[{"article_processing_charge":"No","type":"journal_article","month":"04","oa_version":"Published Version","_id":"9146","volume":5,"doi":"10.1088/1748-9326/5/2/025207","day":"09","publication_identifier":{"issn":["1748-9326"]},"article_number":"025207","article_type":"original","publisher":"IOP Publishing","abstract":[{"text":"The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.","lang":"eng"}],"oa":1,"date_updated":"2022-01-24T13:51:02Z","main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/5/2/025207","open_access":"1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","publication":"Environmental Research Letters","keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"date_created":"2021-02-15T14:40:46Z","citation":{"ista":"O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental Research Letters. 5(2), 025207.","apa":"O’Gorman, P. A., &#38; Muller, C. J. (2010). How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>","ama":"O’Gorman PA, Muller CJ. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. 2010;5(2). doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>","ieee":"P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?,” <i>Environmental Research Letters</i>, vol. 5, no. 2. IOP Publishing, 2010.","mla":"O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>, vol. 5, no. 2, 025207, IOP Publishing, 2010, doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","chicago":"O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>. IOP Publishing, 2010. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>."},"year":"2010","date_published":"2010-04-09T00:00:00Z","extern":"1","publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"O’Gorman","full_name":"O’Gorman, P A","first_name":"P A"},{"first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller"}],"intvolume":"         5","issue":"2"},{"intvolume":"       104","issue":"16","publist_id":"6523","author":[{"first_name":"Thomas","full_name":"Angelini, Thomas","last_name":"Angelini"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"first_name":"Xavier","full_name":"Trepat, Xavier","last_name":"Trepat"},{"full_name":"Fredberg, Jeffrey","first_name":"Jeffrey","last_name":"Fredberg"},{"last_name":"Weitz","full_name":"Weitz, David","first_name":"David"}],"_id":"920","date_published":"2010-04-23T00:00:00Z","year":"2010","volume":104,"status":"public","publication_status":"published","extern":"1","citation":{"chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepat, Jeffrey Fredberg, and David Weitz. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>.","short":"T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review Letters 104 (2010).","mla":"Angelini, Thomas, et al. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>, vol. 104, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>.","ieee":"T. Angelini, E. B. Hannezo, X. Trepat, J. Fredberg, and D. Weitz, “Cell migration driven by cooperative substrate deformation patterns,” <i>Physical Review Letters</i>, vol. 104, no. 16. American Physical Society, 2010.","ama":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. 2010;104(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>","apa":"Angelini, T., Hannezo, E. B., Trepat, X., Fredberg, J., &#38; Weitz, D. (2010). Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>","ista":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. 2010. Cell migration driven by cooperative substrate deformation patterns. Physical Review Letters. 104(16)."},"day":"23","doi":"10.1103/PhysRevLett.104.168104","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:55Z","oa_version":"None","date_created":"2018-12-11T11:49:12Z","acknowledgement":"This work was supported by the NSF (DMR-0602684) and the Harvard MRSEC (DMR-0820484).\r\nWe would like to thank Dr. James Butler for helpful conversations.","title":"Cell migration driven by cooperative substrate deformation patterns","type":"journal_article","publication":"Physical Review Letters","month":"04","article_processing_charge":"No","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration."}]},{"article_processing_charge":"No","scopus_import":"1","page":"916-919","department":[{"_id":"DaZi"}],"oa_version":"None","month":"05","type":"journal_article","volume":328,"_id":"9452","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"doi":"10.1126/science.1186366","day":"14","article_type":"original","publisher":"American Association for the Advancement of Science","abstract":[{"lang":"eng","text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes."}],"pmid":1,"date_updated":"2021-12-14T08:35:37Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-06-04T08:26:08Z","keyword":["Multidisciplinary"],"publication":"Science","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","status":"public","extern":"1","publication_status":"published","year":"2010","date_published":"2010-05-14T00:00:00Z","citation":{"ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["20395474 "]},"issue":"5980","intvolume":"       328","author":[{"last_name":"Zemach","full_name":"Zemach, Assaf ","first_name":"Assaf "},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"first_name":"Pedro","full_name":"Silva, Pedro","last_name":"Silva"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel"}]},{"month":"10","type":"journal_article","oa_version":"Published Version","page":"18729-18734","department":[{"_id":"DaZi"}],"scopus_import":"1","article_processing_charge":"No","article_type":"original","doi":"10.1073/pnas.1009695107","day":"26","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":107,"_id":"9485","publication":"Proceedings of the National Academy of Sciences","title":"Local DNA hypomethylation activates genes in rice endosperm","date_created":"2021-06-07T09:31:01Z","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:40:02Z","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"oa":1,"publisher":"National Academy of Sciences","author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"last_name":"Silva","first_name":"Pedro","full_name":"Silva, Pedro"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"first_name":"Bradley","full_name":"Dotson, Bradley","last_name":"Dotson"},{"last_name":"Brooks","full_name":"Brooks, Matthew D.","first_name":"Matthew D."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"issue":"43","intvolume":"       107","language":[{"iso":"eng"}],"external_id":{"pmid":["20937895"]},"quality_controlled":"1","citation":{"mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734."},"publication_status":"published","status":"public","extern":"1","year":"2010","date_published":"2010-10-26T00:00:00Z"},{"day":"14","doi":"10.1016/j.cub.2010.07.007","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"_id":"9489","volume":20,"article_type":"review","department":[{"_id":"DaZi"}],"page":"R780-R785","scopus_import":"1","article_processing_charge":"No","type":"journal_article","month":"09","oa_version":"Published Version","external_id":{"pmid":["20833323"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785."},"date_published":"2010-09-14T00:00:00Z","year":"2010","extern":"1","status":"public","publication_status":"published","author":[{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"intvolume":"        20","issue":"17","abstract":[{"lang":"eng","text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries."}],"oa":1,"publisher":"Elsevier","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","publication":"Current Biology","date_created":"2021-06-07T09:45:27Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"date_updated":"2021-12-14T08:52:34Z"},{"oa_version":"Published Version","date_created":"2021-08-02T09:45:39Z","month":"07","related_material":{"record":[{"status":"public","id":"3779","relation":"used_in_publication"}]},"type":"research_data_reference","title":"Heterosis and the drift load","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2025-09-30T09:42:52Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","publisher":"Public Library of Science","author":[{"last_name":"Rosas","full_name":"Rosas, Ulises","first_name":"Ulises"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Copsey","first_name":"Lucy","full_name":"Copsey, Lucy"},{"full_name":"Barbier De Reuille, Pierre","first_name":"Pierre","last_name":"Barbier De Reuille"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"doi":"10.1371/journal.pbio.1000429.s003","day":"20","status":"public","_id":"9764","year":"2010","date_published":"2010-07-20T00:00:00Z","citation":{"chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","mla":"Rosas, Ulises, et al. <i>Heterosis and the Drift Load</i>. Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Heterosis and the drift load. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>."}},{"publist_id":"2780","day":"01","doi":"10.1111/j.1558-5646.2010.01019.x","_id":"474","volume":64,"type":"journal_article","month":"09","oa_version":"None","department":[{"_id":"NiBa"}],"page":"2701 - 2715","scopus_import":"1","isi":1,"article_processing_charge":"No","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"intvolume":"        64","issue":"9","language":[{"iso":"eng"}],"external_id":{"isi":["000281636400017"]},"quality_controlled":"1","citation":{"short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. 2010;64(9):2701-2715. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>","apa":"Barton, N. H., Kelleher, J., &#38; Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” <i>Evolution</i>, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>."},"corr_author":"1","date_published":"2010-09-01T00:00:00Z","year":"2010","publication_status":"published","status":"public","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","publication":"Evolution","date_created":"2018-12-11T11:46:40Z","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:50:22Z","abstract":[{"lang":"eng","text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci."}],"publisher":"Wiley-Blackwell"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"doi":"10.4230/LIPIcs.FSTTCS.2010.1","day":"01","volume":8,"_id":"488","conference":{"start_date":"2010-12-15","end_date":"2010-12-18","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","location":"Chennai, India"},"publist_id":"7331","isi":1,"ddc":["005"],"scopus_import":"1","page":"1 - 12","department":[{"_id":"ToHe"}],"article_processing_charge":"No","oa_version":"Published Version","month":"01","type":"conference","pubrep_id":"948","quality_controlled":"1","external_id":{"isi":["000310361000001"]},"language":[{"iso":"eng"}],"status":"public","publication_status":"published","date_published":"2010-01-01T00:00:00Z","year":"2010","corr_author":"1","citation":{"ieee":"R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12.","apa":"Alur, R., &#38; Cerny, P. (2010). Expressiveness of streaming string transducers (Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>","ama":"Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>","ista":"Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 1–12.","mla":"Alur, Rajeev, and Pavol Cerny. <i>Expressiveness of Streaming String Transducers</i>. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>.","short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12.","chicago":"Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>."},"file_date_updated":"2020-07-14T12:46:35Z","alternative_title":["LIPIcs"],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":"         8","author":[{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"}],"oa":1,"abstract":[{"text":"Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of &quot;regular&quot; transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. ","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:08:29Z","file_id":"4690","access_level":"open_access","date_updated":"2020-07-14T12:46:35Z","relation":"main_file","content_type":"application/pdf","checksum":"5845be5aa19791830f7407d8853f2df0","creator":"system","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf","file_size":492344}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:46:45Z","title":"Expressiveness of streaming string transducers","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:49:32Z"},{"publist_id":"7332","_id":"489","volume":25,"conference":{"start_date":"2010-06-17","name":"GandALF: Games, Automata, Logic, and Formal Verification","end_date":"2010-06-18","location":"Minori, Amalfi Coast, Italy"},"doi":"10.4204/EPTCS.25.7","day":"09","oa_version":"Published Version","type":"conference","month":"06","article_processing_charge":"No","scopus_import":"1","department":[{"_id":"KrCh"}],"page":"30 - 39","intvolume":"        25","author":[{"first_name":"Julien","full_name":"Cristau, Julien","last_name":"Cristau"},{"last_name":"David","first_name":"Claire","full_name":"David, Claire"},{"last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","full_name":"Horn, Florian","first_name":"Florian"}],"date_published":"2010-06-09T00:00:00Z","year":"2010","status":"public","publication_status":"published","citation":{"mla":"Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?” <i>Proceedings of GandALF 2010</i>, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>.","ista":"Cristau J, David C, Horn F. 2010. How do we remember the past in randomised strategies? Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 30–39.","ieee":"J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies?,” in <i>Proceedings of GandALF 2010</i>, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.","ama":"Cristau J, David C, Horn F. How do we remember the past in randomised strategies? In: <i>Proceedings of GandALF 2010</i>. Vol 25. Open Publishing Association; 2010:30-39. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>","apa":"Cristau, J., David, C., &#38; Horn, F. (2010). How do we remember the past in randomised strategies? In <i>Proceedings of GandALF 2010</i> (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>","chicago":"Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies?” In <i>Proceedings of GandALF 2010</i>, 25:30–39. Open Publishing Association, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>.","short":"J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39."},"corr_author":"1","alternative_title":["EPTCS"],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1006.1404"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-11T08:14:27Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1006.1404"}],"arxiv":1,"date_created":"2018-12-11T11:46:45Z","title":"How do we remember the past in randomised strategies?","publication":"Proceedings of GandALF 2010","publisher":"Open Publishing Association","oa":1,"abstract":[{"lang":"eng","text":"Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies."}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:48:58Z","date_created":"2018-12-11T11:47:01Z","publication":"Formal Methods in System Design","title":"Doomed program points","publisher":"Springer","abstract":[{"lang":"eng","text":"Any programming error that can be revealed before compiling a program saves precious time for the programmer. While integrated development environments already do a good job by detecting, e.g., data-flow abnormalities, current static analysis tools suffer from false positives (&quot;noise&quot;) or require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, regardless of which state it is started in. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on experiments with a prototype tool."}],"issue":"2-3","intvolume":"        37","author":[{"last_name":"Hoenicke","full_name":"Hoenicke, Jochen","first_name":"Jochen"},{"last_name":"Leino","first_name":"Kari","full_name":"Leino, Kari"},{"last_name":"Podelski","first_name":"Andreas","full_name":"Podelski, Andreas"},{"first_name":"Martin","full_name":"Schäf, Martin","last_name":"Schäf"},{"first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas","last_name":"Wies"}],"publication_status":"published","status":"public","year":"2010","date_published":"2010-12-01T00:00:00Z","corr_author":"1","citation":{"chicago":"Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” <i>Formal Methods in System Design</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>.","short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199.","mla":"Hoenicke, Jochen, et al. “Doomed Program Points.” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>.","ama":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. <i>Formal Methods in System Design</i>. 2010;37(2-3):171-199. doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>","ieee":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.","apa":"Hoenicke, J., Leino, K., Podelski, A., Schäf, M., &#38; Wies, T. (2010). Doomed program points. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>","ista":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points. Formal Methods in System Design. 37(2–3), 171–199."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000286631700004"]},"oa_version":"None","month":"12","type":"journal_article","article_processing_charge":"No","isi":1,"scopus_import":"1","page":"171 - 199","department":[{"_id":"ToHe"}],"publist_id":"7284","volume":37,"_id":"533","doi":"10.1007/s10703-010-0102-0","day":"01"},{"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"first_name":"Rohit","full_name":"Singh, Rohit","last_name":"Singh"}],"has_accepted_license":"1","_id":"5388","date_published":"2010-10-07T00:00:00Z","year":"2010","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:46:42Z","citation":{"short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>."},"alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2010-0004","day":"07","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T08:12:00Z","pubrep_id":"24","oa_version":"Published Version","date_created":"2018-12-12T11:39:03Z","type":"technical_report","title":"Quantitative synthesis for concurrent programs","related_material":{"record":[{"id":"3366","relation":"later_version","status":"public"}]},"month":"10","publisher":"IST Austria","ddc":["000","005"],"oa":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file":[{"file_size":429101,"file_name":"IST-2010-0004_IST-2010-0004.pdf","creator":"system","checksum":"da38782d2388a6fa32109d10bb9bad67","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:46:42Z","access_level":"open_access","date_created":"2018-12-12T11:53:53Z","file_id":"5515"}],"abstract":[{"lang":"eng","text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements."}],"page":"17"},{"author":[{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"}],"has_accepted_license":"1","publication_status":"published","status":"public","year":"2010","_id":"5389","date_published":"2010-06-04T00:00:00Z","citation":{"chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p."},"alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:42Z","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"day":"04","doi":"10.15479/AT:IST-2010-0003","date_updated":"2025-09-30T07:46:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"25","date_created":"2018-12-12T11:39:03Z","oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"4393","status":"public"},{"relation":"later_version","id":"3249","status":"public"}]},"month":"06","type":"technical_report","title":"Simulation distances","publisher":"IST Austria","ddc":["005"],"oa":1,"page":"24","file":[{"date_updated":"2020-07-14T12:46:42Z","access_level":"open_access","file_id":"5547","date_created":"2018-12-12T11:54:25Z","file_name":"IST-2010-0003_IST-2010-0003.pdf","file_size":367246,"creator":"system","checksum":"284ded99764e32a583a8ea83fcea254b","content_type":"application/pdf","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes."}],"department":[{"_id":"ToHe"}]},{"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël"}],"has_accepted_license":"1","_id":"5390","year":"2010","date_published":"2010-06-04T00:00:00Z","publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:46:43Z","citation":{"chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p."},"alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"day":"04","doi":"10.15479/AT:IST-2010-0002","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2020-07-14T23:04:41Z","pubrep_id":"26","oa_version":"Published Version","date_created":"2018-12-12T11:39:03Z","type":"technical_report","title":"Topological, automata-theoretic and logical characterization of finitary languages","month":"06","publisher":"IST Austria","ddc":["000"],"oa":1,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:43Z","date_created":"2018-12-12T11:54:10Z","file_id":"5532","file_size":395662,"file_name":"IST-2010-0002_IST-2010-0002.pdf","creator":"system","checksum":"283d3604d76dd4d5161585d4c8625fbe","content_type":"application/pdf","relation":"main_file"}],"department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages."}],"page":"21"},{"author":[{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"},{"last_name":"Radhakrishna","first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zufferey","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien"},{"full_name":"Chaudhuri, Swarat","first_name":"Swarat","last_name":"Chaudhuri"},{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"}],"has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"citation":{"chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p."},"file_date_updated":"2020-07-14T12:46:43Z","date_published":"2010-04-19T00:00:00Z","_id":"5391","year":"2010","status":"public","publication_status":"published","doi":"10.15479/AT:IST-2010-0001","day":"19","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"27","date_updated":"2024-10-21T06:03:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Model checking of linearizability of concurrent list implementations","type":"technical_report","related_material":{"record":[{"relation":"later_version","id":"4390","status":"public"}]},"month":"04","oa_version":"Published Version","date_created":"2018-12-12T11:39:04Z","publisher":"IST Austria","department":[{"_id":"ToHe"}],"file":[{"date_updated":"2020-07-14T12:46:43Z","access_level":"open_access","file_id":"5505","date_created":"2018-12-12T11:53:44Z","file_size":372286,"file_name":"IST-2010-0001_IST-2010-0001.pdf","creator":"system","checksum":"986645caad7dd85a6a091488f6c646dc","content_type":"application/pdf","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable."}],"page":"27","ddc":["004"],"oa":1},{"oa_version":"None","date_created":"2019-02-08T09:33:41Z","type":"book_chapter","title":"Instance Deadlock: A Mystery behind Frozen Programs","publication":"Applications and Theory of Petri Nets","date_updated":"2022-04-01T13:45:24Z","user_id":"4A997E50-F248-11E8-B48F-1D18A9856A87","page":"1-17","article_processing_charge":"No","publisher":"Springer Berlin Heidelberg","author":[{"last_name":"Juhás","full_name":"Juhás, Gabriel","first_name":"Gabriel"},{"last_name":"Kazlov","first_name":"Igor","id":"4A997E50-F248-11E8-B48F-1D18A9856A87","full_name":"Kazlov, Igor"},{"full_name":"Juhásová, Ana","first_name":"Ana","last_name":"Juhásová"}],"publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["9783642136740","9783642136757"]},"doi":"10.1007/978-3-642-13675-7_1","language":[{"iso":"eng"}],"year":"2010","_id":"5940","date_published":"2010-01-01T00:00:00Z","status":"public","publication_status":"published","extern":"1","place":"Berlin, Heidelberg","citation":{"chicago":"Juhás, Gabriel, Igor Kazlov, and Ana Juhásová. “Instance Deadlock: A Mystery behind Frozen Programs.” In <i>Applications and Theory of Petri Nets</i>, 1–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>.","short":"G. Juhás, I. Kazlov, A. Juhásová, in:, Applications and Theory of Petri Nets, Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, pp. 1–17.","mla":"Juhás, Gabriel, et al. “Instance Deadlock: A Mystery behind Frozen Programs.” <i>Applications and Theory of Petri Nets</i>, Springer Berlin Heidelberg, 2010, pp. 1–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>.","ama":"Juhás G, Kazlov I, Juhásová A. Instance Deadlock: A Mystery behind Frozen Programs. In: <i>Applications and Theory of Petri Nets</i>. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010:1-17. doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>","ieee":"G. Juhás, I. Kazlov, and A. Juhásová, “Instance Deadlock: A Mystery behind Frozen Programs,” in <i>Applications and Theory of Petri Nets</i>, Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp. 1–17.","apa":"Juhás, G., Kazlov, I., &#38; Juhásová, A. (2010). Instance Deadlock: A Mystery behind Frozen Programs. In <i>Applications and Theory of Petri Nets</i> (pp. 1–17). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>","ista":"Juhás G, Kazlov I, Juhásová A. 2010.Instance Deadlock: A Mystery behind Frozen Programs. In: Applications and Theory of Petri Nets. , 1–17."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:05:28Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932482/","open_access":"1"}],"date_created":"2018-12-11T11:47:24Z","oa_version":"None","publication":"Nature Structural and Molecular Biology","month":"06","type":"journal_article","title":"P53 activates transcription by directing structural shifts in Mediator","article_processing_charge":"No","publisher":"Nature Publishing Group","oa":1,"page":"753 - 760","abstract":[{"lang":"eng","text":"It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes."}],"issue":"6","intvolume":"        17","publist_id":"7210","author":[{"last_name":"Meyer","first_name":"Krista","full_name":"Meyer, Krista"},{"first_name":"Shih","full_name":"Lin, Shih","last_name":"Lin"},{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"},{"full_name":"Gao, Yuefeng","first_name":"Yuefeng","last_name":"Gao"},{"first_name":"Dylan","full_name":"Taatjes, Dylan","last_name":"Taatjes"}],"extern":"1","status":"public","volume":17,"publication_status":"published","year":"2010","_id":"598","date_published":"2010-06-01T00:00:00Z","citation":{"mla":"Meyer, Krista, et al. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6, Nature Publishing Group, 2010, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>.","ama":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. 2010;17(6):753-760. doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>","apa":"Meyer, K., Lin, S., Bernecky, C., Gao, Y., &#38; Taatjes, D. (2010). P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>","ieee":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, and D. Taatjes, “P53 activates transcription by directing structural shifts in Mediator,” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6. Nature Publishing Group, pp. 753–760, 2010.","ista":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. 2010. P53 activates transcription by directing structural shifts in Mediator. Nature Structural and Molecular Biology. 17(6), 753–760.","chicago":"Meyer, Krista, Shih Lin, Carrie Bernecky, Yuefeng Gao, and Dylan Taatjes. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>.","short":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, D. Taatjes, Nature Structural and Molecular Biology 17 (2010) 753–760."},"language":[{"iso":"eng"}],"day":"01","doi":"10.1038/nsmb.1816"},{"oa_version":"Published Version","type":"journal_article","month":"11","ddc":["570"],"article_number":"e13922","_id":"6142","volume":5,"publication_identifier":{"issn":["1932-6203"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1371/journal.pone.0013922","day":"11","date_updated":"2021-01-12T08:06:20Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"date_created":"2019-03-20T15:20:30Z","title":"Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans","publication":"PLoS ONE","publisher":"Public Library of Science","oa":1,"file":[{"checksum":"a01e6bbe15f044c0c79a26d7d881953e","relation":"main_file","content_type":"application/pdf","file_name":"2010_PLOS_Weber.PDF","file_size":578059,"creator":"kschuh","file_id":"6143","date_created":"2019-03-20T15:22:48Z","date_updated":"2020-07-14T12:47:20Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication."}],"intvolume":"         5","issue":"11","author":[{"last_name":"Weber","full_name":"Weber, Katherine P.","first_name":"Katherine P."},{"full_name":"De, Subhajyoti","first_name":"Subhajyoti","last_name":"De"},{"last_name":"Kozarewa","full_name":"Kozarewa, Iwanka","first_name":"Iwanka"},{"last_name":"Turner","first_name":"Daniel J.","full_name":"Turner, Daniel J."},{"first_name":"M. Madan","full_name":"Babu, M. Madan","last_name":"Babu"},{"last_name":"de Bono","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"has_accepted_license":"1","date_published":"2010-11-11T00:00:00Z","year":"2010","status":"public","extern":"1","publication_status":"published","citation":{"short":"K.P. Weber, S. De, I. Kozarewa, D.J. Turner, M.M. Babu, M. de Bono, PLoS ONE 5 (2010).","chicago":"Weber, Katherine P., Subhajyoti De, Iwanka Kozarewa, Daniel J. Turner, M. Madan Babu, and Mario de Bono. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>.","ista":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. 2010. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS ONE. 5(11), e13922.","apa":"Weber, K. P., De, S., Kozarewa, I., Turner, D. J., Babu, M. M., &#38; de Bono, M. (2010). Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>","ama":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. 2010;5(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>","ieee":"K. P. Weber, S. De, I. Kozarewa, D. J. Turner, M. M. Babu, and M. de Bono, “Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans,” <i>PLoS ONE</i>, vol. 5, no. 11. Public Library of Science, 2010.","mla":"Weber, Katherine P., et al. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>, vol. 5, no. 11, e13922, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>."},"file_date_updated":"2020-07-14T12:47:20Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["21085631"]}},{"_id":"619","year":"2010","date_published":"2010-01-01T00:00:00Z","publication_status":"published","status":"public","extern":1,"citation":{"ista":"Zacharasiewicz W, Kirsch F. 2010.“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien. , 173–179.","ama":"Zacharasiewicz W, Kirsch F. “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>. Facultas.WUV; 2010:173-179.","apa":"Zacharasiewicz, W., &#38; Kirsch, F. (2010). “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i> (pp. 173–179). Facultas.WUV.","ieee":"W. Zacharasiewicz and F. Kirsch, “‘This is a fundamentalist town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House,” in <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i>, Facultas.WUV, 2010, pp. 173–179.","mla":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, Facultas.WUV, 2010, pp. 173–79.","short":"W. Zacharasiewicz, F. Kirsch, in:, Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien, Facultas.WUV, 2010, pp. 173–179.","chicago":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” In <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, 173–79. Facultas.WUV, 2010."},"quality_controlled":0,"day":"01","publist_id":"7185","author":[{"first_name":"Waldemar","full_name":"Zacharasiewicz, Waldemar","last_name":"Zacharasiewicz"},{"first_name":"Fritz","full_name":"Kirsch, Fritz Peter","last_name":"Kirsch"}],"publisher":"Facultas.WUV","abstract":[{"text":"Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place.","lang":"eng"}],"page":"173 - 179","date_updated":"2021-01-12T08:06:40Z","date_created":"2018-12-11T11:47:32Z","type":"book_chapter","title":"“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House","month":"01","publication":"Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien"},{"language":[{"iso":"eng"}],"external_id":{"pmid":["21102461"]},"day":"21","doi":"10.1038/nm.2245","publication_identifier":{"issn":["1078-8956","1546-170x"]},"quality_controlled":"1","citation":{"ama":"Zhou L, Li F, Xu H, et al. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. 2010;16(12):1439-1443. doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>","ieee":"L. Zhou <i>et al.</i>, “Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95,” <i>Nature Medicine</i>, vol. 16, no. 12. Nature Publishing Group, pp. 1439–1443, 2010.","apa":"Zhou, L., Li, F., Xu, H., Luo, C., Wu, H., Zhu, M., … Zhu, D. (2010). Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>","ista":"Zhou L, Li F, Xu H, Luo C, Wu H, Zhu M, Lu W, Ji X, Zhou Q, Zhu D. 2010. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nature Medicine. 16(12), 1439–1443.","mla":"Zhou, L., et al. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>, vol. 16, no. 12, Nature Publishing Group, 2010, pp. 1439–43, doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>.","short":"L. Zhou, F. Li, H. Xu, C. Luo, H. Wu, M. Zhu, W. Lu, X. Ji, Q. Zhou, D. Zhu, Nature Medicine 16 (2010) 1439–1443.","chicago":"Zhou, L, F Li, Haibing Xu, CX Luo, HY Wu, MM Zhu, W Lu, X Ji, QG Zhou, and DY Zhu. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>."},"publication_status":"published","volume":16,"status":"public","extern":"1","_id":"6198","year":"2010","date_published":"2010-11-21T00:00:00Z","author":[{"last_name":"Zhou","first_name":"L","full_name":"Zhou, L"},{"last_name":"Li","first_name":"F","full_name":"Li, F"},{"full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","last_name":"Xu"},{"last_name":"Luo","first_name":"CX","full_name":"Luo, CX"},{"last_name":"Wu","first_name":"HY","full_name":"Wu, HY"},{"first_name":"MM","full_name":"Zhu, MM","last_name":"Zhu"},{"last_name":"Lu","full_name":"Lu, W","first_name":"W"},{"last_name":"Ji","first_name":"X","full_name":"Ji, X"},{"last_name":"Zhou","full_name":"Zhou, QG","first_name":"QG"},{"full_name":"Zhu, DY","first_name":"DY","last_name":"Zhu"}],"issue":"12","intvolume":"        16","page":"1439-1443","abstract":[{"lang":"eng","text":"Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. "}],"publisher":"Nature Publishing Group","month":"11","publication":"Nature Medicine","title":"Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95","type":"journal_article","oa_version":"None","date_created":"2019-04-04T14:55:32Z","date_updated":"2021-01-12T08:06:43Z","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"issue":"18","intvolume":"        82","author":[{"first_name":"E. K. H.","full_name":"Salje, E. K. H.","last_name":"Salje"},{"last_name":"Safarik","first_name":"D. J.","full_name":"Safarik, D. J."},{"first_name":"Kimberly A","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic"},{"first_name":"J. E.","full_name":"Gubernatis, J. E.","last_name":"Gubernatis"},{"last_name":"Cooley","first_name":"J. C.","full_name":"Cooley, J. C."},{"last_name":"Taylor","first_name":"R. D.","full_name":"Taylor, R. D."},{"first_name":"B.","full_name":"Mihaila, B.","last_name":"Mihaila"},{"full_name":"Saxena, A.","first_name":"A.","last_name":"Saxena"},{"first_name":"T.","full_name":"Lookman, T.","last_name":"Lookman"},{"last_name":"Smith","first_name":"J. L.","full_name":"Smith, J. L."},{"last_name":"Fisher","full_name":"Fisher, R. A.","first_name":"R. A."},{"first_name":"M.","full_name":"Pasternak, M.","last_name":"Pasternak"},{"last_name":"Opeil","full_name":"Opeil, C. P.","first_name":"C. P."},{"last_name":"Siegrist","first_name":"T.","full_name":"Siegrist, T."},{"first_name":"P. B.","full_name":"Littlewood, P. B.","last_name":"Littlewood"},{"last_name":"Lashley","first_name":"J. C.","full_name":"Lashley, J. C."}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1011.1445"]},"extern":"1","status":"public","publication_status":"published","year":"2010","date_published":"2010-11-18T00:00:00Z","citation":{"short":"E.K.H. Salje, D.J. Safarik, K.A. Modic, J.E. Gubernatis, J.C. Cooley, R.D. Taylor, B. Mihaila, A. Saxena, T. Lookman, J.L. Smith, R.A. Fisher, M. Pasternak, C.P. Opeil, T. Siegrist, P.B. Littlewood, J.C. Lashley, Physical Review B 82 (2010).","chicago":"Salje, E. K. H., D. J. Safarik, Kimberly A Modic, J. E. Gubernatis, J. C. Cooley, R. D. Taylor, B. Mihaila, et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>. APS, 2010. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>.","ista":"Salje EKH, Safarik DJ, Modic KA, Gubernatis JE, Cooley JC, Taylor RD, Mihaila B, Saxena A, Lookman T, Smith JL, Fisher RA, Pasternak M, Opeil CP, Siegrist T, Littlewood PB, Lashley JC. 2010. Tin telluride: A weakly co-elastic metal. Physical Review B. 82(18), 184112.","ieee":"E. K. H. Salje <i>et al.</i>, “Tin telluride: A weakly co-elastic metal,” <i>Physical Review B</i>, vol. 82, no. 18. APS, 2010.","apa":"Salje, E. K. H., Safarik, D. J., Modic, K. A., Gubernatis, J. E., Cooley, J. C., Taylor, R. D., … Lashley, J. C. (2010). Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. APS. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>","ama":"Salje EKH, Safarik DJ, Modic KA, et al. Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. 2010;82(18). doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>","mla":"Salje, E. K. H., et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>, vol. 82, no. 18, 184112, APS, 2010, doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>."},"date_created":"2019-11-19T13:46:28Z","publication":"Physical Review B","title":"Tin telluride: A weakly co-elastic metal","date_updated":"2021-01-12T08:11:44Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1011.1445"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa":1,"abstract":[{"text":"We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other.","lang":"eng"}],"publisher":"APS","article_type":"original","article_number":"184112","publication_identifier":{"issn":["1098-0121","1550-235X"]},"doi":"10.1103/physrevb.82.184112","day":"18","volume":82,"_id":"7078","oa_version":"Preprint","month":"11","type":"journal_article","article_processing_charge":"No"}]