"Mitteregger, Barbara","first_name":"Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","last_name":"Mitteregger"},{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","last_name":"Barone","full_name":"Barone, Vanessa"},{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","full_name":"Konrad, Matthias"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"department":[{"_id":"SyCr"},{"_id":"CaHe"}]},{"date_updated":"2025-09-29T13:26:21Z","publication_status":"published","status":"public","doi":"10.1016/j.comgeo.2012.02.010","oa_version":"None","volume":46,"day":"01","article_processing_charge":"No","citation":{"ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>.","mla":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>.","short":"C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447.","ista":"Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.","apa":"Chen, C., &#38; Kerber, M. (2013). An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. 2013;46(4):435-447. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>"},"year":"2013","external_id":{"isi":["000314437000004"]},"month":"05","publication":"Computational Geometry: Theory and Applications","corr_author":"1","type":"journal_article","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3367"}]},"title":"An output sensitive algorithm for persistent homology","department":[{"_id":"HeEd"}],"author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ &gt; 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} &gt; 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n)."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publisher":"Elsevier","publist_id":"3796","date_created":"2018-12-11T12:00:27Z","issue":"4","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper.","date_published":"2013-05-01T00:00:00Z","intvolume":"        46","_id":"2939","page":"435 - 447"},{"type":"conference","related_material":{"record":[{"id":"1479","status":"public","relation":"later_version"}]},"title":"A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it","department":[{"_id":"KrPi"}],"author":[{"last_name":"Krenn","first_name":"Stephan","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2835-9093","full_name":"Krenn, Stephan"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Akshay","last_name":"Wadia","full_name":"Wadia, Akshay"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)&gt;= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)&gt;= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but  $H(X|Y)&gt;&gt;H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","conference":{"start_date":"2013-03-03","location":"Tokyo, Japan","name":"TCC: Theory of Cryptography Conference","end_date":"2013-03-06"},"publist_id":"3795","date_created":"2018-12-11T12:00:27Z","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2013-01-29T00:00:00Z","alternative_title":["LNCS"],"_id":"2940","intvolume":"      7785","page":"23 - 39","editor":[{"full_name":"Sahai, Amit","first_name":"Amit","last_name":"Sahai"}],"date_updated":"2025-09-18T11:37:22Z","ddc":["000"],"status":"public","publication_status":"published","doi":"10.1007/978-3-642-36594-2_2","oa":1,"oa_version":"Submitted Version","volume":7785,"day":"29","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"file":[{"creator":"dernst","file_size":414823,"date_updated":"2020-07-14T12:45:54Z","content_type":"application/pdf","date_created":"2019-01-22T14:11:11Z","file_name":"2013_LNCS_Krenn.pdf","file_id":"5875","access_level":"open_access","checksum":"beb0cc1c0579da2d2e84394230a5da78","relation":"main_file"}],"file_date_updated":"2020-07-14T12:45:54Z","citation":{"ieee":"S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39.","apa":"Krenn, S., Pietrzak, K. Z., &#38; Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>","ama":"Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>.","ista":"Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39.","mla":"Krenn, Stephan, et al. <i>A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It</i>. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>."},"year":"2013","has_accepted_license":"1","month":"01","ec_funded":1},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"author":[{"last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Aeschbacher, Simon"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"}],"department":[{"_id":"NiBa"}],"title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","related_material":{"record":[{"relation":"research_data","status":"public","id":"9758"}]},"corr_author":"1","type":"journal_article","page":"987 - 1002","_id":"2944","intvolume":"        22","date_published":"2013-02-01T00:00:00Z","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","language":[{"iso":"eng"}],"scopus_import":"1","issue":"4","date_created":"2018-12-11T12:00:28Z","publist_id":"3788","publisher":"Wiley-Blackwell","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","day":"01","volume":22,"oa_version":"None","doi":"10.1111/mec.12165","status":"public","publication_status":"published","date_updated":"2025-09-29T13:25:36Z","month":"02","publication":"Molecular Ecology","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["000314220900008"]},"year":"2013","citation":{"ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>"}},{"month":"04","has_accepted_license":"1","year":"2013","citation":{"apa":"Tommasi, T., Quadrianto, N., Caputo, B., &#38; Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>","ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>","mla":"Tommasi, Tatiana, et al. <i>Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer</i>. Vol. 7724, Springer, 2013, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>.","ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.","chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>.","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013."},"day":"04","volume":7724,"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:55Z","file_size":1513620,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"a0a7234a89e2192af655b0d0ae3bf445","file_name":"2012_ACCV_Tommasi.pdf","file_id":"5874","date_created":"2019-01-22T14:03:11Z"}],"file_date_updated":"2020-07-14T12:45:55Z","oa":1,"oa_version":"Submitted Version","ddc":["000"],"doi":"10.1007/978-3-642-37331-2_1","publication_status":"published","status":"public","date_updated":"2020-08-11T10:09:54Z","date_published":"2013-04-04T00:00:00Z","page":"1 - 15","alternative_title":["LNCS"],"_id":"2948","intvolume":"      7724","scopus_import":1,"date_created":"2018-12-11T12:00:30Z","acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","language":[{"iso":"eng"}],"conference":{"end_date":"2012-11-09","name":"ACCV: Asian Conference on Computer Vision","location":"Daejeon, Korea","start_date":"2012-11-05"},"publist_id":"3784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","abstract":[{"text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.","lang":"eng"}],"department":[{"_id":"ChLa"}],"author":[{"full_name":"Tommasi, Tatiana","last_name":"Tommasi","first_name":"Tatiana"},{"last_name":"Quadrianto","first_name":"Novi","full_name":"Quadrianto, Novi"},{"full_name":"Caputo, Barbara","first_name":"Barbara","last_name":"Caputo"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"series_title":"Lecture Notes in Computer Science","title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","type":"conference"},{"oa":1,"oa_version":"Submitted Version","pubrep_id":"198","day":"01","file":[{"date_updated":"2020-07-14T12:45:31Z","file_size":294689,"creator":"system","content_type":"application/pdf","file_id":"5086","file_name":"IST-2014-198-v1+1_popl128-henzinger-clean.pdf","date_created":"2018-12-12T10:14:33Z","relation":"main_file","checksum":"adf465e70948f4e80e48057524516456","access_level":"open_access"}],"file_date_updated":"2020-07-14T12:45:31Z","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"date_updated":"2023-02-21T16:06:49Z","ddc":["000","004"],"doi":"10.1145/2429069.2429109","publication_status":"published","status":"public","publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","month":"01","ec_funded":1,"year":"2013","citation":{"ieee":"T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 317–328.","chicago":"Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 317–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>.","ista":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.","mla":"Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 317–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>.","short":"T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328.","ama":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:317-328. doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>","apa":"Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., &#38; Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 317–328). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>"},"has_accepted_license":"1","department":[{"_id":"ToHe"}],"author":[{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"}],"abstract":[{"lang":"eng","text":"There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all &quot;legal&quot; sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones."}],"quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-1832-7"]},"type":"conference","related_material":{"record":[{"status":"deleted","relation":"later_version","id":"10901"}]},"title":"Quantitative relaxation of concurrent data structures","scopus_import":1,"date_created":"2018-12-11T11:56:11Z","acknowledgement":" and an Elise Richter Fellowship (Austrian Science Fund V00125). ","language":[{"iso":"eng"}],"date_published":"2013-01-01T00:00:00Z","page":"317 - 328","_id":"2181","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","conference":{"name":"POPL: Principles of Programming Languages","location":"Rome, Italy","start_date":"2013-01-23","end_date":"2013-01-25"},"publist_id":"4801"},{"status":"public","publication_status":"published","doi":"10.1145/2429069.2429085","title":"Quantitative abstraction refinement","corr_author":"1","date_updated":"2024-10-09T20:55:21Z","type":"conference","day":"01","quality_controlled":"1","abstract":[{"lang":"eng","text":"We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed."}],"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ToHe"}],"author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun"}],"oa_version":"None","publist_id":"4800","conference":{"name":"POPL: Principles of Programming Languages","location":"Rome, Italy","start_date":"2013-07-23","end_date":"2013-01-25"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative abstraction refinement,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 115–128.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Abstraction Refinement.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 115–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429085\">https://doi.org/10.1145/2429069.2429085</a>.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–128.","mla":"Cerny, Pavol, et al. “Quantitative Abstraction Refinement.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 115–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429085\">10.1145/2429069.2429085</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2013. Quantitative abstraction refinement. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 115–128.","ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative abstraction refinement. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:115-128. doi:<a href=\"https://doi.org/10.1145/2429069.2429085\">10.1145/2429069.2429085</a>","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2013). Quantitative abstraction refinement. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 115–128). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429085\">https://doi.org/10.1145/2429069.2429085</a>"},"year":"2013","publisher":"ACM","date_published":"2013-01-01T00:00:00Z","ec_funded":1,"_id":"2182","page":"115 - 128","date_created":"2018-12-11T11:56:11Z","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","month":"01"},{"scopus_import":1,"date_created":"2018-12-11T11:51:39Z","language":[{"iso":"eng"}],"date_published":"2013-09-01T00:00:00Z","page":"181 - 196","_id":"1374","alternative_title":["LIPIcs"],"intvolume":"        23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"5837","conference":{"end_date":"2013-09-05","start_date":"203-09-02","name":"CSL: Computer Science Logic","location":"Torino, Italy"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"quality_controlled":"1","abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","corr_author":"1","type":"conference","series_title":"Leibniz International Proceedings in Informatics","title":"Infinite-state games with finitary conditions","month":"09","publication":"22nd EACSL Annual Conference on Computer Science Logic","ec_funded":1,"year":"2013","citation":{"ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in <i>22nd EACSL Annual Conference on Computer Science Logic</i>, Torino, Italy, 2013, vol. 23, pp. 181–196.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In <i>22nd EACSL Annual Conference on Computer Science Logic</i>, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>.","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” <i>22nd EACSL Annual Conference on Computer Science Logic</i>, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>.","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2013). Infinite-state games with finitary conditions. In <i>22nd EACSL Annual Conference on Computer Science Logic</i> (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: <i>22nd EACSL Annual Conference on Computer Science Logic</i>. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>"},"has_accepted_license":"1","oa":1,"oa_version":"Published Version","pubrep_id":"624","day":"01","volume":23,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"file_date_updated":"2020-07-14T12:44:47Z","file":[{"date_updated":"2020-07-14T12:44:47Z","file_size":547296,"creator":"system","content_type":"application/pdf","file_id":"5023","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","date_created":"2018-12-12T10:13:38Z","relation":"main_file","access_level":"open_access","checksum":"b7091a3866db573c0db5ec486952255e"}],"date_updated":"2024-10-09T20:55:23Z","ddc":["000"],"doi":"10.4230/LIPIcs.CSL.2013.181","publication_status":"published","status":"public"},{"related_material":{"record":[{"id":"5406","status":"public","relation":"earlier_version"}]},"title":"Distributed synthesis for LTL fragments","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15479/AT:IST-2013-130-v1-1"}],"type":"conference","corr_author":"1","abstract":[{"lang":"eng","text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition."}],"quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"conference":{"location":"Portland, OR, United States","name":"FMCAD: Formal Methods in Computer-Aided Design","start_date":"2013-10-20","end_date":"2013-10-23"},"publist_id":"5835","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","date_published":"2013-12-11T00:00:00Z","page":"18 - 25","_id":"1376","scopus_import":"1","OA_place":"repository","date_created":"2018-12-11T11:51:40Z","language":[{"iso":"eng"}],"doi":"10.1109/FMCAD.2013.6679386","status":"public","publication_status":"published","date_updated":"2025-06-26T08:33:43Z","day":"11","article_processing_charge":"No","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"oa_version":"Preprint","OA_type":"green","year":"2013","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 18–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, 18–25. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 18–25, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In <i>13th International Conference on Formal Methods in Computer-Aided Design</i> (pp. 18–25). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: <i>13th International Conference on Formal Methods in Computer-Aided Design</i>. IEEE; 2013:18-25. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>"},"ec_funded":1,"month":"12","publication":"13th International Conference on Formal Methods in Computer-Aided Design"},{"author":[{"last_name":"Hofferek","first_name":"Georg","full_name":"Hofferek, Georg"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"last_name":"Könighofer","first_name":"Bettina","full_name":"Könighofer, Bettina"},{"last_name":"Jiang","first_name":"Jie","full_name":"Jiang, Jie"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"department":[{"_id":"ToHe"}],"quality_controlled":"1","abstract":[{"text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.","lang":"eng"}],"arxiv":1,"type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.4767"}],"title":"Synthesizing multiple boolean functions using interpolation on a single proof","acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND  (FP7-2009-IST-4-248613), and  QUAINT  (I774-N23),  ","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2018-12-11T11:51:43Z","page":"77 - 84","_id":"1385","date_published":"2013-12-11T00:00:00Z","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2013-10-23","location":"Portland, OR, United States","name":"FMCAD: Formal Methods in Computer-Aided Design","start_date":"2013-10-20"},"publist_id":"5825","oa_version":"Preprint","oa":1,"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"day":"11","date_updated":"2024-10-21T06:02:56Z","doi":"10.1109/FMCAD.2013.6679394","status":"public","publication_status":"published","publication":"2013 Formal Methods in Computer-Aided Design","month":"12","ec_funded":1,"external_id":{"arxiv":["1308.4767"]},"citation":{"ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84.","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>.","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>.","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>"},"year":"2013"},{"publist_id":"5823","conference":{"start_date":"2013-07-08","location":"Riga, Latvia","name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12"},"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"_id":"1387","intvolume":"      7966","page":"89 - 100","date_published":"2013-07-01T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"and ERC Grant QUALITY.","issue":"PART 2","date_created":"2018-12-11T11:51:44Z","scopus_import":1,"title":"Nondeterminism in the presence of a diverse or unknown future","series_title":"Lecture Notes in Computer Science","type":"conference","quality_controlled":"1","abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"author":[{"last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"last_name":"Kuperberg","first_name":"Denis","full_name":"Kuperberg, Denis"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"},{"full_name":"Skrzypczak, Michał","first_name":"Michał","last_name":"Skrzypczak"}],"department":[{"_id":"ToHe"}],"has_accepted_license":"1","citation":{"ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013."},"year":"2013","ec_funded":1,"month":"07","publication_status":"published","status":"public","doi":"10.1007/978-3-642-39212-2_11","ddc":["000"],"date_updated":"2020-08-11T10:09:09Z","file_date_updated":"2020-07-14T12:44:48Z","file":[{"date_created":"2020-05-15T11:05:50Z","file_name":"2013_ICALP_Boker.pdf","file_id":"7857","checksum":"98bc02e3793072e279ec8d364b381ff3","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":276982,"date_updated":"2020-07-14T12:44:48Z","content_type":"application/pdf"}],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"volume":7966,"day":"01","article_processing_charge":"No","oa_version":"Submitted Version","oa":1},{"language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","date_created":"2018-12-11T11:51:50Z","OA_place":"publisher","_id":"1405","alternative_title":["ISTA Thesis"],"page":"134","date_published":"2013-09-05T00:00:00Z","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publist_id":"5802","author":[{"last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien"}],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point."}],"corr_author":"1","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"title":"Analysis of dynamic message passing programs","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"4361"},{"status":"public","relation":"part_of_dissertation","id":"3251"},{"id":"2847","status":"public","relation":"part_of_dissertation"}]},"month":"09","degree_awarded":"PhD","ec_funded":1,"citation":{"ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>.","mla":"Zufferey, Damien. <i>Analysis of Dynamic Message Passing Programs</i>. Institute of Science and Technology Austria, 2013, doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>.","short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria.","apa":"Zufferey, D. (2013). <i>Analysis of dynamic message passing programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>","ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>"},"supervisor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"year":"2013","has_accepted_license":"1","oa_version":"Published Version","oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"file":[{"access_level":"open_access","checksum":"ed2d7b52933d134e8dc69d569baa284e","relation":"main_file","date_created":"2021-02-22T11:28:36Z","success":1,"file_id":"9176","file_name":"2013_Zufferey_thesis_final.pdf","content_type":"application/pdf","creator":"dernst","date_updated":"2021-02-22T11:28:36Z","file_size":1514906},{"content_type":"application/pdf","date_updated":"2021-11-17T13:47:58Z","file_size":1378313,"creator":"cchlebak","relation":"main_file","checksum":"cecc4c4b14225bee973d32e3dba91a55","access_level":"closed","file_name":"2013_Zufferey_thesis_final_pdfa.pdf","file_id":"10298","date_created":"2021-11-16T14:42:52Z"}],"file_date_updated":"2021-11-17T13:47:58Z","article_processing_charge":"No","day":"05","date_updated":"2026-04-09T14:35:24Z","status":"public","publication_status":"published","doi":"10.15479/at:ista:1405","ddc":["000"]},{"oa_version":"None","author":[{"full_name":"Campinho, Pedro","last_name":"Campinho","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416"}],"department":[{"_id":"CaHe"}],"abstract":[{"text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading.","lang":"eng"}],"article_processing_charge":"No","day":"01","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T14:34:43Z","corr_author":"1","type":"dissertation","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","status":"public","publication_status":"published","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"10","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2018-12-11T11:51:50Z","page":"123","alternative_title":["ISTA Thesis"],"_id":"1406","date_published":"2013-10-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2013","citation":{"ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publist_id":"5801"},{"type":"journal_article","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","author":[{"last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Rowell","full_name":"Rowell, David"},{"first_name":"Andrew","last_name":"Young","full_name":"Young, Andrew"}],"department":[{"_id":"NiBa"}],"abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Royal Society, The","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"7372","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:32Z","issue":"1750","intvolume":"       280","_id":"450","article_number":"2058","pmid":1,"date_published":"2013-01-07T00:00:00Z","date_updated":"2025-09-30T07:30:35Z","status":"public","publication_status":"published","doi":"10.1098/rspb.2012.2058","oa_version":"Submitted Version","oa":1,"volume":280,"article_processing_charge":"No","day":"07","citation":{"ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, The, 2013."},"year":"2013","external_id":{"isi":["000311943100012"],"pmid":["23173202"]},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","month":"01"},{"type":"journal_article","title":"Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions","author":[{"last_name":"Dickerson","id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","full_name":"Dickerson, Desiree"},{"first_name":"David","last_name":"Bilkey","full_name":"Bilkey, David"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JoCs"}],"abstract":[{"text":"Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. ","lang":"eng"}],"quality_controlled":"1","publisher":"Frontiers Research Foundation","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"7346","language":[{"iso":"eng"}],"issue":"DEC","date_created":"2018-12-11T11:46:41Z","intvolume":"         7","_id":"476","date_published":"2013-12-27T00:00:00Z","date_updated":"2025-09-30T07:30:04Z","doi":"10.3389/fnbeh.2013.00217","publication_status":"published","status":"public","ddc":["571"],"oa_version":"Published Version","oa":1,"file_date_updated":"2020-07-14T12:46:35Z","file":[{"file_size":530134,"date_updated":"2020-07-14T12:46:35Z","creator":"system","content_type":"application/pdf","file_id":"5128","file_name":"IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf","date_created":"2018-12-12T10:15:10Z","relation":"main_file","access_level":"open_access","checksum":"cd7183121e56251176100ccac165c95c"}],"pubrep_id":"953","day":"27","article_processing_charge":"No","volume":7,"external_id":{"isi":["000329175600001"]},"citation":{"ieee":"D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC. Frontiers Research Foundation, 2013.","apa":"Dickerson, D., &#38; Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>","ama":"Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. 2013;7(DEC). doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>","ista":"Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).","short":"D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).","mla":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>.","chicago":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>."},"year":"2013","has_accepted_license":"1","month":"12","publication":"Frontiers in Behavioral Neuroscience"},{"publist_id":"7321","publisher":"American Association for the Advancement of Science","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"91 - 95","_id":"499","intvolume":"       339","date_published":"2013-01-04T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2018-12-11T11:46:48Z","issue":"6115","title":"Dynamic persistence of antibiotic-stressed mycobacteria","type":"journal_article","quality_controlled":"1","abstract":[{"lang":"eng","text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing &quot;persisters.&quot; Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure."}],"author":[{"first_name":"Yurichi","last_name":"Wakamoto","full_name":"Wakamoto, Yurichi"},{"last_name":"Dhar","first_name":"Neraaj","full_name":"Dhar, Neraaj"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait","full_name":"Chait, Remy P"},{"full_name":"Schneider, Katrin","last_name":"Schneider","first_name":"Katrin"},{"full_name":"Signorino Gelo, François","first_name":"François","last_name":"Signorino Gelo"},{"first_name":"Stanislas","last_name":"Leibler","full_name":"Leibler, Stanislas"},{"full_name":"Mckinney, John","last_name":"Mckinney","first_name":"John"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"external_id":{"isi":["000312985800059"]},"year":"2013","citation":{"ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. 2013;339(6115):91-95. doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>","apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &#38; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>.","ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>.","ieee":"Y. Wakamoto <i>et al.</i>, “Dynamic persistence of antibiotic-stressed mycobacteria,” <i>Science</i>, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013."},"publication":"Science","month":"01","doi":"10.1126/science.1229858","publication_status":"published","status":"public","date_updated":"2025-09-30T07:29:30Z","article_processing_charge":"No","day":"04","volume":339,"oa_version":"None"},{"month":"10","publication":"BMC Evolutionary Biology","has_accepted_license":"1","external_id":{"isi":["000326620200001"]},"citation":{"ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., &#38; Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>.","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 222, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>.","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013)."},"year":"2013","day":"09","pubrep_id":"941","article_processing_charge":"No","volume":13,"file_date_updated":"2020-07-14T12:46:36Z","file":[{"creator":"system","file_size":1150052,"date_updated":"2020-07-14T12:46:36Z","content_type":"application/pdf","date_created":"2018-12-12T10:08:59Z","file_id":"4722","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","access_level":"open_access","checksum":"52cf48a7c1794676ae8b0029573a84a9","relation":"main_file"}],"oa":1,"oa_version":"Published Version","ddc":["576"],"doi":"10.1186/1471-2148-13-222","status":"public","publication_status":"published","date_updated":"2025-09-30T07:28:51Z","date_published":"2013-10-09T00:00:00Z","article_number":"222","intvolume":"        13","_id":"500","scopus_import":"1","date_created":"2018-12-11T11:46:49Z","issue":"1","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","language":[{"iso":"eng"}],"publist_id":"7320","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"BioMed Central","isi":1,"quality_controlled":"1","abstract":[{"text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JoBo"}],"author":[{"last_name":"Ward","first_name":"Melissa","full_name":"Ward, Melissa"},{"full_name":"Lycett, Samantha","first_name":"Samantha","last_name":"Lycett"},{"full_name":"Avila, Dorita","last_name":"Avila","first_name":"Dorita"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"full_name":"Leigh Brown, Andrew","first_name":"Andrew","last_name":"Leigh Brown"}],"title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","type":"journal_article"}]