[{"oa":1,"publication_identifier":{"issn":["09254773"]},"status":"public","ec_funded":1,"month":"06","year":"2017","abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}],"date_updated":"2021-01-12T08:09:20Z","_id":"685","ddc":["571"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:42Z","intvolume":"       145","citation":{"chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>.","apa":"Briscoe, J., &#38; Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>","ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>, vol. 145, Elsevier, 2017, pp. 26–31, doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. 2017;145:26-31. doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” <i>Mechanisms of Development</i>, vol. 145. Elsevier, pp. 26–31, 2017.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31."},"doi":"10.1016/j.mod.2017.03.005","publication_status":"published","date_published":"2017-06-01T00:00:00Z","oa_version":"Submitted Version","title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","day":"01","pmid":1,"file":[{"date_created":"2019-04-17T07:58:48Z","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","creator":"dernst","file_id":"6335","checksum":"727043d2e4199fbef6b3704e6d1ac105","file_size":652313,"content_type":"application/pdf","relation":"main_file"}],"author":[{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"pubrep_id":"985","publist_id":"7025","quality_controlled":"1","volume":145,"external_id":{"pmid":["28366718"]},"publication":"Mechanisms of Development","date_created":"2018-12-11T11:47:55Z","page":"26 - 31","has_accepted_license":"1","department":[{"_id":"AnKi"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"date_published":"2017-06-01T00:00:00Z","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication":"Mechanisms of Development","date_created":"2018-12-11T11:47:55Z","page":"32 - 37","doi":"10.1016/j.mod.2017.03.006","publication_status":"published","intvolume":"       145","citation":{"ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” <i>Mechanisms of Development</i>, vol. 145, Elsevier, 2017, pp. 32–37, doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">10.1016/j.mod.2017.03.006</a>.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">https://doi.org/10.1016/j.mod.2017.03.006</a>","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” <i>Mechanisms of Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">https://doi.org/10.1016/j.mod.2017.03.006</a>.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. <i>Mechanisms of Development</i>. 2017;145:32-37. doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">10.1016/j.mod.2017.03.006</a>","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” <i>Mechanisms of Development</i>, vol. 145. Elsevier, pp. 32–37, 2017."},"volume":145,"quality_controlled":"1","publist_id":"7024","scopus_import":1,"_id":"686","author":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2017","day":"01","abstract":[{"text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology.","lang":"eng"}],"date_updated":"2021-01-12T08:09:23Z","month":"06","publication_identifier":{"issn":["09254773"]},"title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","status":"public"},{"_id":"687","abstract":[{"text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs.","lang":"eng"}],"issue":"2","date_updated":"2021-01-12T08:09:24Z","year":"2017","month":"06","ec_funded":1,"status":"public","publication_identifier":{"issn":["00335606"]},"oa":1,"oa_version":"Submitted Version","date_published":"2017-06-01T00:00:00Z","doi":"10.1093/qmath/haw053","publication_status":"published","intvolume":"        68","citation":{"mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>.","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","ama":"Davison B. The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. 2017;68(2):635-703. doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"scopus_import":1,"author":[{"full_name":"Davison, Ben","orcid":"0000-0002-8944-4390","first_name":"Ben","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","last_name":"Davison"}],"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","title":"The critical CoHA of a quiver with potential","type":"journal_article","department":[{"_id":"TaHa"}],"language":[{"iso":"eng"}],"publication":"Quarterly Journal of Mathematics","page":"635 - 703","date_created":"2018-12-11T11:47:55Z","quality_controlled":"1","volume":68,"publist_id":"7022"},{"file_date_updated":"2020-07-14T12:47:42Z","scopus_import":1,"ddc":["514","516"],"citation":{"ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. <i>Topological Data Analysis with Bregman Divergences</i>. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>.","apa":"Edelsbrunner, H., &#38; Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916."},"intvolume":"        77","doi":"10.4230/LIPIcs.SoCG.2017.39","conference":{"end_date":"2017-07-07","location":"Brisbane, Australia","start_date":"2017-07-04","name":"Symposium on Computational Geometry, SoCG"},"publication_status":"published","oa_version":"Published Version","date_published":"2017-06-01T00:00:00Z","status":"public","oa":1,"publication_identifier":{"issn":["18688969"]},"month":"06","abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"date_updated":"2021-01-12T08:09:26Z","year":"2017","_id":"688","pubrep_id":"895","publist_id":"7021","volume":77,"quality_controlled":"1","has_accepted_license":"1","date_created":"2018-12-11T11:47:56Z","page":"391-3916","type":"conference","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Topological data analysis with Bregman divergences","alternative_title":["LIPIcs"],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Wagner, Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert"}],"file":[{"file_size":990546,"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:03Z","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_id":"4856","creator":"system","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3"}]},{"scopus_import":1,"publist_id":"7019","quality_controlled":"1","intvolume":"         9","citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” <i>Science Translational Medicine</i>, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","ama":"Novarino G. Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. 2017;9(393). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>."},"volume":9,"publication":"Science Translational Medicine","date_created":"2018-12-11T11:47:56Z","doi":"10.1126/scitranslmed.aan8196","publication_status":"published","department":[{"_id":"GaNo"}],"date_published":"2017-06-07T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publication_identifier":{"issn":["19466234"]},"title":"Rett syndrome modeling goes simian","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"American Association for the Advancement of Science","month":"06","year":"2017","day":"07","issue":"393","abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"date_updated":"2021-01-12T08:09:29Z","_id":"689","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"article_number":"eaan8196"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","pmid":1,"day":"27","author":[{"full_name":"Miki, Takafumi","last_name":"Miki","first_name":"Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"last_name":"Malagon","first_name":"Gerardo","full_name":"Malagon, Gerardo"},{"first_name":"Laura","last_name":"Gomez","full_name":"Gomez, Laura"},{"first_name":"Katsuhiko","last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Marty, Alain","first_name":"Alain","last_name":"Marty"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":2721544,"checksum":"2ab75d554f3df4a34d20fa8040589b7e","creator":"kschuh","file_id":"7223","access_level":"open_access","file_name":"2017_PNAS_Miki.pdf","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z"}],"article_processing_charge":"Yes (in subscription journal)","publist_id":"7013","volume":114,"quality_controlled":"1","external_id":{"pmid":["28607047"]},"has_accepted_license":"1","publication":"PNAS","date_created":"2018-12-11T11:47:57Z","page":"E5246 - E5255","type":"journal_article","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"publication_identifier":{"issn":["00278424"]},"month":"06","issue":"26","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"date_updated":"2023-02-23T12:54:57Z","year":"2017","_id":"693","file_date_updated":"2020-07-14T12:47:44Z","scopus_import":1,"ddc":["570"],"intvolume":"       114","citation":{"apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255."},"doi":"10.1073/pnas.1704470114","publication_status":"published","oa_version":"Published Version","date_published":"2017-06-27T00:00:00Z"},{"month":"07","publication_identifier":{"isbn":["9781450349925"]},"title":"LCL problems on grids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM Press","status":"public","_id":"6932","author":[{"last_name":"Brandt","first_name":"Sebastian","full_name":"Brandt, Sebastian"},{"full_name":"Hirvonen, Juho","first_name":"Juho","last_name":"Hirvonen"},{"full_name":"Korhonen, Janne H.","last_name":"Korhonen","first_name":"Janne H."},{"first_name":"Tuomo","last_name":"Lempiäinen","full_name":"Lempiäinen, Tuomo"},{"full_name":"Östergård, Patric R.J.","first_name":"Patric R.J.","last_name":"Östergård"},{"full_name":"Purcell, Christopher","last_name":"Purcell","first_name":"Christopher"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","orcid":"0000-0002-6432-6646"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"},{"full_name":"Uznański, Przemysław","first_name":"Przemysław","last_name":"Uznański"}],"extern":"1","year":"2017","day":"01","abstract":[{"text":"LCLs or locally checkable labelling problems (e.g. maximal independent set, maximal matching, and vertex colouring) in the LOCAL model of computation are very well-understood in cycles (toroidal 1-dimensional grids): every problem has a complexity of O(1), Θ(log* n), or Θ(n), and the design of optimal algorithms can be fully automated. This work develops the complexity theory of LCL problems for toroidal 2-dimensional grids. The complexity classes are the same as in the 1-dimensional case: O(1), Θ(log* n), and Θ(n). However, given an LCL problem it is undecidable whether its complexity is Θ(log* n) or Θ(n) in 2-dimensional grids.\r\nNevertheless, if we correctly guess that the complexity of a problem is Θ(log* n), we can completely automate the design of optimal algorithms. For any problem we can find an algorithm that is of a normal form A' o Sk, where A' is a finite function, Sk is an algorithm for finding a maximal independent set in kth power of the grid, and k is a constant.\r\nFinally, partially with the help of automated design tools, we classify the complexity of several concrete LCL problems related to colourings and orientations.","lang":"eng"}],"date_updated":"2021-01-12T08:09:39Z","quality_controlled":"1","citation":{"apa":"Brandt, S., Hirvonen, J., Korhonen, J. H., Lempiäinen, T., Östergård, P. R. J., Purcell, C., … Uznański, P. (2017). LCL problems on grids (pp. 101–110). Presented at the PODC: Principles of Distributed Computing, Washington, DC, United States: ACM Press. <a href=\"https://doi.org/10.1145/3087801.3087833\">https://doi.org/10.1145/3087801.3087833</a>","ista":"Brandt S, Hirvonen J, Korhonen JH, Lempiäinen T, Östergård PRJ, Purcell C, Rybicki J, Suomela J, Uznański P. 2017. LCL problems on grids. PODC: Principles of Distributed Computing, 101–110.","mla":"Brandt, Sebastian, et al. <i>LCL Problems on Grids</i>. ACM Press, 2017, pp. 101–10, doi:<a href=\"https://doi.org/10.1145/3087801.3087833\">10.1145/3087801.3087833</a>.","chicago":"Brandt, Sebastian, Juho Hirvonen, Janne H. Korhonen, Tuomo Lempiäinen, Patric R.J. Östergård, Christopher Purcell, Joel Rybicki, Jukka Suomela, and Przemysław Uznański. “LCL Problems on Grids,” 101–10. ACM Press, 2017. <a href=\"https://doi.org/10.1145/3087801.3087833\">https://doi.org/10.1145/3087801.3087833</a>.","short":"S. Brandt, J. Hirvonen, J.H. Korhonen, T. Lempiäinen, P.R.J. Östergård, C. Purcell, J. Rybicki, J. Suomela, P. Uznański, in:, ACM Press, 2017, pp. 101–110.","ama":"Brandt S, Hirvonen J, Korhonen JH, et al. LCL problems on grids. In: ACM Press; 2017:101-110. doi:<a href=\"https://doi.org/10.1145/3087801.3087833\">10.1145/3087801.3087833</a>","ieee":"S. Brandt <i>et al.</i>, “LCL problems on grids,” presented at the PODC: Principles of Distributed Computing, Washington, DC, United States, 2017, pp. 101–110."},"article_processing_charge":"No","date_published":"2017-07-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","oa_version":"None","date_created":"2019-10-08T12:47:46Z","page":"101-110","doi":"10.1145/3087801.3087833","conference":{"location":"Washington, DC, United States","end_date":"2017-07-27","name":"PODC: Principles of Distributed Computing","start_date":"2017-07-25"},"publication_status":"published"},{"doi":"10.1242/jcs.200899","publication_status":"published","date_published":"2017-07-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:45Z","intvolume":"       130","citation":{"chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>"},"year":"2017","abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"issue":"13","date_updated":"2021-01-12T08:09:41Z","_id":"694","publication_identifier":{"issn":["00219533"]},"oa":1,"status":"public","month":"07","publication":"Journal of Cell Science","date_created":"2018-12-11T11:47:58Z","page":"2172 - 2184","has_accepted_license":"1","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","publist_id":"7008","volume":130,"quality_controlled":"1","external_id":{"pmid":["28515231"]},"day":"01","pmid":1,"file":[{"date_created":"2019-10-24T09:43:56Z","date_updated":"2020-07-14T12:47:45Z","file_name":"2017_CellScience_Vess.pdf","access_level":"open_access","creator":"dernst","file_id":"6966","checksum":"42c81a0a4fc3128883b391c3af3f74bc","file_size":10847596,"relation":"main_file","content_type":"application/pdf"}],"author":[{"last_name":"Veß","first_name":"Astrid","full_name":"Veß, Astrid"},{"last_name":"Blache","first_name":"Ulrich","full_name":"Blache, Ulrich"},{"full_name":"Leitner, Laura","last_name":"Leitner","first_name":"Laura"},{"last_name":"Kurz","first_name":"Angela","full_name":"Kurz, Angela"},{"first_name":"Anja","last_name":"Ehrenpfordt","full_name":"Ehrenpfordt, Anja"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Posern","first_name":"Guido","full_name":"Posern, Guido"}],"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists"},{"publist_id":"7007","intvolume":"       232","quality_controlled":"1","citation":{"ama":"Etl F, Franschitz A, Aguiar A, Schönenberger J, Dötterl S. A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini. <i>Flora: Morphology, Distribution, Functional Ecology of Plants</i>. 2017;232:7-15. doi:<a href=\"https://doi.org/10.1016/j.flora.2017.02.020\">10.1016/j.flora.2017.02.020</a>","ieee":"F. Etl, A. Franschitz, A. Aguiar, J. Schönenberger, and S. Dötterl, “A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini,” <i>Flora: Morphology, Distribution, Functional Ecology of Plants</i>, vol. 232. Elsevier, pp. 7–15, 2017.","short":"F. Etl, A. Franschitz, A. Aguiar, J. Schönenberger, S. Dötterl, Flora: Morphology, Distribution, Functional Ecology of Plants 232 (2017) 7–15.","apa":"Etl, F., Franschitz, A., Aguiar, A., Schönenberger, J., &#38; Dötterl, S. (2017). A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini. <i>Flora: Morphology, Distribution, Functional Ecology of Plants</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.flora.2017.02.020\">https://doi.org/10.1016/j.flora.2017.02.020</a>","mla":"Etl, Florian, et al. “A Perfume Collecting Male Oil Bee? Evidences of a Novel Pollination System Involving Anthurium Acutifolium Araceae and Paratetrapedia Chocoensis Apidae Tapinotaspidini.” <i>Flora: Morphology, Distribution, Functional Ecology of Plants</i>, vol. 232, Elsevier, 2017, pp. 7–15, doi:<a href=\"https://doi.org/10.1016/j.flora.2017.02.020\">10.1016/j.flora.2017.02.020</a>.","ista":"Etl F, Franschitz A, Aguiar A, Schönenberger J, Dötterl S. 2017. A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini. Flora: Morphology, Distribution, Functional Ecology of Plants. 232, 7–15.","chicago":"Etl, Florian, Anna Franschitz, Antonio Aguiar, Jürg Schönenberger, and Stefan Dötterl. “A Perfume Collecting Male Oil Bee? Evidences of a Novel Pollination System Involving Anthurium Acutifolium Araceae and Paratetrapedia Chocoensis Apidae Tapinotaspidini.” <i>Flora: Morphology, Distribution, Functional Ecology of Plants</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.flora.2017.02.020\">https://doi.org/10.1016/j.flora.2017.02.020</a>."},"volume":232,"publication":"Flora: Morphology, Distribution, Functional Ecology of Plants","page":"7 - 15","date_created":"2018-12-11T11:47:58Z","doi":"10.1016/j.flora.2017.02.020","publication_status":"published","date_published":"2017-07-01T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication_identifier":{"issn":["03672530"]},"title":"A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","status":"public","month":"07","extern":"1","year":"2017","day":"01","abstract":[{"lang":"eng","text":"It has been known since Stefan Vogel's observations in 1969 that solitary female oil bees collect fatty floral oils from specialized oil-secreting plants with the aid of hairy patches on either their legs or abdomen, a reward used as food for their larvae and/or to line their brood cells. Similar adaptations are also known from male oil bees, although the purpose of their oil-collecting behavior has not yet been clarified. Here, we describe a novel pollination system involving male Paratetrapedia oil bees and the tropical herb Anthurium acutifolium. We present ultrastructural morphological details of bee and plant structures involved in this interaction and the composition of floral scents likely mediating pollinator attraction. Inflorescences of A. acutifolium were visited almost exclusively by male P. chocoensis oil bees. The bees mopped with a hairy patch of their abdominal sterna 3 across the inflorescence surface. During this activity on both staminate and pistillate stage inflorescences, bees’ abdomens and legs became loaded with pollen and contacted receptive stigmas. In contrast to what has been observed in other angiosperms visited for the collection of fatty floral oils, the inflorescences/flowers of A. acutifolium do not have structures specialized in oil secretion, i.e., elaiophores. These inflorescences, nonetheless, were strongly scented during the time interval they were visited by the bees. Gas chromatography/mass spectrometry (GC/MS) analyses of dynamic headspace floral samples revealed that inflorescences of both anthetic phases emitted scent bouquets consisting mainly of aliphatic esters, indole and uncommmon terpenoids (megastigmanes). Interestingly enough, our data suggest that the unusual floral scent of A. acutifolium is a perfume reward collected by male P. chocoensis oil bees. This pollination system thus bears a remarkable resemblence with the interactions between perfume-collecting male euglossine bees and their preferred flowers, discovered by Stefan Vogel half a century ago."}],"date_updated":"2021-01-12T08:09:44Z","_id":"695","author":[{"last_name":"Etl","first_name":"Florian","full_name":"Etl, Florian"},{"last_name":"Franschitz","id":"480826C8-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Franschitz, Anna"},{"first_name":"Antonio","last_name":"Aguiar","full_name":"Aguiar, Antonio"},{"first_name":"Jürg","last_name":"Schönenberger","full_name":"Schönenberger, Jürg"},{"first_name":"Stefan","last_name":"Dötterl","full_name":"Dötterl, Stefan"}]},{"_id":"696","article_number":"e1005609","year":"2017","issue":"7","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"date_updated":"2024-03-25T23:30:14Z","ec_funded":1,"month":"07","publication_identifier":{"issn":["1553734X"]},"oa":1,"status":"public","date_published":"2017-07-18T00:00:00Z","oa_version":"Published Version","doi":"10.1371/journal.pcbi.1005609","publication_status":"published","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609."},"intvolume":"        13","ddc":["576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:46Z","file":[{"date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","creator":"system","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":3775716}],"author":[{"full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X","first_name":"Sebastian"},{"full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"}],"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"day":"18","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:47:58Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9849"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"id":"9852","status":"public","relation":"research_data"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"volume":13,"quality_controlled":"1","pubrep_id":"894","article_type":"original","publist_id":"7004"},{"date_created":"2018-12-11T11:47:59Z","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"type":"conference","publist_id":"7003","pubrep_id":"893","quality_controlled":"1","volume":80,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","relation":"main_file","file_size":601004,"file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z","file_id":"4701","checksum":"e95618a001692f1af2d68f5fde43bc1f","creator":"system","access_level":"open_access"}],"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"author":[{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","full_name":"Skórski, Maciej"}],"title":"Non uniform attacks against pseudoentropy","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"conference":{"start_date":"2017-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2017-07-14","location":"Warsaw, Poland"},"publication_status":"published","doi":"10.4230/LIPIcs.ICALP.2017.39","date_published":"2017-07-01T00:00:00Z","oa_version":"Published Version","ddc":["005"],"file_date_updated":"2020-07-14T12:47:46Z","scopus_import":1,"intvolume":"        80","citation":{"chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>.","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"year":"2017","date_updated":"2021-01-12T08:11:15Z","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"_id":"697","article_number":"39","publication_identifier":{"issn":["18688969"]},"oa":1,"status":"public","ec_funded":1,"month":"07"},{"_id":"698","year":"2017","date_updated":"2021-01-12T08:11:17Z","issue":"14","abstract":[{"text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. ","lang":"eng"}],"month":"07","oa":1,"publication_identifier":{"issn":["10591524"]},"status":"public","date_published":"2017-07-07T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1091/mbc.E16-12-0825","citation":{"short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009."},"intvolume":"        28","ddc":["519"],"file_date_updated":"2020-07-14T12:47:46Z","scopus_import":1,"file":[{"date_created":"2018-12-12T10:10:53Z","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","creator":"system","checksum":"de01dac9e30970cfa6ae902480a4e04d","file_id":"4844","file_size":1086097,"content_type":"application/pdf","relation":"main_file"}],"project":[{"call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35"}],"author":[{"full_name":"Wang, Yejun","first_name":"Yejun","last_name":"Wang"},{"first_name":"Mallika","last_name":"Nagarajan","full_name":"Nagarajan, Mallika"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","full_name":"Uhler, Caroline"},{"full_name":"Shivashankar, Gv","last_name":"Shivashankar","first_name":"Gv"}],"day":"07","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","publisher":"American Society for Cell Biology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"CaUh"}],"type":"journal_article","page":"1997 - 2009","date_created":"2018-12-11T11:47:59Z","publication":"Molecular Biology of the Cell","has_accepted_license":"1","volume":28,"quality_controlled":"1","publist_id":"7001","pubrep_id":"892"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","title":"The red queen and king in finite populations","pmid":1,"day":"03","author":[{"full_name":"Veller, Carl","last_name":"Veller","first_name":"Carl"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"}],"publist_id":"7002","quality_controlled":"1","volume":114,"external_id":{"pmid":["28630336"]},"publication":"PNAS","date_created":"2018-12-11T11:48:00Z","page":"E5396 - E5405","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"publication_identifier":{"issn":["00278424"]},"month":"07","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"issue":"27","date_updated":"2021-01-12T08:11:21Z","year":"2017","_id":"699","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/"}],"citation":{"ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405."},"intvolume":"       114","doi":"10.1073/pnas.1702020114","publication_status":"published","oa_version":"Submitted Version","date_published":"2017-07-03T00:00:00Z"},{"publist_id":"6997","quality_controlled":"1","volume":96,"date_created":"2018-12-11T11:48:00Z","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"type":"journal_article","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","publisher":"American Institute of Physics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"12","project":[{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","call_identifier":"H2020"}],"author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh"},{"first_name":"Vahid","last_name":"Salari","full_name":"Salari, Vahid"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"last_name":"Simon","first_name":"Christoph","full_name":"Simon, Christoph"}],"main_file_link":[{"url":"https://arxiv.org/pdf/1612.07061.pdf","open_access":"1"}],"scopus_import":1,"citation":{"ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>"},"intvolume":"        96","publication_status":"published","doi":"10.1103/PhysRevE.96.012404","date_published":"2017-07-12T00:00:00Z","oa_version":"Submitted Version","oa":1,"publication_identifier":{"issn":["24700045"]},"status":"public","ec_funded":1,"month":"07","year":"2017","date_updated":"2023-02-23T12:56:35Z","abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"issue":"1","_id":"700","article_number":"012404"},{"type":"journal_article","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"The Electronic Journal of Combinatorics","date_created":"2018-12-11T11:48:00Z","page":"1-44","quality_controlled":"1","volume":24,"pubrep_id":"984","publist_id":"6996","author":[{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":544042,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5077","checksum":"a431e573e31df13bc0f66de3061006ec","date_created":"2018-12-12T10:14:25Z","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","date_updated":"2020-07-14T12:47:47Z"}],"day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"International Press","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","oa_version":"Submitted Version","date_published":"2017-07-14T00:00:00Z","publication_status":"published","intvolume":"        24","citation":{"short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. 2017;24(3):1-44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, pp. 1–44, 2017.","apa":"Kynčl, J., &#38; Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. International Press.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3, International Press, 2017, pp. 1–44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>. International Press, 2017."},"file_date_updated":"2020-07-14T12:47:47Z","ddc":["500"],"_id":"701","abstract":[{"lang":"eng","text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2."}],"issue":"3","date_updated":"2021-01-12T08:11:28Z","year":"2017","month":"07","status":"public","publication_identifier":{"issn":["10778926"]},"oa":1},{"doi":"10.1126/scitranslmed.aao0972","publication_status":"published","publication":"Science Translational Medicine","date_created":"2018-12-11T11:48:01Z","page":"eaao0972","oa_version":"None","type":"journal_article","department":[{"_id":"GaNo"}],"date_published":"2017-07-19T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"6993","scopus_import":1,"volume":9,"citation":{"mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” <i>Science Translational Medicine</i>, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. 2017;9(399):eaao0972. doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>"},"intvolume":"         9","quality_controlled":"1","issue":"399","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"date_updated":"2021-01-12T08:11:31Z","year":"2017","day":"19","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"_id":"702","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","status":"public","publication_identifier":{"issn":["19466234"]},"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","month":"07"},{"has_accepted_license":"1","date_created":"2018-12-11T11:48:01Z","publication":"eLife","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"publist_id":"6990","pubrep_id":"890","volume":6,"quality_controlled":"1","related_material":{"record":[{"id":"5564","status":"public","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"day":"25","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719","first_name":"Magdalena","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":2092088,"creator":"system","file_id":"4975","checksum":"6b908b5db9f61f6820ebd7f8fa815571","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","date_created":"2018-12-12T10:12:54Z"},{"access_level":"open_access","checksum":"ca21530389b720243552678125fdba35","file_id":"4976","creator":"system","date_created":"2018-12-12T10:12:55Z","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","date_updated":"2020-07-14T12:47:48Z","file_size":3428681,"relation":"main_file","content_type":"application/pdf"}],"publisher":"eLife Sciences Publications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","publication_status":"published","doi":"10.7554/eLife.25100","oa_version":"Published Version","date_published":"2017-07-25T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:47:48Z","ddc":["576"],"intvolume":"         6","citation":{"chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017)."},"date_updated":"2024-03-25T23:30:14Z","abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"year":"2017","article_number":"e25100","_id":"704","status":"public","oa":1,"publication_identifier":{"issn":["2050084X"]},"month":"07"},{"year":"2017","day":"01","abstract":[{"text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.","lang":"eng"}],"issue":"8","date_updated":"2021-01-12T08:11:37Z","_id":"706","author":[{"full_name":"Geng, Xiaoqi","first_name":"Xiaoqi","id":"3395256A-F248-11E8-B48F-1D18A9856A87","last_name":"Geng"},{"first_name":"Tomohiko","last_name":"Maruo","full_name":"Maruo, Tomohiko"},{"full_name":"Mandai, Kenji","last_name":"Mandai","first_name":"Kenji"},{"full_name":"Supriyanto, Irwan","first_name":"Irwan","last_name":"Supriyanto"},{"last_name":"Miyata","first_name":"Muneaki","full_name":"Miyata, Muneaki"},{"first_name":"Shotaro","last_name":"Sakakibara","full_name":"Sakakibara, Shotaro"},{"full_name":"Mizoguchi, Akira","last_name":"Mizoguchi","first_name":"Akira"},{"last_name":"Takai","first_name":"Yoshimi","full_name":"Takai, Yoshimi"},{"last_name":"Mori","first_name":"Masahiro","full_name":"Mori, Masahiro"}],"publication_identifier":{"issn":["13569597"]},"title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","status":"public","month":"08","publication":"Genes to Cells","date_created":"2018-12-11T11:48:02Z","page":"715 - 722","doi":"10.1111/gtc.12508","publication_status":"published","department":[{"_id":"PeJo"}],"date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","scopus_import":1,"publist_id":"6987","quality_controlled":"1","volume":22,"intvolume":"        22","citation":{"short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. 2017;22(8):715-722. doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>","ieee":"X. Geng <i>et al.</i>, “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” <i>Genes to Cells</i>, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>."}},{"date_created":"2019-11-19T13:11:55Z","publication":"Nature Communications","has_accepted_license":"1","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","volume":8,"quality_controlled":"1","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"extern":"1","file":[{"date_updated":"2020-07-14T12:47:48Z","file_name":"2017_NatureComm_Modic.pdf","date_created":"2019-11-20T14:12:54Z","checksum":"57fcd59d2f274b6b16cc89ea03cfd440","file_id":"7091","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":1242958}],"author":[{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","full_name":"Modic, Kimberly A"},{"full_name":"Ramshaw, B. J.","last_name":"Ramshaw","first_name":"B. J."},{"full_name":"Betts, J. B.","last_name":"Betts","first_name":"J. B."},{"last_name":"Breznay","first_name":"Nicholas P.","full_name":"Breznay, Nicholas P."},{"full_name":"Analytis, James G.","last_name":"Analytis","first_name":"James G."},{"last_name":"McDonald","first_name":"Ross D.","full_name":"McDonald, Ross D."},{"last_name":"Shekhter","first_name":"Arkady","full_name":"Shekhter, Arkady"}],"title":"Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1038/s41467-017-00264-6","date_published":"2017-08-01T00:00:00Z","oa_version":"Published Version","ddc":["530"],"file_date_updated":"2020-07-14T12:47:48Z","intvolume":"         8","citation":{"chicago":"Modic, Kimberly A, B. J. Ramshaw, J. B. Betts, Nicholas P. Breznay, James G. Analytis, Ross D. McDonald, and Arkady Shekhter. “Robust Spin Correlations at High Magnetic Fields in the Harmonic Honeycomb Iridates.” <i>Nature Communications</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00264-6\">https://doi.org/10.1038/s41467-017-00264-6</a>.","mla":"Modic, Kimberly A., et al. “Robust Spin Correlations at High Magnetic Fields in the Harmonic Honeycomb Iridates.” <i>Nature Communications</i>, vol. 8, no. 1, 180, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00264-6\">10.1038/s41467-017-00264-6</a>.","apa":"Modic, K. A., Ramshaw, B. J., Betts, J. B., Breznay, N. P., Analytis, J. G., McDonald, R. D., &#38; Shekhter, A. (2017). Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-00264-6\">https://doi.org/10.1038/s41467-017-00264-6</a>","ista":"Modic KA, Ramshaw BJ, Betts JB, Breznay NP, Analytis JG, McDonald RD, Shekhter A. 2017. Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates. Nature Communications. 8(1), 180.","ama":"Modic KA, Ramshaw BJ, Betts JB, et al. Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00264-6\">10.1038/s41467-017-00264-6</a>","ieee":"K. A. Modic <i>et al.</i>, “Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates,” <i>Nature Communications</i>, vol. 8, no. 1. Springer Nature, 2017.","short":"K.A. Modic, B.J. Ramshaw, J.B. Betts, N.P. Breznay, J.G. Analytis, R.D. McDonald, A. Shekhter, Nature Communications 8 (2017)."},"year":"2017","date_updated":"2021-01-12T08:11:39Z","issue":"1","abstract":[{"lang":"eng","text":"The complex antiferromagnetic orders observed in the honeycomb iridates are a double-edged sword in the search for a quantum spin-liquid: both attesting that the magnetic interactions provide many of the necessary ingredients, while simultaneously impeding access. Focus has naturally been drawn to the unusual magnetic orders that hint at the underlying spin correlations. However, the study of any particular broken symmetry state generally provides little clue about the possibility of other nearby ground states. Here we use magnetic fields approaching 100 Tesla to reveal the extent of the spin correlations in γ-lithium iridate. We find that a small component of field along the magnetic easy-axis melts long-range order, revealing a bistable, strongly correlated spin state. Far from the usual destruction of antiferromagnetism via spin polarization, the high-field state possesses only a small fraction of the total iridium moment, without evidence for long-range order up to the highest attainable magnetic fields."}],"_id":"7064","article_number":"180","publication_identifier":{"issn":["2041-1723"]},"oa":1,"status":"public","month":"08"},{"issue":"12","abstract":[{"lang":"eng","text":"Magneto-quantum oscillation experiments in high-temperature superconductors show a strong thermally induced suppression of the oscillation amplitude approaching the critical dopings [B. J. Ramshaw et al., Science 348, 317 (2014); H. Shishido et al., Phys. Rev. Lett. 104, 057008 (2010); P. Walmsley et al., Phys. Rev. Lett. 110, 257002 (2013)]—in support of a quantum-critical origin of their phase diagrams. We suggest that, in addition to a thermodynamic mass enhancement, these experiments may directly indicate the increasing role of quantum fluctuations that suppress the quantum oscillation amplitude through inelastic scattering. We show that the traditional theoretical approaches beyond Lifshitz-Kosevich to calculate the oscillation amplitude in correlated metals result in a contradiction with the third law of thermodynamics and suggest a way to rectify this problem."}],"date_updated":"2021-01-12T08:11:39Z","year":"2017","extern":"1","day":"27","author":[{"last_name":"Shekhter","first_name":"Arkady","full_name":"Shekhter, Arkady"},{"orcid":"0000-0001-9760-3147","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","full_name":"Modic, Kimberly A"},{"full_name":"McDonald, R. D.","first_name":"R. D.","last_name":"McDonald"},{"full_name":"Ramshaw, B. J.","first_name":"B. J.","last_name":"Ramshaw"}],"article_number":"121106","_id":"7065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"APS","status":"public","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"title":"Thermodynamic constraints on the amplitude of quantum oscillations","month":"03","doi":"10.1103/physrevb.95.121106","publication_status":"published","publication":"Physical Review B","date_created":"2019-11-19T13:12:27Z","type":"journal_article","oa_version":"None","date_published":"2017-03-27T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","citation":{"short":"A. Shekhter, K.A. Modic, R.D. McDonald, B.J. Ramshaw, Physical Review B 95 (2017).","ama":"Shekhter A, Modic KA, McDonald RD, Ramshaw BJ. Thermodynamic constraints on the amplitude of quantum oscillations. <i>Physical Review B</i>. 2017;95(12). doi:<a href=\"https://doi.org/10.1103/physrevb.95.121106\">10.1103/physrevb.95.121106</a>","ieee":"A. Shekhter, K. A. Modic, R. D. McDonald, and B. J. Ramshaw, “Thermodynamic constraints on the amplitude of quantum oscillations,” <i>Physical Review B</i>, vol. 95, no. 12. APS, 2017.","chicago":"Shekhter, Arkady, Kimberly A Modic, R. D. McDonald, and B. J. Ramshaw. “Thermodynamic Constraints on the Amplitude of Quantum Oscillations.” <i>Physical Review B</i>. APS, 2017. <a href=\"https://doi.org/10.1103/physrevb.95.121106\">https://doi.org/10.1103/physrevb.95.121106</a>.","ista":"Shekhter A, Modic KA, McDonald RD, Ramshaw BJ. 2017. Thermodynamic constraints on the amplitude of quantum oscillations. Physical Review B. 95(12), 121106.","apa":"Shekhter, A., Modic, K. A., McDonald, R. D., &#38; Ramshaw, B. J. (2017). Thermodynamic constraints on the amplitude of quantum oscillations. <i>Physical Review B</i>. APS. <a href=\"https://doi.org/10.1103/physrevb.95.121106\">https://doi.org/10.1103/physrevb.95.121106</a>","mla":"Shekhter, Arkady, et al. “Thermodynamic Constraints on the Amplitude of Quantum Oscillations.” <i>Physical Review B</i>, vol. 95, no. 12, 121106, APS, 2017, doi:<a href=\"https://doi.org/10.1103/physrevb.95.121106\">10.1103/physrevb.95.121106</a>."},"intvolume":"        95","volume":95,"quality_controlled":"1"}]