[{"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000459890700008"],"pmid":["30778205"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41596-018-0117-3","month":"03","department":[{"_id":"JoDa"},{"_id":"Bio"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"year":"2019","volume":14,"date_created":"2019-02-24T22:59:20Z","date_updated":"2023-08-24T14:48:33Z","author":[{"last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G"}],"ec_funded":1,"file_date_updated":"2021-06-29T14:41:46Z","page":"832–863","article_type":"original","citation":{"apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3","chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3."},"publication":"Nature Protocols","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 14","title":"A practical guide to optimization in X10 expansion microscopy","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6052","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":84478958,"creator":"kschuh","relation":"main_file","file_id":"9619","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","success":1,"date_updated":"2021-06-29T14:41:46Z","date_created":"2021-06-29T14:41:46Z"}],"type":"journal_article","issue":"3","abstract":[{"text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.","lang":"eng"}]},{"month":"02","quality_controlled":"1","isi":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000458025300001"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.7554/eLife.42093","article_number":"e42093","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"publisher":"eLife Sciences Publications","year":"2019","date_updated":"2023-08-24T14:46:01Z","date_created":"2019-02-17T22:59:22Z","volume":8,"author":[{"full_name":"Capek, Daniel","last_name":"Capek","first_name":"Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Smutny, Michael","first_name":"Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090"},{"full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy","first_name":"Alexandra Madelaine"},{"last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","full_name":"Morri, Maurizio"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"eLife","citation":{"ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093","ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol. 8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093."},"date_published":"2019-02-06T00:00:00Z","type":"journal_article","abstract":[{"text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.","lang":"eng"}],"ddc":["570"],"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","status":"public","intvolume":" 8","_id":"6025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6041","checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","date_created":"2019-02-18T15:17:21Z","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","file_name":"2019_elife_Capek.pdf","file_size":5500707,"content_type":"application/pdf","creator":"dernst"}]},{"_id":"6022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Genetic dissection of assortative mating behavior","intvolume":" 17","oa_version":"Published Version","file":[{"file_name":"2019_PLOS_Merrill.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2005949,"file_id":"6036","relation":"main_file","date_created":"2019-02-18T14:57:24Z","date_updated":"2020-07-14T12:47:17Z","checksum":"5f34001617ee729314ca520c049b1112"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation."}],"issue":"2","publication":"PLoS Biology","citation":{"ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902."},"date_published":"2019-02-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","author":[{"last_name":"Merrill","first_name":"Richard M.","full_name":"Merrill, Richard M."},{"full_name":"Rastas, Pasi","last_name":"Rastas","first_name":"Pasi"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"last_name":"Davey","first_name":"John","full_name":"Davey, John"},{"full_name":"Mcmillan, W. Owen","last_name":"Mcmillan","first_name":"W. Owen"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9801"}]},"date_updated":"2023-08-24T14:46:23Z","date_created":"2019-02-17T22:59:21Z","volume":17,"article_number":"e2005902","file_date_updated":"2020-07-14T12:47:17Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"external_id":{"isi":["000460317100001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pbio.2005902","language":[{"iso":"eng"}],"month":"02"},{"scopus_import":"1","day":"08","article_processing_charge":"No","publication":"Nature Plants","citation":{"ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","ieee":"S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6.","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166."},"page":"160-166","date_published":"2019-02-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"issue":"2","_id":"6023","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","intvolume":" 5","oa_version":"Submitted Version","month":"02","external_id":{"isi":["000460479600014"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1038/s41477-019-0363-6","language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"author":[{"full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Der Schuren","first_name":"Alja","full_name":"Van Der Schuren, Alja"},{"first_name":"Maritza","last_name":"Van Dop","full_name":"Van Dop, Maritza"},{"full_name":"Van Galen, Luc","first_name":"Luc","last_name":"Van Galen"},{"full_name":"Saiga, Shunsuke","first_name":"Shunsuke","last_name":"Saiga"},{"last_name":"Adibi","first_name":"Milad","full_name":"Adibi, Milad"},{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"full_name":"Ten Hove, Colette A.","first_name":"Colette A.","last_name":"Ten Hove"},{"full_name":"Marhavy, Peter","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"date_updated":"2023-08-24T14:46:47Z","date_created":"2019-02-17T22:59:21Z","volume":5},{"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://authors.library.caltech.edu/92123/","open_access":"1"}],"oa":1,"external_id":{"isi":["000463195700014"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41565-019-0377-2","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"month":"04","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","volume":14,"date_updated":"2023-08-24T14:48:08Z","date_created":"2019-02-24T22:59:21Z","author":[{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"full_name":"Mirhosseini, Mohammad","last_name":"Mirhosseini","first_name":"Mohammad"},{"full_name":"Dieterle, Paul B.","last_name":"Dieterle","first_name":"Paul B."},{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"}],"page":"334–339","article_type":"original","citation":{"ama":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2","ieee":"M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.","apa":"Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2","ista":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339.","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","mla":"Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2.","chicago":"Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2."},"publication":"Nature Nanotechnology","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 14","status":"public","title":"Quantum electromechanics of a hypersonic crystal","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6053","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information."}]},{"abstract":[{"lang":"eng","text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. "}],"type":"journal_article","oa_version":"Preprint","intvolume":" 147","status":"public","title":"Two circles and only a straightedge","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6050","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-01-01T00:00:00Z","page":"91-102","citation":{"ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","apa":"Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.","mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240.","short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240."},"publication":"Proceedings of the American Mathematical Society","volume":147,"date_updated":"2023-08-24T14:48:59Z","date_created":"2019-02-24T22:59:19Z","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"full_name":"Fedorov, Roman","first_name":"Roman","last_name":"Fedorov"}],"publisher":"AMS","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","month":"01","language":[{"iso":"eng"}],"doi":"10.1090/proc/14240","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1709.02562"],"isi":["000450363900008"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}]},{"date_published":"2019-03-01T00:00:00Z","publication":"Molecular Ecology","citation":{"ieee":"R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972."},"page":"1375-1393","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"relation":"main_file","file_id":"6097","date_created":"2019-03-11T16:12:54Z","date_updated":"2020-07-14T12:47:19Z","checksum":"f915885756057ec0ca5912a41f46a887","file_name":"2019_MolecularEcology_Faria.pdf","access_level":"open_access","file_size":1510715,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"6095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","ddc":["570"],"intvolume":" 28","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"issue":"6","type":"journal_article","doi":"10.1111/mec.14972","language":[{"iso":"eng"}],"external_id":{"isi":["000465219200013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9837"}]},"date_created":"2019-03-10T22:59:21Z","date_updated":"2023-08-24T14:50:27Z","volume":28,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:19Z"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","article_number":"045002","volume":52,"date_updated":"2023-08-24T14:49:23Z","date_created":"2019-02-24T22:59:19Z","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"}],"publisher":"IOP Publishing","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2019","month":"01","language":[{"iso":"eng"}],"doi":"10.1088/1751-8121/aaf2dd","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000455379500001"]},"issue":"4","abstract":[{"text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.","lang":"eng"}],"type":"journal_article","file":[{"file_size":1804557,"content_type":"application/pdf","creator":"kschuh","file_name":"2019_IOP_DeMartino.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-04-19T12:18:57Z","checksum":"1112304ad363a6d8afaeccece36473cf","relation":"main_file","file_id":"6344"}],"oa_version":"Published Version","intvolume":" 52","ddc":["570"],"status":"public","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6049","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"07","scopus_import":"1","date_published":"2019-01-07T00:00:00Z","citation":{"ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd","ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd."},"publication":"Journal of Physics A: Mathematical and Theoretical"},{"article_number":"e41563","file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","volume":8,"date_updated":"2023-08-24T14:50:50Z","date_created":"2019-03-10T22:59:20Z","author":[{"last_name":"Henderson","first_name":"Nathan T.","full_name":"Henderson, Nathan T."},{"full_name":"Le Marchand, Sylvain J.","last_name":"Le Marchand","first_name":"Sylvain J."},{"full_name":"Hruska, Martin","first_name":"Martin","last_name":"Hruska"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"last_name":"Dalva","first_name":"Matthew B.","full_name":"Dalva, Matthew B."}],"month":"02","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000459380600001"],"pmid":["30789343"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.41563","type":"journal_article","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"intvolume":" 8","ddc":["570"],"title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","status":"public","_id":"6091","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":7260753,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_eLife_Henderson.pdf","checksum":"7b0800d003f14cd06b1802dea0c52941","date_created":"2019-03-11T16:15:37Z","date_updated":"2020-07-14T12:47:19Z","relation":"main_file","file_id":"6098"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"21","citation":{"ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563","ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563","mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563."},"publication":"eLife","date_published":"2019-02-21T00:00:00Z"},{"month":"02","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.15252/msb.20188470","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000459628300003"],"pmid":["30765425"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425"}],"article_number":"e8470","volume":15,"date_created":"2019-02-24T22:59:18Z","date_updated":"2023-08-24T14:49:53Z","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"publisher":"Embo Press","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2019-02-14T00:00:00Z","citation":{"short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470."},"publication":"Molecular systems biology","issue":"2","abstract":[{"lang":"eng","text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 15","status":"public","title":"Temporal order and precision of complex stress responses in individual bacteria","_id":"6046","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"eissn":["13652656"],"issn":["00218790"]},"month":"04","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000467994800007"]},"language":[{"iso":"eng"}],"doi":"10.1111/1365-2656.12953","ec_funded":1,"file_date_updated":"2020-07-14T12:47:19Z","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","year":"2019","volume":88,"date_updated":"2023-08-25T08:04:53Z","date_created":"2019-03-17T22:59:15Z","related_material":{"record":[{"id":"9806","relation":"research_data","status":"public"}]},"author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","first_name":"Megan","last_name":"Kutzer","full_name":"Kutzer, Megan"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"full_name":"Armitage, Sophie A.O.","first_name":"Sophie A.O.","last_name":"Armitage"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"566-578","article_type":"original","citation":{"ama":"Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance,” Journal of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Journal of Animal Ecology. 88(4), 566–578.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019) 566–578.","mla":"Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology, vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953."},"publication":"Journal of Animal Ecology","date_published":"2019-04-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":" Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.\r\n Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.\r\n We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.\r\n"}],"intvolume":" 88","ddc":["570"],"status":"public","title":"A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","_id":"6105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6107","relation":"main_file","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T07:43:06Z","checksum":"405cde15120de26018b3bd0dfa29986c","file_name":"2019_JournalAnimalEcology_Kutzer.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1460662}],"oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"No","day":"07","page":"1379-1392.e14","article_type":"original","citation":{"ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019","ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","apa":"Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019."},"publication":"Cell","date_published":"2019-03-07T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.","lang":"eng"}],"intvolume":" 176","status":"public","title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","_id":"6087","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"03","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.01.019","open_access":"1"}],"external_id":{"isi":["000460509600013"],"pmid":["30773315"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"doi":"10.1016/j.cell.2019.01.019","ec_funded":1,"department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","volume":176,"date_updated":"2023-08-25T08:02:23Z","date_created":"2019-03-10T22:59:19Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"first_name":"Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756","full_name":"Xia, Peng"},{"id":"381929CE-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}]},{"article_processing_charge":"No","day":"05","month":"02","doi":"10.5061/dryad.9kj41f0","date_published":"2019-02-05T00:00:00Z","citation":{"ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.","mla":"Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}],"abstract":[{"text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-08-25T08:04:52Z","date_created":"2021-08-06T12:06:40Z","related_material":{"record":[{"id":"6105","status":"public","relation":"used_in_publication"}]},"author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","first_name":"Megan","last_name":"Kutzer","full_name":"Kutzer, Megan"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"last_name":"Armitage","first_name":"Sophie A.O.","full_name":"Armitage, Sophie A.O."}],"publisher":"Dryad","department":[{"_id":"SyCr"}],"title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","status":"public","_id":"9806","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019"},{"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1601.06118"],"isi":["000459725600012"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.06118"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1017/etds.2017.52","month":"04","publisher":"Cambridge University Press","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2019","volume":39,"date_updated":"2023-08-25T08:03:30Z","date_created":"2019-03-10T22:59:18Z","author":[{"first_name":"Christian","last_name":"Sadel","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8255-3968","full_name":"Sadel, Christian"},{"full_name":"Xu, Disheng","last_name":"Xu","first_name":"Disheng"}],"ec_funded":1,"page":"1082-1098","citation":{"ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098.","apa":"Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2017.52","ieee":"C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019.","ama":"Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098. doi:10.1017/etds.2017.52","chicago":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52.","mla":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52.","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098."},"publication":"Ergodic Theory and Dynamical Systems","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 39","status":"public","title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6086","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part."}]},{"date_published":"2019-03-06T00:00:00Z","citation":{"apa":"Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., & Rotenberg, N. (2019). A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. Springer Nature. https://doi.org/10.1038/s41377-019-0124-3","ieee":"B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial mapping of nanophotonic light fields,” Light: Science and Applications, vol. 8, no. 1. Springer Nature, 2019.","ista":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.","ama":"Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping of nanophotonic light fields. Light: Science and Applications. 2019;8(1). doi:10.1038/s41377-019-0124-3","chicago":"Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications. Springer Nature, 2019. https://doi.org/10.1038/s41377-019-0124-3.","short":"B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science and Applications 8 (2019).","mla":"Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and Applications, vol. 8, no. 1, 28, Springer Nature, 2019, doi:10.1038/s41377-019-0124-3."},"publication":"Light: Science and Applications","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6108","checksum":"d71e528cff9c56f70ccc29dd7005257f","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-18T08:08:22Z","access_level":"open_access","file_name":"2019_Light_LeFeber.pdf","content_type":"application/pdf","file_size":1119947,"creator":"dernst"}],"intvolume":" 8","status":"public","ddc":["530"],"title":"A full vectorial mapping of nanophotonic light fields","_id":"6102","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"lang":"eng","text":"Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41377-019-0124-3","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1803.10145"],"isi":["000460470700004"]},"publication_identifier":{"eissn":["20477538"],"issn":["20955545"]},"month":"03","volume":8,"date_created":"2019-03-17T22:59:13Z","date_updated":"2023-08-25T08:06:10Z","author":[{"first_name":"B.","last_name":"Le Feber","full_name":"Le Feber, B."},{"full_name":"Sipe, J. E.","first_name":"J. E.","last_name":"Sipe"},{"full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuipers, L.","last_name":"Kuipers","first_name":"L."},{"last_name":"Rotenberg","first_name":"N.","full_name":"Rotenberg, N."}],"department":[{"_id":"JoFi"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:19Z","article_number":"28"},{"date_published":"2019-03-19T00:00:00Z","page":"5344-5349","citation":{"ama":"Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116","apa":"Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1813255116","ieee":"P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning in biphasic biological tissues,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12. National Academy of Sciences, pp. 5344–5349, 2019.","ista":"Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning in biphasic biological tissues. Proceedings of the National Academy of Sciences of the United States of America. 116(12), 5344–5349.","short":"P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 5344–5349.","mla":"Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49, doi:10.1073/pnas.1813255116.","chicago":"Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1813255116."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","file":[{"file_id":"6193","relation":"main_file","date_updated":"2020-07-14T12:47:23Z","date_created":"2019-04-03T14:10:30Z","checksum":"8b67eee0ea8e5db61583e4d485215258","file_name":"2019_PNAS_Recho.pdf","access_level":"open_access","creator":"dernst","file_size":3456045,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 116","ddc":["570"],"status":"public","title":"Theory of mechanochemical patterning in biphasic biological tissues","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6191","issue":"12","abstract":[{"text":"The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1813255116","project":[{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30819884"],"isi":["000461679000027"]},"oa":1,"publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"03","volume":116,"date_updated":"2023-08-25T08:57:30Z","date_created":"2019-03-31T21:59:13Z","related_material":{"link":[{"relation":"supplementary_material","url":"www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental"}]},"author":[{"last_name":"Recho","first_name":"Pierre","full_name":"Recho, Pierre"},{"last_name":"Hallou","first_name":"Adrien","full_name":"Hallou, Adrien"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"department":[{"_id":"EdHa"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:23Z"},{"author":[{"first_name":"Marko","last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko"},{"first_name":"Darya","last_name":"Protsyuk","full_name":"Protsyuk, Darya"},{"full_name":"Becker, Paul F.","first_name":"Paul F.","last_name":"Becker"},{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"full_name":"Gorzelanny, Christian","first_name":"Christian","last_name":"Gorzelanny"},{"full_name":"Glaus Garzon, Jesus F.","first_name":"Jesus F.","last_name":"Glaus Garzon"},{"full_name":"Knopfova, Lucia","last_name":"Knopfova","first_name":"Lucia"},{"first_name":"Mathias","last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias"},{"first_name":"Bruno","last_name":"Luckow","full_name":"Luckow, Bruno"},{"last_name":"Schneider","first_name":"Stefan W.","full_name":"Schneider, Stefan W."},{"full_name":"Borsig, Lubor","first_name":"Lubor","last_name":"Borsig"}],"volume":17,"date_updated":"2023-08-25T08:57:01Z","date_created":"2019-03-31T21:59:12Z","pmid":1,"year":"2019","publisher":"AACR","department":[{"_id":"DaSi"}],"publication_status":"published","publication_identifier":{"eissn":["15573125"],"issn":["15417786"]},"month":"03","doi":"10.1158/1541-7786.MCR-18-0530","language":[{"iso":"eng"}],"external_id":{"isi":["000460099800012"],"pmid":["30552233"]},"main_file_link":[{"url":"https://doi.org/10.1158/1541-7786.MCR-18-0530","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","issue":"3","abstract":[{"text":"Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"6190","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 17","title":"CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","citation":{"chicago":"Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research. AACR, 2019. https://doi.org/10.1158/1541-7786.MCR-18-0530.","short":"M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular Cancer Research 17 (2019) 783–793.","mla":"Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research, vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:10.1158/1541-7786.MCR-18-0530.","ieee":"M. Roblek et al., “CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis,” Molecular Cancer Research, vol. 17, no. 3. AACR, pp. 783–793, 2019.","apa":"Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530","ista":"Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 17(3), 783–793.","ama":"Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530"},"publication":"Molecular Cancer Research","page":"783-793","article_type":"original"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6230","title":"Why structure matters","status":"public","ddc":["570"],"intvolume":" 8","file":[{"file_size":298466,"content_type":"application/pdf","creator":"dernst","file_name":"2019_eLife_Barton.pdf","access_level":"open_access","date_created":"2019-04-11T11:43:38Z","date_updated":"2020-07-14T12:47:24Z","checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","file_id":"6293"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"publication":"eLife","citation":{"ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380."},"date_published":"2019-03-21T00:00:00Z","scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"No","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"},{"full_name":"Nordborg, Magnus","last_name":"Nordborg","first_name":"Magnus"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2019-04-07T21:59:15Z","date_updated":"2023-08-25T08:59:38Z","volume":8,"article_number":"e45380","file_date_updated":"2020-07-14T12:47:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000461988300001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.45380","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2050084X"]}},{"language":[{"iso":"eng"}],"doi":"10.1214/18-AOP1272","isi":1,"quality_controlled":"1","external_id":{"isi":["000459681900005"],"arxiv":["1705.05364"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05364"}],"month":"03","publication_identifier":{"issn":["00911798"]},"date_updated":"2023-08-25T08:59:11Z","date_created":"2019-04-07T21:59:15Z","volume":47,"author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"}],"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"year":"2019","date_published":"2019-03-01T00:00:00Z","page":"804-834","publication":"Annals of Probability","citation":{"short":"M. Gerencser, Annals of Probability 47 (2019) 804–834.","mla":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272.","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability. 2019;47(2):804-834. doi:10.1214/18-AOP1272","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272","ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Boundary regularity of stochastic PDEs","status":"public","intvolume":" 47","_id":"6232","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.","lang":"eng"}],"issue":"2","type":"journal_article"},{"intvolume":" 98","title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","ddc":["580"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6262","oa_version":"Published Version","file":[{"file_name":"2019_PlantJournal_Rakusov.pdf","access_level":"open_access","file_size":1383100,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6304","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-15T09:38:43Z","checksum":"ad3b5e270b67ba2a45f894ce3be27920"}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development."}],"page":"1048-1059","article_type":"original","citation":{"mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301","ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059.","apa":"Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019."},"publication":"The Plant Journal","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2019","volume":98,"date_updated":"2023-08-25T10:11:03Z","date_created":"2019-04-09T08:46:44Z","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Valošek","full_name":"Valošek, Petr"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:25Z","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30821050"],"isi":["000473644100008"]},"language":[{"iso":"eng"}],"doi":"10.1111/tpj.14301","publication_identifier":{"eissn":["1365-313x"],"issn":["0960-7412"]},"month":"06"},{"abstract":[{"text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","file_size":4444339,"content_type":"application/pdf","file_name":"2018_MatrixBiology_Davies.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:27Z","date_created":"2020-05-14T09:02:07Z","checksum":"790878cd78bfc54a147ddcc7c8f286a0","file_id":"7825","relation":"main_file"}],"oa_version":"Submitted Version","_id":"6297","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2019-05-01T00:00:00Z","citation":{"ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002","ieee":"H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier, 2019. https://doi.org/10.1016/j.matbio.2018.12.002.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59."},"publication":"Matrix Biology","page":"47-59","article_type":"original","file_date_updated":"2020-07-14T12:47:27Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S.","full_name":"Baranova, Natalia S."},{"full_name":"El Amri, Nouha","last_name":"El Amri","first_name":"Nouha"},{"last_name":"Coche-Guérente","first_name":"Liliane","full_name":"Coche-Guérente, Liliane"},{"full_name":"Verdier, Claude","first_name":"Claude","last_name":"Verdier"},{"first_name":"Lionel","last_name":"Bureau","full_name":"Bureau, Lionel"},{"last_name":"Richter","first_name":"Ralf P.","full_name":"Richter, Ralf P."},{"full_name":"Débarre, Delphine","last_name":"Débarre","first_name":"Delphine"}],"volume":"78-79","date_created":"2019-04-11T20:55:01Z","date_updated":"2023-08-25T10:11:28Z","year":"2019","publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"published","publication_identifier":{"issn":["0945-053X"]},"month":"05","doi":"10.1016/j.matbio.2018.12.002","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000468707600005"]},"isi":1,"quality_controlled":"1"},{"page":"920-940","publication":"Advances in Mathematics","citation":{"short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.","mla":"Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp. 920–40, doi:10.1016/j.aim.2019.04.031.","chicago":"Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.","ama":"Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031","apa":"Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.","ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940."},"date_published":"2019-06-20T00:00:00Z","scopus_import":"1","day":"20","has_accepted_license":"1","article_processing_charge":"No","title":"Counting rational points on biquadratic hypersurfaces","status":"public","ddc":["512"],"intvolume":" 349","_id":"6310","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"file_size":379158,"content_type":"application/pdf","creator":"tbrownin","file_name":"wliqun.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-16T09:12:20Z","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","relation":"main_file","file_id":"6311"}],"type":"journal_article","abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method."}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000468857300025"],"arxiv":["1810.08426"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2019.04.031","month":"06","publication_identifier":{"eissn":["10902082"],"issn":["00018708"]},"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Elsevier","year":"2019","date_updated":"2023-08-25T10:11:55Z","date_created":"2019-04-16T09:13:25Z","volume":349,"author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"full_name":"Hu, L.Q.","first_name":"L.Q.","last_name":"Hu"}],"file_date_updated":"2020-07-14T12:47:27Z"},{"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"05","oa":1,"external_id":{"pmid":["30787134"],"isi":["000466860800010"]},"main_file_link":[{"url":"https://doi.org/10.1104/pp.18.01305","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1104/pp.18.01305","language":[{"iso":"eng"}],"pmid":1,"year":"2019","publisher":"ASPB","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"first_name":"Y","last_name":"Wang","full_name":"Wang, Y"},{"full_name":"Gong, Z","last_name":"Gong","first_name":"Z"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"}],"volume":180,"date_updated":"2023-08-25T10:10:23Z","date_created":"2019-04-09T08:46:17Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp. 22–25, 2019.","apa":"Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305","ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305","chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25."},"publication":"Plant Physiology","page":"22-25","article_type":"letter_note","date_published":"2019-05-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Nitrate regulation of root stem cell activity is auxin-dependent."}],"_id":"6261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 180","status":"public","title":"Nitrate modulates the differentiation of root distal stem cells","oa_version":"Published Version"},{"publication":"Molecular Biology Reports","citation":{"ieee":"A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019.","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z."},"date_published":"2019-04-12T00:00:00Z","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"status":"public","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","_id":"6352","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1948014,"content_type":"application/pdf","file_name":"2019_MolecularBioReport_Temnov.pdf","access_level":"open_access","date_created":"2019-04-30T09:52:36Z","date_updated":"2020-07-14T12:47:28Z","checksum":"45bf040bbce1cea274f6013fa18ba21b","file_id":"6362","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure.","lang":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000470332600049"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11033-019-04765-z","month":"04","publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","year":"2019","date_created":"2019-04-28T21:59:14Z","date_updated":"2023-08-25T10:14:26Z","author":[{"first_name":"Andrey Alexandrovich","last_name":"Temnov","full_name":"Temnov, Andrey Alexandrovich"},{"full_name":"Rogov, Konstantin Arkadevich","last_name":"Rogov","first_name":"Konstantin Arkadevich"},{"last_name":"Sklifas","first_name":"Alla Nikolaevna","full_name":"Sklifas, Alla Nikolaevna"},{"last_name":"Klychnikova","first_name":"Elena Valerievna","full_name":"Klychnikova, Elena Valerievna"},{"full_name":"Hartl, Markus","first_name":"Markus","last_name":"Hartl"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"},{"full_name":"Charnagalov, Alexej","first_name":"Alexej","last_name":"Charnagalov","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:28Z"},{"_id":"6348","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Resonant electro-optic frequency comb","status":"public","intvolume":" 568","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"issue":"7752","publication":"Nature","citation":{"ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x."},"page":"378-381","date_published":"2019-04-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"author":[{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"date_created":"2019-04-28T21:59:13Z","date_updated":"2023-08-25T10:15:25Z","volume":568,"main_file_link":[{"url":"https://arxiv.org/abs/1808.10608","open_access":"1"}],"oa":1,"external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-019-1110-x","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]}},{"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Elsevier","author":[{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","last_name":"Stella","full_name":"Stella, Federico"},{"full_name":"Baracskay, Peter","first_name":"Peter","last_name":"Baracskay","id":"361CC00E-F248-11E8-B48F-1D18A9856A87"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/"}]},"date_updated":"2023-08-25T10:13:07Z","date_created":"2019-04-17T08:28:59Z","volume":102,"ec_funded":1,"oa":1,"external_id":{"pmid":["30819547"],"isi":["000465169700017"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511"},{"name":"Interneuro Plasticity During Spatial Learning","call_identifier":"FWF","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.neuron.2019.01.052","language":[{"iso":"eng"}],"month":"04","_id":"6338","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","intvolume":" 102","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning."}],"publication":"Neuron","citation":{"chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.","mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.","apa":"Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019.","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.","ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052"},"article_type":"original","page":"450-461","date_published":"2019-04-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al."}],"intvolume":" 29","title":"State space geometry of the chaotic pilot-wave hydrodynamics","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5878","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"22","article_type":"original","citation":{"ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.","apa":"Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279","ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019)."},"publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_published":"2019-01-22T00:00:00Z","article_number":"013122","publisher":"AIP Publishing","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":29,"date_updated":"2023-08-25T10:16:11Z","date_created":"2019-01-23T08:35:09Z","related_material":{"link":[{"url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157","relation":"erratum"}]},"author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fleury, Marc","first_name":"Marc","last_name":"Fleury"}],"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"month":"01","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1812.09011"],"isi":["000457409100028"]},"main_file_link":[{"url":"https://arxiv.org/abs/1812.09011","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.5058279"},{"date_updated":"2023-08-25T10:19:23Z","date_created":"2019-05-13T08:13:46Z","author":[{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"first_name":"Alexandre","last_name":"Donzé","full_name":"Donzé, Alexandre"},{"first_name":"Hisahiro","last_name":"Ito","full_name":"Ito, Hisahiro"},{"full_name":"Kapinski, James","last_name":"Kapinski","first_name":"James"}],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","year":"2019","file_date_updated":"2020-10-08T17:25:45Z","language":[{"iso":"eng"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control","location":"Montreal, Canada","start_date":"2019-04-16","end_date":"2019-04-18"},"doi":"10.1145/3302504.3311800","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"oa":1,"external_id":{"isi":["000516713900007"]},"month":"04","publication_identifier":{"isbn":["9781450362825"]},"file":[{"creator":"dernst","content_type":"application/pdf","file_size":1055421,"file_name":"2019_ACM_Ferrere.pdf","access_level":"open_access","date_updated":"2020-10-08T17:25:45Z","date_created":"2020-10-08T17:25:45Z","success":1,"checksum":"b8e967081e051d1c55ca5d18fb187890","file_id":"8633","relation":"main_file"}],"oa_version":"Submitted Version","status":"public","ddc":["000"],"title":"Interface-aware signal temporal logic","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6428","abstract":[{"lang":"eng","text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system."}],"type":"conference","date_published":"2019-04-16T00:00:00Z","page":"57-66","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","citation":{"short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66."},"day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000475740600104"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3306346.3323002","month":"07","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","year":"2019","volume":38,"date_updated":"2023-08-25T10:18:46Z","date_created":"2019-05-14T07:04:06Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/"}]},"author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck"},{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"article_number":"130","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","citation":{"ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002."},"publication":"ACM Transactions on Graphics","date_published":"2019-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 38","ddc":["000","005"],"status":"public","title":"Fundamental solutions for water wave animation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6442","oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Schreck.pdf","access_level":"open_access","file_size":44328918,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6443","date_created":"2019-05-14T07:03:55Z","date_updated":"2020-07-14T12:47:30Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673"}],"type":"journal_article","issue":"4","abstract":[{"text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.","lang":"eng"}]},{"date_created":"2019-05-13T07:58:35Z","date_updated":"2023-08-25T10:19:55Z","volume":117,"author":[{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"last_name":"Plana","first_name":"Carlos","full_name":"Plana, Carlos"},{"full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"year":"2019","language":[{"iso":"eng"}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"oa":1,"external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"month":"08","publication_identifier":{"issn":["03019322"]},"oa_version":"Preprint","status":"public","title":"Phase-field simulation of core-annular pipe flow","intvolume":" 117","_id":"6413","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"type":"journal_article","date_published":"2019-08-01T00:00:00Z","article_type":"original","page":"14-24","publication":"International Journal of Multiphase Flow","citation":{"ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"eissn":["15537404"]},"month":"04","doi":"10.1371/journal.pgen.1008079","language":[{"iso":"eng"}],"external_id":{"isi":["000466866000029"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","article_number":"e1008079","related_material":{"record":[{"relation":"research_data","status":"public","id":"9789"},{"id":"9790","relation":"research_data","status":"public"},{"id":"9797","relation":"research_data","status":"public"}]},"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"last_name":"Espinar","first_name":"Lorena","full_name":"Espinar, Lorena"},{"last_name":"Sarkisyan","first_name":"Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"first_name":"Natalya S.","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S."},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"},{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"last_name":"Filion","first_name":"Guillaume J.","full_name":"Filion, Guillaume J."},{"last_name":"Carey","first_name":"Lucas B.","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"}],"volume":15,"date_created":"2019-05-13T07:58:38Z","date_updated":"2023-08-25T10:30:37Z","year":"2019","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2019-04-10T00:00:00Z","citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079."},"publication":"PLoS Genetics","issue":"4","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"type":"journal_article","file":[{"creator":"dernst","file_size":3726017,"content_type":"application/pdf","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","access_level":"open_access","date_created":"2019-05-14T08:26:08Z","date_updated":"2020-07-14T12:47:30Z","checksum":"cf3889c8a8a16053dacf9c3776cbe217","file_id":"6445","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6419","intvolume":" 15","ddc":["570"],"status":"public","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape"},{"oa_version":"Published Version","file":[{"date_created":"2019-05-14T08:45:51Z","date_updated":"2020-07-14T12:47:29Z","checksum":"6550a328335396c856db4cbdda7d2994","file_id":"6448","relation":"main_file","creator":"dernst","file_size":1223647,"content_type":"application/pdf","file_name":"2019_NatureComm_Moussa.pdf","access_level":"open_access"}],"status":"public","ddc":["570"],"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","intvolume":" 10","_id":"6412","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2019-04-29T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6"},"day":"29","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-08-25T10:31:56Z","date_created":"2019-05-13T07:58:35Z","volume":10,"author":[{"full_name":"Moussa, Hagar F.","first_name":"Hagar F.","last_name":"Moussa"},{"full_name":"Bsteh, Daniel","last_name":"Bsteh","first_name":"Daniel"},{"last_name":"Yelagandula","first_name":"Ramesh","full_name":"Yelagandula, Ramesh"},{"full_name":"Pribitzer, Carina","first_name":"Carina","last_name":"Pribitzer"},{"last_name":"Stecher","first_name":"Karin","full_name":"Stecher, Karin"},{"first_name":"Katarina","last_name":"Bartalska","id":"4D883232-F248-11E8-B48F-1D18A9856A87","full_name":"Bartalska, Katarina"},{"full_name":"Michetti, Luca","first_name":"Luca","last_name":"Michetti"},{"last_name":"Wang","first_name":"Jingkui","full_name":"Wang, Jingkui"},{"full_name":"Zepeda-Martinez, Jorge A.","last_name":"Zepeda-Martinez","first_name":"Jorge A."},{"last_name":"Elling","first_name":"Ulrich","full_name":"Elling, Ulrich"},{"full_name":"Stuckey, Jacob I.","first_name":"Jacob I.","last_name":"Stuckey"},{"full_name":"James, Lindsey I.","last_name":"James","first_name":"Lindsey I."},{"full_name":"Frye, Stephen V.","first_name":"Stephen V.","last_name":"Frye"},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","year":"2019","file_date_updated":"2020-07-14T12:47:29Z","article_number":"1931","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-09628-6","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000466118700002"]},"month":"04","publication_identifier":{"eissn":["20411723"]}},{"conference":{"location":"New York, NY, United States","start_date":"2019-07-13","end_date":"2019-07-18","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-030-25540-4_36","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491468000036"]},"quality_controlled":"1","isi":1,"project":[{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"month":"07","publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"author":[{"last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Bettina","last_name":"Konighofer","full_name":"Konighofer, Bettina"},{"full_name":"Pranger, Stefan","last_name":"Pranger","first_name":"Stefan"}],"date_updated":"2023-08-25T10:33:27Z","date_created":"2019-05-16T11:22:30Z","volume":11561,"year":"2019","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:31Z","date_published":"2019-07-12T00:00:00Z","publication":"31st International Conference on Computer-Aided Verification","citation":{"apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36","chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36."},"page":"630-649","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2019_CAV_Avni.pdf","file_size":659766,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6816","checksum":"c231579f2485c6fd4df17c9443a4d80b","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-08-14T09:35:24Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6462","ddc":["000"],"title":"Run-time optimization for learned controllers through quantitative games","status":"public","intvolume":" 11561","abstract":[{"text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"article_number":"021001","file_date_updated":"2020-07-14T12:47:31Z","year":"2019","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","author":[{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"full_name":"Altman, Ehud","last_name":"Altman","first_name":"Ehud"},{"last_name":"Bloch","first_name":"Immanuel","full_name":"Bloch, Immanuel"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"volume":91,"date_created":"2019-05-23T07:38:43Z","date_updated":"2023-08-25T10:37:56Z","publication_identifier":{"issn":["1539-0756"],"eissn":["0034-6861"]},"month":"05","oa":1,"external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"isi":1,"quality_controlled":"1","doi":"10.1103/revmodphys.91.021001","language":[{"iso":"eng"}],"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6477","intvolume":" 91","status":"public","title":"Colloquium: Many-body localization, thermalization, and entanglement","ddc":["530"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"RevModPhys.91.021001.pdf","creator":"mserbyn","file_size":1695677,"content_type":"application/pdf","file_id":"6478","relation":"main_file","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","date_created":"2019-05-23T07:39:05Z","date_updated":"2020-07-14T12:47:31Z"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"22","citation":{"ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.","apa":"Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001","ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001."},"publication":"Reviews of Modern Physics","article_type":"original","date_published":"2019-05-22T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6466","title":"Breaking down barriers in morning glories","status":"public","ddc":["580","576"],"intvolume":" 28","file":[{"file_size":367711,"content_type":"application/pdf","creator":"dernst","file_name":"2019_MolecularEcology_Field.pdf","access_level":"open_access","date_created":"2019-05-20T11:49:06Z","date_updated":"2020-07-14T12:47:31Z","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","relation":"main_file","file_id":"6472"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"issue":"7","publication":"Molecular ecology","citation":{"ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048."},"page":"1579-1581","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","author":[{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"date_updated":"2023-08-25T10:37:30Z","date_created":"2019-05-19T21:59:15Z","volume":28,"file_date_updated":"2020-07-14T12:47:31Z","external_id":{"isi":["000474808300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/mec.15048","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1365294X"]}},{"article_number":"2013","file_date_updated":"2020-07-14T12:47:31Z","year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaGu"}],"author":[{"first_name":"Hélène","last_name":"Chassin","full_name":"Chassin, Hélène"},{"full_name":"Müller, Marius","first_name":"Marius","last_name":"Müller"},{"full_name":"Tigges, Marcel","first_name":"Marcel","last_name":"Tigges"},{"full_name":"Scheller, Leo","last_name":"Scheller","first_name":"Leo"},{"first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Fussenegger, Martin","last_name":"Fussenegger","first_name":"Martin"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-023-36111-0","relation":"erratum"}]},"date_created":"2019-05-19T21:59:14Z","date_updated":"2023-08-25T10:33:51Z","volume":10,"month":"05","publication_identifier":{"eissn":["20411723"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000466338600006"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-019-09974-5","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.","lang":"eng"}],"issue":"1","_id":"6465","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"A modular degron library for synthetic circuits in mammalian cells","status":"public","intvolume":" 10","file":[{"access_level":"open_access","file_name":"2019_NatureComm_Chassin.pdf","creator":"dernst","file_size":1191827,"content_type":"application/pdf","file_id":"6471","relation":"main_file","checksum":"e214d3e4f8c81e35981583c4569b51b8","date_created":"2019-05-20T07:33:54Z","date_updated":"2020-07-14T12:47:31Z"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"chicago":"Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5.","short":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019).","mla":"Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5.","ieee":"H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","apa":"Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5","ista":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013.","ama":"Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5"},"date_published":"2019-05-01T00:00:00Z"},{"ec_funded":1,"article_number":"0881","author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9798"},{"id":"9799","relation":"research_data","status":"public"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}]},"date_created":"2019-05-19T21:59:15Z","date_updated":"2023-08-25T10:34:41Z","volume":15,"year":"2019","pmid":1,"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"month":"04","publication_identifier":{"eissn":["1744957X"],"issn":["17449561"]},"doi":"10.1098/rsbl.2018.0881","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"issue":"4","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6467","title":"The distribution of epistasis on simple fitness landscapes","status":"public","intvolume":" 15","day":"03","article_processing_charge":"No","scopus_import":"1","date_published":"2019-04-03T00:00:00Z","publication":"Biology Letters","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881"},"article_type":"original"},{"type":"journal_article","abstract":[{"text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ","lang":"eng"}],"issue":"11","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","status":"public","intvolume":" 597","_id":"6470","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"2925–2947","publication":"Journal of Physiology","citation":{"ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947."},"date_published":"2019-06-01T00:00:00Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"GaNo"}],"year":"2019","pmid":1,"date_updated":"2023-08-25T10:34:15Z","date_created":"2019-05-19T21:59:17Z","volume":597,"author":[{"last_name":"Éltes","first_name":"Tímea","full_name":"Éltes, Tímea"},{"last_name":"Szoboszlay","first_name":"Miklos","full_name":"Szoboszlay, Miklos"},{"full_name":"Szigeti, Margit Katalin","first_name":"Margit Katalin","last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9500-8758"},{"full_name":"Nusser, Zoltan","last_name":"Nusser","first_name":"Zoltan"}],"month":"06","publication_identifier":{"issn":["00223751"],"eissn":["14697793"]},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1113/JP277681"},{"publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"month":"07","doi":"10.1007/978-3-030-25540-4_16","conference":{"name":"CAV: Computer-Aided Verification","end_date":"2019-07-18","start_date":"2019-07-15","location":"New York City, NY, USA"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000491468000016"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:32Z","author":[{"full_name":"Garcia Soto, Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","first_name":"Miriam","last_name":"Garcia Soto"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"},{"last_name":"Zeleznik","first_name":"Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","full_name":"Zeleznik, Luka"}],"volume":11561,"date_updated":"2023-08-25T10:40:41Z","date_created":"2019-05-27T07:09:53Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","keyword":["Synthesis","Linear hybrid automaton","Membership"],"date_published":"2019-07-12T00:00:00Z","citation":{"short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.","mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314."},"publication":"31st International Conference on Computer-Aided Verification","page":"297-314","abstract":[{"lang":"eng","text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements."}],"type":"conference","alternative_title":["LNCS"],"file":[{"creator":"dernst","file_size":674795,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_CAV_GarciaSoto.pdf","checksum":"1f1d61b83a151031745ef70a501da3d6","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-08-14T11:05:30Z","file_id":"6817","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6493","intvolume":" 11561","status":"public","title":"Membership-based synthesis of linear hybrid automata","ddc":["000"]},{"isi":1,"quality_controlled":"1","external_id":{"pmid":["31111487"],"isi":["000487184200024"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/nph.15932","month":"10","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"date_updated":"2023-08-28T08:40:13Z","date_created":"2019-05-28T14:33:26Z","volume":224,"author":[{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"first_name":"P","last_name":"He","full_name":"He, P"},{"full_name":"Ma, X","first_name":"X","last_name":"Ma"},{"full_name":"Yang, Z","first_name":"Z","last_name":"Yang"},{"last_name":"Pang","first_name":"C","full_name":"Pang, C"},{"full_name":"Yu, J","last_name":"Yu","first_name":"J"},{"full_name":"Wang, G","first_name":"G","last_name":"Wang"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"}],"file_date_updated":"2020-10-14T08:59:33Z","article_type":"original","page":"761-774","publication":"New Phytologist","citation":{"ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774."},"date_published":"2019-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","title":"Auxin-mediated statolith production for root gravitropism","status":"public","ddc":["580"],"intvolume":" 224","_id":"6504","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2019_NewPhytologist_Zhang_accepted.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1099061,"creator":"dernst","relation":"main_file","file_id":"8661","date_created":"2020-10-14T08:59:33Z","date_updated":"2020-10-14T08:59:33Z","checksum":"6488243334538f5c39099a701cbf76b9","success":1}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"issue":"2"},{"date_published":"2019-07-01T00:00:00Z","citation":{"ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y."},"publication":"Nature Microbiology","page":"1221–1230","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6506","intvolume":" 4","status":"public","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","issue":"7","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41564-019-0412-y","language":[{"iso":"eng"}],"external_id":{"isi":["000480348200017"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/340828v2"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2058-5276"]},"month":"07","author":[{"full_name":"Noda-García, Lianet","last_name":"Noda-García","first_name":"Lianet"},{"first_name":"Dan","last_name":"Davidi","full_name":"Davidi, Dan"},{"full_name":"Korenblum, Elisa","first_name":"Elisa","last_name":"Korenblum"},{"full_name":"Elazar, Assaf","first_name":"Assaf","last_name":"Elazar"},{"id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Putintseva","full_name":"Putintseva, Ekaterina"},{"full_name":"Aharoni, Asaph","last_name":"Aharoni","first_name":"Asaph"},{"first_name":"Dan S.","last_name":"Tawfik","full_name":"Tawfik, Dan S."}],"volume":4,"date_created":"2019-05-29T13:03:30Z","date_updated":"2023-08-28T08:39:47Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published"},{"publication_identifier":{"issn":["0304-3940"]},"month":"08","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"},{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000486094600037"],"pmid":["31158432"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neulet.2019.134310","article_number":"134310","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"SaSi"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","volume":707,"date_updated":"2023-08-28T09:30:57Z","date_created":"2019-06-05T13:16:24Z","author":[{"full_name":"Maes, Margaret E","last_name":"Maes","first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","first_name":"Gloria","full_name":"Colombo, Gloria"},{"last_name":"Schulz","first_name":"Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","full_name":"Schulz, Rouven"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","article_type":"original","citation":{"short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310."},"publication":"Neuroscience Letters","date_published":"2019-08-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies.","lang":"eng"}],"intvolume":" 707","ddc":["570"],"status":"public","title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6521","file":[{"file_size":1779287,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_Neuroscience_Maes.pdf","checksum":"553c9dbd39727fbed55ee991c51ca4d1","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-08T11:44:20Z","relation":"main_file","file_id":"6551"}],"oa_version":"Published Version"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-019-1212-5","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"month":"06","pmid":1,"year":"2019","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Jordi","last_name":"Guiu","full_name":"Guiu, Jordi"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Shiro","last_name":"Yui","full_name":"Yui, Shiro"},{"last_name":"Demharter","first_name":"Samuel","full_name":"Demharter, Samuel"},{"first_name":"Svetlana","last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana"},{"last_name":"Maimets","first_name":"Martti","full_name":"Maimets, Martti"},{"first_name":"Anne","last_name":"Jørgensen","full_name":"Jørgensen, Anne"},{"full_name":"Perlman, Signe","last_name":"Perlman","first_name":"Signe"},{"last_name":"Lundvall","first_name":"Lene","full_name":"Lundvall, Lene"},{"last_name":"Mamsen","first_name":"Linn Salto","full_name":"Mamsen, Linn Salto"},{"full_name":"Larsen, Agnete","first_name":"Agnete","last_name":"Larsen"},{"last_name":"Olesen","first_name":"Rasmus H.","full_name":"Olesen, Rasmus H."},{"full_name":"Andersen, Claus Yding","last_name":"Andersen","first_name":"Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","first_name":"Lea Langhoff","last_name":"Thuesen"},{"first_name":"Kristine Juul","last_name":"Hare","full_name":"Hare, Kristine Juul"},{"last_name":"Pers","first_name":"Tune H.","full_name":"Pers, Tune H."},{"last_name":"Khodosevich","first_name":"Konstantin","full_name":"Khodosevich, Konstantin"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"volume":570,"date_created":"2019-06-02T21:59:14Z","date_updated":"2023-08-28T09:30:23Z","citation":{"ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5."},"publication":"Nature","page":"107-111","article_type":"original","date_published":"2019-06-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6513","intvolume":" 570","status":"public","title":"Tracing the origin of adult intestinal stem cells","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property.","lang":"eng"}]},{"publication_identifier":{"issn":["00222836"],"eissn":["10898638"]},"month":"08","doi":"10.1016/j.jmb.2019.05.033","language":[{"iso":"eng"}],"external_id":{"isi":["000482872100002"]},"oa":1,"main_file_link":[{"url":"http://www.biorxiv.org/content/10.1101/583369v1","open_access":"1"}],"isi":1,"quality_controlled":"1","author":[{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine","last_name":"Tichy"},{"last_name":"Gerrard","first_name":"Elliot J.","full_name":"Gerrard, Elliot J."},{"last_name":"Legrand","first_name":"Julien M.D.","full_name":"Legrand, Julien M.D."},{"first_name":"Robin M.","last_name":"Hobbs","full_name":"Hobbs, Robin M."},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"volume":431,"date_created":"2019-06-16T21:59:14Z","date_updated":"2023-08-28T09:39:22Z","year":"2019","publisher":"Elsevier","department":[{"_id":"HaJa"}],"publication_status":"published","article_processing_charge":"No","day":"09","scopus_import":"1","date_published":"2019-08-09T00:00:00Z","citation":{"ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033."},"publication":"Journal of Molecular Biology","page":"3046-3055","article_type":"original","issue":"17","abstract":[{"lang":"eng","text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology."}],"type":"journal_article","oa_version":"Preprint","_id":"6564","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 431","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","status":"public"},{"scopus_import":"1","article_processing_charge":"No","day":"03","citation":{"short":"S. Cremer, Current Biology 29 (2019) R458–R463.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.","chicago":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035.","ama":"Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035","ieee":"S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","apa":"Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463."},"publication":"Current Biology","page":"R458-R463","article_type":"original","date_published":"2019-06-03T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). "}],"_id":"6552","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 29","status":"public","title":"Social immunity in insects","oa_version":"Published Version","publication_identifier":{"issn":["09609822"]},"month":"06","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2019.03.035","open_access":"1"}],"oa":1,"external_id":{"isi":["000470902000023"],"pmid":["31163158"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2019.03.035","language":[{"iso":"eng"}],"pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"volume":29,"date_created":"2019-06-09T21:59:10Z","date_updated":"2023-08-28T09:38:00Z"},{"abstract":[{"lang":"eng","text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N)."}],"issue":"3","type":"journal_article","oa_version":"Preprint","_id":"6511","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Local single ring theorem on optimal scale","status":"public","intvolume":" 47","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-01T00:00:00Z","publication":"Annals of Probability","citation":{"ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284.","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284."},"page":"1270-1334","ec_funded":1,"author":[{"full_name":"Bao, Zhigang","first_name":"Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","first_name":"Kevin","full_name":"Schnelli, Kevin"}],"date_created":"2019-06-02T21:59:13Z","date_updated":"2023-08-28T09:32:29Z","volume":47,"year":"2019","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"month":"05","publication_identifier":{"issn":["00911798"]},"doi":"10.1214/18-AOP1284","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000466616100003"],"arxiv":["1612.05920"]},"main_file_link":[{"url":"https://arxiv.org/abs/1612.05920","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}]},{"keyword":["colloidal nanoparticles","asymmetric nanoparticles","inorganic ligands","heterostructures","catalyst assisted growth","nanocomposites","thermoelectrics"],"scopus_import":"1","day":"25","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","article_type":"original","page":"6572-6580","publication":"ACS Nano","citation":{"chicago":"Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical Society, 2019. https://doi.org/10.1021/acsnano.9b00346.","short":"M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580.","mla":"Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano, vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346.","apa":"Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., … Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b00346","ieee":"M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks,” ACS Nano, vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019.","ista":"Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la, Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 13(6), 6572–6580.","ama":"Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346"},"date_published":"2019-06-25T00:00:00Z","type":"journal_article","abstract":[{"text":"Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K.","lang":"eng"}],"issue":"6","title":"Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks","status":"public","ddc":["540"],"intvolume":" 13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6566","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2019-07-16T14:17:09Z","relation":"main_file","file_id":"6644","file_size":8628690,"content_type":"application/pdf","creator":"dernst","file_name":"2019_ACSNano_Ibanez.pdf","access_level":"open_access"}],"month":"06","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000473248300043"],"pmid":["31185159"]},"language":[{"iso":"eng"}],"doi":"10.1021/acsnano.9b00346","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"year":"2019","pmid":1,"date_updated":"2023-08-28T12:20:53Z","date_created":"2019-06-18T13:54:34Z","volume":13,"author":[{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"first_name":"Oleksandr","last_name":"Dobrozhan","full_name":"Dobrozhan, Oleksandr"},{"last_name":"Nazarenko","first_name":"Olga","full_name":"Nazarenko, Olga"},{"full_name":"Mata, María de la","last_name":"Mata","first_name":"María de la"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."}]},{"file_date_updated":"2020-07-14T12:47:34Z","article_number":"9139","volume":9,"date_updated":"2023-08-28T12:26:51Z","date_created":"2019-07-07T21:59:19Z","author":[{"full_name":"Nguyen, Chi Huu","first_name":"Chi Huu","last_name":"Nguyen"},{"full_name":"Glüxam, Tobias","last_name":"Glüxam","first_name":"Tobias"},{"last_name":"Schlerka","first_name":"Angela","full_name":"Schlerka, Angela"},{"id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","first_name":"Katharina","full_name":"Bauer, Katharina"},{"full_name":"Grandits, Alexander M.","last_name":"Grandits","first_name":"Alexander M."},{"full_name":"Hackl, Hubert","last_name":"Hackl","first_name":"Hubert"},{"last_name":"Dovey","first_name":"Oliver","full_name":"Dovey, Oliver"},{"full_name":"Zöchbauer-Müller, Sabine","first_name":"Sabine","last_name":"Zöchbauer-Müller"},{"full_name":"Cooper, Jonathan L.","last_name":"Cooper","first_name":"Jonathan L."},{"last_name":"Vassiliou","first_name":"George S.","full_name":"Vassiliou, George S."},{"full_name":"Stoiber, Dagmar","last_name":"Stoiber","first_name":"Dagmar"},{"last_name":"Wieser","first_name":"Rotraud","full_name":"Wieser, Rotraud"},{"full_name":"Heller, Gerwin","first_name":"Gerwin","last_name":"Heller"}],"publisher":"Nature Publishing Group","department":[{"_id":"PreCl"}],"publication_status":"published","year":"2019","month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s41598-019-45579-0","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000472597400042"]},"oa":1,"issue":"1","abstract":[{"text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically.","lang":"eng"}],"type":"journal_article","file":[{"creator":"kschuh","file_size":2017352,"content_type":"application/pdf","access_level":"open_access","file_name":"nature_2019_Nguyen.pdf","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:15:28Z","file_id":"6623","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 9","title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","ddc":["576"],"status":"public","_id":"6607","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","date_published":"2019-06-24T00:00:00Z","citation":{"short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019).","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0.","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0","apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0","ieee":"C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139."},"publication":"Scientific Reports"},{"abstract":[{"lang":"eng","text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons."}],"type":"journal_article","oa_version":"Preprint","title":"Stationary entangled radiation from micromechanical motion","status":"public","intvolume":" 570","_id":"6609","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-27T00:00:00Z","page":"480-483","publication":"Nature","citation":{"chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” Nature. Nature Publishing Group, 2019. https://doi.org/10.1038/s41586-019-1320-2.","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” Nature, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:10.1038/s41586-019-1320-2.","short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483.","ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","ieee":"S. Barzanjeh et al., “Stationary entangled radiation from micromechanical motion,” Nature, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., & Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-019-1320-2","ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. Nature. 2019;570:480-483. doi:10.1038/s41586-019-1320-2"},"ec_funded":1,"date_created":"2019-07-07T21:59:20Z","date_updated":"2023-08-28T12:29:56Z","volume":570,"author":[{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"},{"last_name":"Peruzzo","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"},{"first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias"},{"full_name":"Lewis, Dylan","last_name":"Lewis","first_name":"Dylan"},{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoFi"}],"year":"2019","month":"06","acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1320-2","quality_controlled":"1","isi":1,"project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","call_identifier":"H2020","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.05865"}],"external_id":{"isi":["000472860000042"],"arxiv":["1809.05865"]},"oa":1},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","citation":{"chicago":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics. Springer, 2019. https://doi.org/10.1007/s00025-019-1061-4.","short":"Y. Shehu, Results in Mathematics 74 (2019).","mla":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” Results in Mathematics, vol. 74, no. 4, 138, Springer, 2019, doi:10.1007/s00025-019-1061-4.","ieee":"Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces,” Results in Mathematics, vol. 74, no. 4. Springer, 2019.","apa":"Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. Springer. https://doi.org/10.1007/s00025-019-1061-4","ista":"Shehu Y. 2019. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138.","ama":"Shehu Y. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 2019;74(4). doi:10.1007/s00025-019-1061-4"},"publication":"Results in Mathematics","article_type":"original","issue":"4","abstract":[{"text":"It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper.","lang":"eng"}],"type":"journal_article","file":[{"file_size":466942,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"Springer_2019_Shehu.pdf","checksum":"c6d18cb1e16fc0c36a0e0f30b4ebbc2d","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-03T15:20:40Z","relation":"main_file","file_id":"6605"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6596","intvolume":" 74","ddc":["000"],"title":"Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces","status":"public","publication_identifier":{"issn":["1422-6383"],"eissn":["1420-9012"]},"month":"12","doi":"10.1007/s00025-019-1061-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000473237500002"],"arxiv":["2101.09068"]},"oa":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","article_number":"138","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini"}],"volume":74,"date_created":"2019-06-29T10:11:30Z","date_updated":"2023-08-28T12:26:22Z","year":"2019","publisher":"Springer","department":[{"_id":"VlKo"}],"publication_status":"published"},{"oa_version":"Published Version","_id":"6601","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 178","title":"Mechanochemical feedback loops in development and disease","status":"public","issue":"1","abstract":[{"lang":"eng","text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease."}],"type":"journal_article","date_published":"2019-07-27T00:00:00Z","citation":{"ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052."},"publication":"Cell","page":"12-25","article_type":"review","article_processing_charge":"No","day":"27","scopus_import":"1","author":[{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"volume":178,"date_created":"2019-06-30T21:59:11Z","date_updated":"2023-08-28T12:25:21Z","pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publication_status":"published","ec_funded":1,"doi":"10.1016/j.cell.2019.05.052","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"oa":1,"external_id":{"isi":["000473002700005"],"pmid":["31251912"]},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00928674"]},"month":"07"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00205-019-01400-w","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1807.00834"],"isi":["000482386000006"]},"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"month":"11","volume":234,"date_created":"2019-07-07T21:59:23Z","date_updated":"2023-08-28T12:31:21Z","author":[{"first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"}],"publisher":"Springer","department":[{"_id":"JuFi"}],"publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:34Z","date_published":"2019-11-01T00:00:00Z","page":"635–726","article_type":"original","citation":{"short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726.","mla":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w.","chicago":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w.","ama":"Fischer JL. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 2019;234(2):635–726. doi:10.1007/s00205-019-01400-w","apa":"Fischer, J. L. (2019). The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w","ieee":"J. L. Fischer, “The choice of representative volumes in the approximation of effective properties of random materials,” Archive for Rational Mechanics and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019.","ista":"Fischer JL. 2019. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 234(2), 635–726."},"publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"Springer_2019_Fischer.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1377659,"creator":"kschuh","relation":"main_file","file_id":"6626","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:56:47Z","checksum":"4cff75fa6addb0770991ad9c474ab404"}],"intvolume":" 234","ddc":["500"],"title":"The choice of representative volumes in the approximation of effective properties of random materials","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6617","issue":"2","abstract":[{"text":"The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably.","lang":"eng"}],"type":"journal_article"},{"doi":"10.3390/biom9060222","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31181636"],"isi":["000475301500018"]},"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"isi":1,"quality_controlled":"1","month":"06","author":[{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"volume":9,"date_created":"2019-07-07T21:59:21Z","date_updated":"2023-08-28T12:30:24Z","pmid":1,"year":"2019","department":[{"_id":"JiFr"}],"publisher":"MDPI","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","article_number":"222","date_published":"2019-06-07T00:00:00Z","citation":{"ieee":"M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6. MDPI, 2019.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. MDPI. https://doi.org/10.3390/biom9060222","ista":"Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222.","ama":"Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules. MDPI, 2019. https://doi.org/10.3390/biom9060222.","short":"M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019).","mla":"Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019, doi:10.3390/biom9060222."},"publication":"Biomolecules","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"biomolecules-2019-Matous.pdf","access_level":"open_access","creator":"kschuh","file_size":1066773,"content_type":"application/pdf","file_id":"6625","relation":"main_file","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:46:32Z","checksum":"1ce1bd36038fe5381057a1bcc6760083"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6611","intvolume":" 9","title":"PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton","ddc":["580"],"status":"public","issue":"6","abstract":[{"text":"Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1007/s11425-018-9543-8","language":[{"iso":"eng"}],"external_id":{"isi":["000509102200001"],"arxiv":["1709.09476"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1709.09476","open_access":"1"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["16747283"]},"month":"12","author":[{"full_name":"De La Bretèche, Régis","first_name":"Régis","last_name":"De La Bretèche"},{"full_name":"Destagnol, Kevin N","last_name":"Destagnol","first_name":"Kevin N","id":"44DDECBC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Liu","first_name":"Jianya","full_name":"Liu, Jianya"},{"first_name":"Jie","last_name":"Wu","full_name":"Wu, Jie"},{"full_name":"Zhao, Yongqiang","last_name":"Zhao","first_name":"Yongqiang"}],"volume":62,"date_updated":"2023-08-28T12:32:20Z","date_created":"2019-07-07T21:59:25Z","year":"2019","publisher":"Springer","department":[{"_id":"TiBr"}],"publication_status":"published","date_published":"2019-12-01T00:00:00Z","citation":{"short":"R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China Mathematics 62 (2019) 2435–2446.","mla":"De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8.","chicago":"De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics. Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8.","ama":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8","apa":"De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019). On a certain non-split cubic surface. Science China Mathematics. Springer. https://doi.org/10.1007/s11425-018-9543-8","ieee":"R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer, pp. 2435–2446, 2019.","ista":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split cubic surface. Science China Mathematics. 62(12), 2435–2446."},"publication":"Science China Mathematics","page":"2435–2446","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"6620","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 62","title":"On a certain non-split cubic surface","status":"public","issue":"12","abstract":[{"lang":"eng","text":"This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures.\r\n"}],"type":"journal_article"},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","article_type":"original","page":"1356-1374","publication":"Evolution","citation":{"chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784"},"abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","file":[{"creator":"apreinsp","file_size":815416,"content_type":"application/pdf","file_name":"2019_Evolution_TrubenovaBarbora.pdf","access_level":"open_access","date_created":"2019-07-16T06:08:31Z","date_updated":"2020-07-14T12:47:34Z","checksum":"9831ca65def2d62498c7b08338b6d237","file_id":"6643","relation":"main_file"}],"status":"public","title":"Surfing on the seascape: Adaptation in a changing environment","ddc":["576"],"intvolume":" 73","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6637","month":"07","language":[{"iso":"eng"}],"doi":"10.1111/evo.13784","quality_controlled":"1","isi":1,"project":[{"grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000474031600001"]},"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"date_created":"2019-07-14T21:59:20Z","date_updated":"2023-08-29T06:31:14Z","volume":73,"author":[{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"},{"last_name":"Krejca","first_name":"Martin ","full_name":"Krejca, Martin "},{"last_name":"Lehre","first_name":"Per Kristian","full_name":"Lehre, Per Kristian"},{"full_name":"Kötzing, Timo","last_name":"Kötzing","first_name":"Timo"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","year":"2019"},{"page":"457-490","publication":"Topological Methods in Nonlinear Analysis","citation":{"chicago":"Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008.","short":"A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis 53 (2019) 457–490.","mla":"Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008.","apa":"Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008","ieee":"A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53, no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019.","ista":"Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490.","ama":"Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490. doi:10.12775/TMNA.2019.008"},"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Lower and upper bounds for the waists of different spaces","intvolume":" 53","_id":"6634","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure.","lang":"eng"}],"issue":"2","isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000472541600004"],"arxiv":["1612.06926"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.06926"}],"language":[{"iso":"eng"}],"doi":"10.12775/TMNA.2019.008","month":"06","publication_status":"published","publisher":"Akademicka Platforma Czasopism","department":[{"_id":"HeEd"}],"year":"2019","date_created":"2019-07-14T21:59:19Z","date_updated":"2023-08-29T06:32:48Z","volume":53,"author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"first_name":"Alfredo","last_name":"Hubard","full_name":"Hubard, Alfredo"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"ec_funded":1},{"author":[{"full_name":"Silva, André ","last_name":"Silva","first_name":"André "},{"full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","first_name":"Alan M","last_name":"Arroyo Guevara"},{"last_name":"Richter","first_name":"Bruce","full_name":"Richter, Bruce"},{"full_name":"Lee, Orlando","last_name":"Lee","first_name":"Orlando"}],"volume":342,"date_updated":"2023-08-29T06:31:41Z","date_created":"2019-07-14T21:59:20Z","year":"2019","department":[{"_id":"UlWa"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"doi":"10.1016/j.disc.2019.06.031","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1901.09955"],"isi":["000486358100025"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.09955"}],"project":[{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0012-365X"]},"month":"11","oa_version":"Preprint","_id":"6638","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 342","status":"public","title":"Graphs with at most one crossing","issue":"11","abstract":[{"lang":"eng","text":"The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one."}],"type":"journal_article","date_published":"2019-11-01T00:00:00Z","citation":{"chicago":"Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031.","short":"A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342 (2019) 3201–3207.","mla":"Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics, vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031.","ieee":"A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207, 2019.","apa":"Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031","ista":"Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one crossing. Discrete Mathematics. 342(11), 3201–3207.","ama":"Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing. Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031"},"publication":"Discrete Mathematics","page":"3201-3207","article_processing_charge":"No","day":"01","scopus_import":"1"},{"article_number":"111","ec_funded":1,"file_date_updated":"2020-07-14T12:47:36Z","year":"2019","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Sumin, Denis","last_name":"Sumin","first_name":"Denis"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"last_name":"Rittig","first_name":"Tobias","full_name":"Rittig, Tobias"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"first_name":"Thomas","last_name":"Nindel","full_name":"Nindel, Thomas"},{"first_name":"Alexander","last_name":"Wilkie","full_name":"Wilkie, Alexander"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"}],"volume":38,"date_updated":"2023-08-29T06:40:49Z","date_created":"2019-07-22T07:22:28Z","publication_identifier":{"issn":["0730-0301"]},"month":"07","oa":1,"external_id":{"isi":["000475740600085"]},"project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3306346.3322992","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers."}],"_id":"6660","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 38","title":"Geometry-aware scattering compensation for 3D printing","status":"public","ddc":["000"],"file":[{"creator":"dernst","file_size":10109800,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_ACM_Sumin_AuthorVersion.pdf","checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","date_updated":"2020-07-14T12:47:36Z","date_created":"2019-07-24T07:36:08Z","file_id":"6669","relation":"main_file"},{"access_level":"open_access","file_name":"sumin19geometry-aware-suppl.zip","creator":"dernst","content_type":"application/zip","file_size":11051245,"file_id":"6938","relation":"supplementary_material","checksum":"f80f365a04e35855fa467ea7ab26b16c","date_updated":"2020-07-14T12:47:36Z","date_created":"2019-10-11T06:51:07Z"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","citation":{"chicago":"Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992.","short":"D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).","mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992","ista":"Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111.","ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992"},"publication":"ACM Transactions on Graphics","date_published":"2019-07-04T00:00:00Z"},{"citation":{"chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118.","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019.","apa":"Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118"},"publication":"Genome Research","page":"1115-1122","date_published":"2019-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6658","intvolume":" 29","ddc":["576"],"title":"Haploid selection drives new gene male germline expression","status":"public","oa_version":"Published Version","file":[{"creator":"apreinsp","content_type":"application/pdf","file_size":2319022,"file_name":"2019_GenomeResearch_Raices.pdf","access_level":"open_access","date_created":"2019-07-24T08:05:56Z","date_updated":"2020-07-14T12:47:35Z","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","file_id":"6670","relation":"main_file"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. "}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000473730600007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1101/gr.238824.118","language":[{"iso":"eng"}],"month":"07","year":"2019","publisher":"CSH Press","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"full_name":"Raices, Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","last_name":"Raices","first_name":"Julia"},{"full_name":"Otto, Paulo","first_name":"Paulo","last_name":"Otto"},{"full_name":"Vibranovski, Maria","first_name":"Maria","last_name":"Vibranovski"}],"volume":29,"date_created":"2019-07-21T21:59:15Z","date_updated":"2023-08-29T06:35:05Z","file_date_updated":"2020-07-14T12:47:35Z","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","citation":{"short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","mla":"Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.","ama":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981","ieee":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981","ista":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110."},"publication":"ACM Transactions on Graphics","issue":"4","abstract":[{"text":"We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"b4562af94672b44d2a501046427412af","date_created":"2019-07-19T06:18:53Z","date_updated":"2020-07-14T12:47:35Z","file_id":"6651","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":74316182,"access_level":"open_access","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf"}],"oa_version":"Submitted Version","_id":"6650","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 38","title":"Volume-aware design of composite molds","status":"public","ddc":["000"],"publication_identifier":{"issn":["0730-0301"]},"month":"07","doi":"10.1145/3306346.3322981","language":[{"iso":"eng"}],"external_id":{"isi":["000475740600084"]},"oa":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:35Z","article_number":"110","related_material":{"link":[{"description":"YouTube Video","relation":"supplementary_material","url":"https://youtu.be/SO349S8-x_w"}]},"author":[{"last_name":"Alderighi","first_name":"Thomas","full_name":"Alderighi, Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"first_name":"Daniela","last_name":"Giorgi","full_name":"Giorgi, Daniela"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"volume":38,"date_updated":"2023-08-29T06:35:52Z","date_created":"2019-07-19T06:18:15Z","year":"2019","publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published"},{"article_number":"1171","file_date_updated":"2020-07-14T12:47:38Z","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Frontiers","year":"2019","date_created":"2019-07-28T21:59:18Z","date_updated":"2023-08-29T06:41:20Z","volume":10,"author":[{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","first_name":"Claudia"},{"last_name":"Abedon","first_name":"Stephen T.","full_name":"Abedon, Stephen T."}],"month":"06","isi":1,"quality_controlled":"1","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000470131200001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2019.01171","type":"journal_article","abstract":[{"text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple.","lang":"eng"}],"ddc":["570"],"title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","status":"public","intvolume":" 10","_id":"6717","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"apreinsp","file_size":246151,"content_type":"application/pdf","file_name":"2019_Frontiers_Igler.pdf","access_level":"open_access","date_created":"2019-07-29T07:51:54Z","date_updated":"2020-07-14T12:47:38Z","checksum":"317a06067e9a8e717bb55f23e0d77ba7","file_id":"6722","relation":"main_file"}],"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Frontiers in Microbiology","citation":{"chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171"},"date_published":"2019-06-03T00:00:00Z"},{"month":"09","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481300600001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.13812","file_date_updated":"2020-07-14T12:47:37Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2019","date_created":"2019-07-25T09:08:28Z","date_updated":"2023-08-29T06:43:58Z","volume":73,"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9802"}]},"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","page":"1729-1745","publication":"Evolution","citation":{"ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812."},"date_published":"2019-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"issue":"9","ddc":["576"],"status":"public","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","intvolume":" 73","_id":"6680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"772ce7035965153959b946a1033de1ca","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-09-17T10:56:27Z","relation":"main_file","file_id":"6881","content_type":"application/pdf","file_size":937573,"creator":"kschuh","access_level":"open_access","file_name":"2019_Evolution_Sachdeva.pdf"}],"oa_version":"Published Version"},{"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6710","intvolume":" 123","status":"public","title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"04","citation":{"mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","chicago":"Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183.","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183"},"publication":"Annals of botany","page":"1119-1131","article_type":"original","date_published":"2019-06-04T00:00:00Z","pmid":1,"year":"2019","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"last_name":"Cossard","first_name":"Guillaume","full_name":"Cossard, Guillaume"},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Pannell, John ","first_name":"John ","last_name":"Pannell"}],"volume":123,"date_created":"2019-07-28T21:59:15Z","date_updated":"2023-08-29T06:42:22Z","publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"month":"06","external_id":{"isi":["000493043500004"],"pmid":["30289430"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"isi":1,"quality_controlled":"1","doi":"10.1093/aob/mcy183","language":[{"iso":"eng"}]},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk."},"doi":"10.5061/dryad.0q2h6tk","date_published":"2019-06-06T00:00:00Z","article_processing_charge":"No","month":"06","day":"06","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","_id":"9804","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-08-29T06:41:51Z","date_created":"2021-08-06T11:52:54Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6713"}]},"author":[{"last_name":"Castro","first_name":"João Pl","full_name":"Castro, João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","first_name":"Stefanie","last_name":"Belohlavy"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","first_name":"Isabella","full_name":"Skuplik, Isabella"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}]},{"year":"2019","_id":"9802","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","related_material":{"record":[{"id":"6680","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"oa_version":"Published Version","date_updated":"2023-08-29T06:43:57Z","date_created":"2021-08-06T11:45:11Z","type":"research_data_reference","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"citation":{"short":"H. Sachdeva, (2019).","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8tp0900","open_access":"1"}],"oa":1,"doi":"10.5061/dryad.8tp0900","date_published":"2019-07-16T00:00:00Z","article_processing_charge":"No","day":"16","month":"07"},{"day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-07-17T00:00:00Z","publication":"Astronomy and Astrophysics","citation":{"ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 2019;627. doi:10.1051/0004-6361/201834916","ista":"Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.","ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019.","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834916","mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics, vol. 627, A163, EDP Sciences, 2019, doi:10.1051/0004-6361/201834916.","short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","chicago":"Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834916."},"article_type":"original","abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":14420451,"access_level":"open_access","file_name":"2019_AstronomyAstrophysics_Pranav.pdf","checksum":"83b9209ed9eefbdcefd89019c5a97805","date_updated":"2020-07-14T12:47:39Z","date_created":"2019-08-05T08:08:59Z","file_id":"6766","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6756","status":"public","ddc":["520","530"],"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","intvolume":" 627","month":"07","publication_identifier":{"issn":["00046361"],"eissn":["14320746"]},"doi":"10.1051/0004-6361/201834916","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1812.07678"],"isi":["000475839300003"]},"isi":1,"quality_controlled":"1","project":[{"_id":"265683E4-B435-11E9-9278-68D0E5697425","grant_number":"M62909-18-1-2038","name":"Toward Computational Information Topology"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"file_date_updated":"2020-07-14T12:47:39Z","article_number":"A163","author":[{"last_name":"Pranav","first_name":"Pratyush","full_name":"Pranav, Pratyush"},{"full_name":"Adler, Robert J.","first_name":"Robert J.","last_name":"Adler"},{"last_name":"Buchert","first_name":"Thomas","full_name":"Buchert, Thomas"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Bernard J.T.","last_name":"Jones","full_name":"Jones, Bernard J.T."},{"full_name":"Schwartzman, Armin","last_name":"Schwartzman","first_name":"Armin"},{"last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"},{"full_name":"Van De Weygaert, Rien","first_name":"Rien","last_name":"Van De Weygaert"}],"date_created":"2019-08-04T21:59:18Z","date_updated":"2023-08-29T07:01:48Z","volume":627,"year":"2019","publication_status":"published","publisher":"EDP Sciences","department":[{"_id":"HeEd"}]},{"department":[{"_id":"BeVi"}],"publisher":"Oxford Academic Press","publication_status":"published","pmid":1,"year":"2019","volume":11,"date_updated":"2023-08-29T06:53:58Z","date_created":"2019-08-04T21:59:18Z","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard","full_name":"Picard, Marion A L"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"},{"last_name":"Roquis","first_name":"David","full_name":"Roquis, David"},{"full_name":"Bulla, Ingo","first_name":"Ingo","last_name":"Bulla"},{"first_name":"Ronaldo C.","last_name":"Augusto","full_name":"Augusto, Ronaldo C."},{"first_name":"Nathalie","last_name":"Arancibia","full_name":"Arancibia, Nathalie"},{"last_name":"Grunau","first_name":"Christoph","full_name":"Grunau, Christoph"},{"full_name":"Boissier, Jérôme","first_name":"Jérôme","last_name":"Boissier"},{"last_name":"Cosseau","first_name":"Céline","full_name":"Cosseau, Céline"}],"file_date_updated":"2020-07-14T12:47:39Z","isi":1,"quality_controlled":"1","external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"CampIT"}],"doi":"10.1093/gbe/evz133","publication_identifier":{"eissn":["1759-6653"]},"month":"07","intvolume":" 11","ddc":["570"],"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6755","file":[{"checksum":"f9e8f6863a406dcc5a36b2be001c138c","date_created":"2019-08-05T07:55:02Z","date_updated":"2020-07-14T12:47:39Z","file_id":"6765","relation":"main_file","creator":"dernst","file_size":580205,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_GenomeBiology_Picard.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.","lang":"eng"}],"page":"1909-1922","article_type":"original","citation":{"chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford Academic Press, 2019. https://doi.org/10.1093/gbe/evz133.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford Academic Press. https://doi.org/10.1093/gbe/evz133","ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133"},"publication":"Genome biology and evolution","date_published":"2019-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"month":"07","publication_identifier":{"eissn":["1557735X"],"issn":["00045411"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1705.01433","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1705.01433"],"isi":["000487714900008"]},"language":[{"iso":"eng"}],"doi":"10.1145/3340295","article_number":"31","publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2019","date_created":"2019-08-04T21:59:16Z","date_updated":"2023-08-29T07:02:13Z","volume":66,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"950"}]},"scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Journal of the ACM","citation":{"mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019."},"date_published":"2019-07-16T00:00:00Z","type":"journal_article","abstract":[{"text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players.","lang":"eng"}],"issue":"4","title":"Infinite-duration bidding games","status":"public","intvolume":" 66","_id":"6752","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"department":[{"_id":"MaLo"}],"publisher":"SPIE","publication_status":"published","year":"2019","volume":11076,"date_created":"2019-11-12T15:10:18Z","date_updated":"2023-08-29T06:54:38Z","author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","last_name":"Baranova","full_name":"Baranova, Natalia S."},{"full_name":"El Amri, Nouha","last_name":"El Amri","first_name":"Nouha"},{"full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente","first_name":"Liliane"},{"first_name":"Claude","last_name":"Verdier","full_name":"Verdier, Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"last_name":"Richter","first_name":"Ralf P.","full_name":"Richter, Ralf P."},{"last_name":"Débarre","first_name":"Delphine","full_name":"Débarre, Delphine"}],"article_number":"110760V","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf"}],"external_id":{"isi":["000535353000023"]},"language":[{"iso":"eng"}],"doi":"10.1117/12.2527058","conference":{"location":"Munich, Germany","start_date":"2019-06-26","end_date":"2019-06-27","name":"European Conferences on Biomedical Optics"},"publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"month":"07","intvolume":" 11076","status":"public","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7010","oa_version":"Published Version","type":"conference","abstract":[{"text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines.","lang":"eng"}],"citation":{"ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058","ieee":"H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019.","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058."},"publication":"Advances in Microscopic Imaging II","date_published":"2019-07-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22"},{"oa_version":"Published Version","file":[{"file_name":"2019_PlosComputBiology_Ruess.pdf","access_level":"open_access","file_size":2200003,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6803","date_created":"2019-08-12T12:27:26Z","date_updated":"2020-07-14T12:47:40Z","checksum":"7ded4721b41c2a0fc66a1c634540416a"}],"ddc":["570"],"status":"public","title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","intvolume":" 15","_id":"6784","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems."}],"issue":"7","type":"journal_article","date_published":"2019-07-02T00:00:00Z","article_type":"original","publication":"PLoS Computational Biology","citation":{"mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019."},"day":"02","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_created":"2019-08-11T21:59:19Z","date_updated":"2023-08-29T07:10:06Z","volume":15,"author":[{"orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob"},{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"9786","relation":"research_data","status":"public"}]},"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2019","file_date_updated":"2020-07-14T12:47:40Z","article_number":"e1007168","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007168","isi":1,"quality_controlled":"1","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level"},{"grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481577700032"]},"oa":1,"month":"07","publication_identifier":{"eissn":["1553-7358"]}},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-11471-8","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000478576500012"],"pmid":["31375675"]},"oa":1,"month":"08","publication_identifier":{"issn":["2041-1723"]},"date_created":"2019-08-09T08:46:26Z","date_updated":"2023-08-29T07:02:44Z","volume":10,"author":[{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xiao","first_name":"G","full_name":"Xiao, G"},{"last_name":"Wang","first_name":"X","full_name":"Wang, X"},{"last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"article_number":"3480","date_published":"2019-08-02T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8.","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8.","ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution of fast root gravitropism in seed plants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11471-8","ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8"},"day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:09:20Z","checksum":"d2c654fdb97f33078f606fe0c298bf6e","relation":"main_file","file_id":"6798","file_size":6406141,"content_type":"application/pdf","creator":"dernst","file_name":"2019_NatureComm_Zhang.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["580"],"title":"Evolution of fast root gravitropism in seed plants","intvolume":" 10","_id":"6778","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land."}],"type":"journal_article"},{"article_type":"original","page":"1447-1460","publication":"Molecular Ecology Resources","citation":{"ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 2019;19(6):1447-1460. doi:10.1111/1755-0998.13062","apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13062","ieee":"M. R. Yourick et al., “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019.","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460.","mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:10.1111/1755-0998.13062.","chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources. Wiley, 2019. https://doi.org/10.1111/1755-0998.13062."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","intvolume":" 19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6821","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined."}],"issue":"6","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727"}],"external_id":{"isi":["000480196800001"],"pmid":["31325910"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.13062","month":"11","publication_identifier":{"eissn":["1755-0998"]},"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Wiley","year":"2019","pmid":1,"date_updated":"2023-08-29T07:10:44Z","date_created":"2019-08-18T22:00:41Z","volume":19,"author":[{"full_name":"Yourick, Miranda R.","last_name":"Yourick","first_name":"Miranda R."},{"last_name":"Sandkam","first_name":"Benjamin A.","full_name":"Sandkam, Benjamin A."},{"orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","first_name":"William J","full_name":"Gammerdinger, William J"},{"full_name":"Escobar-Camacho, Daniel","last_name":"Escobar-Camacho","first_name":"Daniel"},{"full_name":"Nandamuri, Sri Pratima","last_name":"Nandamuri","first_name":"Sri Pratima"},{"full_name":"Clark, Frances E.","last_name":"Clark","first_name":"Frances E."},{"first_name":"Brendan","last_name":"Joyce","full_name":"Joyce, Brendan"},{"full_name":"Conte, Matthew A.","last_name":"Conte","first_name":"Matthew A."},{"last_name":"Kocher","first_name":"Thomas D.","full_name":"Kocher, Thomas D."},{"full_name":"Carleton, Karen L.","last_name":"Carleton","first_name":"Karen L."}]},{"abstract":[{"lang":"eng","text":"We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations."}],"issue":"10","type":"journal_article","file":[{"creator":"dernst","file_size":681139,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_AnnalesHenriPoincare_Leopold.pdf","checksum":"b6dbf0d837d809293d449adf77138904","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T12:05:58Z","file_id":"6801","relation":"main_file"}],"oa_version":"Published Version","ddc":["510"],"status":"public","title":"Mean-field dynamics for the Nelson model with fermions","intvolume":" 20","_id":"6788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"3471–3508","publication":"Annales Henri Poincare","citation":{"ieee":"N. K. Leopold and S. P. Petrat, “Mean-field dynamics for the Nelson model with fermions,” Annales Henri Poincare, vol. 20, no. 10. Springer Nature, pp. 3471–3508, 2019.","apa":"Leopold, N. K., & Petrat, S. P. (2019). Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-019-00828-w","ista":"Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 3471–3508.","ama":"Leopold NK, Petrat SP. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 2019;20(10):3471–3508. doi:10.1007/s00023-019-00828-w","chicago":"Leopold, Nikolai K, and Sören P Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare. Springer Nature, 2019. https://doi.org/10.1007/s00023-019-00828-w.","short":"N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508.","mla":"Leopold, Nikolai K., and Sören P. Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare, vol. 20, no. 10, Springer Nature, 2019, pp. 3471–3508, doi:10.1007/s00023-019-00828-w."},"file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"date_updated":"2023-08-29T07:09:06Z","date_created":"2019-08-11T21:59:21Z","volume":20,"author":[{"last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K"},{"full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","first_name":"Sören P"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"year":"2019","month":"10","publication_identifier":{"issn":["1424-0637"],"eissn":["1424-0661"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-019-00828-w","quality_controlled":"1","isi":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1807.06781"],"isi":["000487036900008"]}},{"publication_identifier":{"eissn":["20457758"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1002/ece3.5484","project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000479973400001"]},"oa":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:40Z","volume":9,"date_updated":"2023-08-29T07:03:10Z","date_created":"2019-08-11T21:59:24Z","author":[{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","page":"9597-9608","article_type":"original","citation":{"short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608."},"publication":"Ecology and Evolution","issue":"17","abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6799","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","checksum":"adcb70af4901977d95b8747eeee01bd7","file_name":"2019_EcologyEvolution_Trubenova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2839636,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 9","status":"public","ddc":["576"],"title":"Green beards in the light of indirect genetic effects","_id":"6795","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","article_type":"original","page":"765-775","publication":"Bulletin of the London Mathematical Society","citation":{"chicago":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society. London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276.","mla":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775.","ista":"Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.","apa":"Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12276","ieee":"A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019.","ama":"Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775. doi:10.1112/blms.12276"},"abstract":[{"text":"The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Preprint","title":"The Regge symmetry, confocal conics, and the Schläfli formula","status":"public","intvolume":" 51","_id":"6793","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","publication_identifier":{"issn":["00246093"],"eissn":["14692120"]},"language":[{"iso":"eng"}],"doi":"10.1112/blms.12276","isi":1,"quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"main_file_link":[{"url":"https://arxiv.org/abs/1903.04929","open_access":"1"}],"oa":1,"external_id":{"isi":["000478560200001"],"arxiv":["1903.04929"]},"ec_funded":1,"date_updated":"2023-08-29T07:08:34Z","date_created":"2019-08-11T21:59:23Z","volume":51,"author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Izmestiev, Ivan","first_name":"Ivan","last_name":"Izmestiev"}],"publication_status":"published","publisher":"London Mathematical Society","department":[{"_id":"HeEd"}],"year":"2019"},{"date_published":"2019-11-01T00:00:00Z","citation":{"ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120."},"publication":"New Phytologist","page":"1108-1120","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"apreinsp","content_type":"application/pdf","file_size":2314016,"file_name":"2019_NewPhytologist_Puixeu.pdf","access_level":"open_access","date_created":"2019-08-27T12:44:54Z","date_updated":"2020-07-14T12:47:42Z","checksum":"6370e7567d96b7b562e77d8b89653f80","file_id":"6833","relation":"main_file"}],"_id":"6831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 224","title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","ddc":["570"],"status":"public","issue":"3","abstract":[{"lang":"eng","text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle."}],"type":"journal_article","doi":"10.1111/nph.16050","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481376500001"]},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1469-8137"]},"month":"11","related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"status":"public","relation":"dissertation_contains","id":"14058"}]},"author":[{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"volume":224,"date_updated":"2023-08-29T07:17:07Z","date_created":"2019-08-25T22:00:51Z","year":"2019","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z"},{"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2019","date_updated":"2023-08-29T07:11:47Z","date_created":"2019-08-22T07:54:13Z","volume":538,"author":[{"id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam","last_name":"Brown","full_name":"Brown, Adam"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1805.04676"],"isi":["000487176300011"]},"main_file_link":[{"url":"https://arxiv.org/abs/1805.04676","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jalgebra.2019.07.027","month":"11","publication_identifier":{"issn":["0021-8693"]},"title":"Arakawa-Suzuki functors for Whittaker modules","status":"public","intvolume":" 538","_id":"6828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper we construct a family of exact functors from the category of Whittaker modules of the simple complex Lie algebra of type to the category of finite-dimensional modules of the graded affine Hecke algebra of type . Using results of Backelin [2] and of Arakawa-Suzuki [1], we prove that these functors map standard modules to standard modules (or zero) and simple modules to simple modules (or zero). Moreover, we show that each simple module of the graded affine Hecke algebra appears as the image of a simple Whittaker module. Since the Whittaker category contains the BGG category as a full subcategory, our results generalize results of Arakawa-Suzuki [1], which in turn generalize Schur-Weyl duality between finite-dimensional representations of and representations of the symmetric group ."}],"article_type":"original","page":"261-289","publication":"Journal of Algebra","citation":{"ista":"Brown A. 2019. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 538, 261–289.","ieee":"A. Brown, “Arakawa-Suzuki functors for Whittaker modules,” Journal of Algebra, vol. 538. Elsevier, pp. 261–289, 2019.","apa":"Brown, A. (2019). Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2019.07.027","ama":"Brown A. Arakawa-Suzuki functors for Whittaker modules. Journal of Algebra. 2019;538:261-289. doi:10.1016/j.jalgebra.2019.07.027","chicago":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra. Elsevier, 2019. https://doi.org/10.1016/j.jalgebra.2019.07.027.","mla":"Brown, Adam. “Arakawa-Suzuki Functors for Whittaker Modules.” Journal of Algebra, vol. 538, Elsevier, 2019, pp. 261–89, doi:10.1016/j.jalgebra.2019.07.027.","short":"A. Brown, Journal of Algebra 538 (2019) 261–289."},"date_published":"2019-11-15T00:00:00Z","day":"15","article_processing_charge":"No"},{"year":"2019","_id":"9803","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"status":"public","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14058"},{"status":"public","relation":"used_in_publication","id":"6831"}]},"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"full_name":"Field, David","first_name":"David","last_name":"Field"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"oa_version":"Published Version","date_updated":"2023-08-29T07:17:07Z","date_created":"2021-08-06T11:48:42Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n1701c9"}],"citation":{"short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9."},"date_published":"2019-07-22T00:00:00Z","doi":"10.5061/dryad.n1701c9","article_processing_charge":"No","month":"07","day":"22"},{"type":"journal_article","issue":"7770","abstract":[{"text":"Direct reciprocity is a powerful mechanism for the evolution of cooperation on the basis of repeated interactions1,2,3,4. It requires that interacting individuals are sufficiently equal, such that everyone faces similar consequences when they cooperate or defect. Yet inequality is ubiquitous among humans5,6 and is generally considered to undermine cooperation and welfare7,8,9,10. Most previous models of reciprocity do not include inequality11,12,13,14,15. These models assume that individuals are the same in all relevant aspects. Here we introduce a general framework to study direct reciprocity among unequal individuals. Our model allows for multiple sources of inequality. Subjects can differ in their endowments, their productivities and in how much they benefit from public goods. We find that extreme inequality prevents cooperation. But if subjects differ in productivity, some endowment inequality can be necessary for cooperation to prevail. Our mathematical predictions are supported by a behavioural experiment in which we vary the endowments and productivities of the subjects. We observe that overall welfare is maximized when the two sources of heterogeneity are aligned, such that more productive individuals receive higher endowments. By contrast, when endowments and productivities are misaligned, cooperation quickly breaks down. Our findings have implications for policy-makers concerned with equity, efficiency and the provisioning of public goods.","lang":"eng"}],"_id":"6836","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 572","ddc":["000"],"title":"Social dilemmas among unequals","status":"public","oa_version":"Submitted Version","file":[{"file_name":"2019_Nature_Hauser.pdf","access_level":"open_access","file_size":18577756,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7828","date_updated":"2020-07-14T12:47:42Z","date_created":"2020-05-14T10:00:32Z","checksum":"a6e0e3168bf62de624e7772cdfaeb26f"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"22","citation":{"ama":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. Social dilemmas among unequals. Nature. 2019;572(7770):524-527. doi:10.1038/s41586-019-1488-5","ista":"Hauser OP, Hilbe C, Chatterjee K, Nowak MA. 2019. Social dilemmas among unequals. Nature. 572(7770), 524–527.","apa":"Hauser, O. P., Hilbe, C., Chatterjee, K., & Nowak, M. A. (2019). Social dilemmas among unequals. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1488-5","ieee":"O. P. Hauser, C. Hilbe, K. Chatterjee, and M. A. Nowak, “Social dilemmas among unequals,” Nature, vol. 572, no. 7770. Springer Nature, pp. 524–527, 2019.","mla":"Hauser, Oliver P., et al. “Social Dilemmas among Unequals.” Nature, vol. 572, no. 7770, Springer Nature, 2019, pp. 524–27, doi:10.1038/s41586-019-1488-5.","short":"O.P. Hauser, C. Hilbe, K. Chatterjee, M.A. Nowak, Nature 572 (2019) 524–527.","chicago":"Hauser, Oliver P., Christian Hilbe, Krishnendu Chatterjee, and Martin A. Nowak. “Social Dilemmas among Unequals.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1488-5."},"publication":"Nature","page":"524-527","article_type":"letter_note","date_published":"2019-08-22T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","year":"2019","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/too-much-inequality-impedes-support-for-public-goods-according-to-research-published-in-nature/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"first_name":"Oliver P.","last_name":"Hauser","full_name":"Hauser, Oliver P."},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"volume":572,"date_updated":"2023-08-29T07:42:54Z","date_created":"2019-09-01T22:00:56Z","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"month":"08","oa":1,"external_id":{"isi":["000482219600045"]},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-019-1488-5","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results."}],"issue":"3","status":"public","title":"A mathematical insight into cell labelling experiments for clonal analysis","ddc":["570"],"intvolume":" 235","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6844","file":[{"checksum":"160f960844b204057f20896e0e1f8ee7","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-02T12:05:18Z","file_id":"6845","relation":"main_file","creator":"dernst","file_size":1192994,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_JournalAnatomy_Picco.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"686-696","publication":"Journal of Anatomy","citation":{"apa":"Picco, N., Hippenmeyer, S., Rodarte, J., Streicher, C., Molnár, Z., Maini, P. K., & Woolley, T. E. (2019). A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. Wiley. https://doi.org/10.1111/joa.13001","ieee":"N. Picco et al., “A mathematical insight into cell labelling experiments for clonal analysis,” Journal of Anatomy, vol. 235, no. 3. Wiley, pp. 686–696, 2019.","ista":"Picco N, Hippenmeyer S, Rodarte J, Streicher C, Molnár Z, Maini PK, Woolley TE. 2019. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 235(3), 686–696.","ama":"Picco N, Hippenmeyer S, Rodarte J, et al. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 2019;235(3):686-696. doi:10.1111/joa.13001","chicago":"Picco, Noemi, Simon Hippenmeyer, Julio Rodarte, Carmen Streicher, Zoltán Molnár, Philip K. Maini, and Thomas E. Woolley. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy. Wiley, 2019. https://doi.org/10.1111/joa.13001.","short":"N. Picco, S. Hippenmeyer, J. Rodarte, C. Streicher, Z. Molnár, P.K. Maini, T.E. Woolley, Journal of Anatomy 235 (2019) 686–696.","mla":"Picco, Noemi, et al. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” Journal of Anatomy, vol. 235, no. 3, Wiley, 2019, pp. 686–96, doi:10.1111/joa.13001."},"date_published":"2019-09-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Wiley","year":"2019","date_updated":"2023-08-29T07:19:39Z","date_created":"2019-09-02T11:57:28Z","volume":235,"author":[{"full_name":"Picco, Noemi","first_name":"Noemi","last_name":"Picco"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"full_name":"Rodarte, Julio","last_name":"Rodarte","first_name":"Julio","id":"3C70A038-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Molnár, Zoltán","first_name":"Zoltán","last_name":"Molnár"},{"full_name":"Maini, Philip K.","last_name":"Maini","first_name":"Philip K."},{"full_name":"Woolley, Thomas E.","first_name":"Thomas E.","last_name":"Woolley"}],"month":"09","publication_identifier":{"eissn":["1469-7580"],"issn":["0021-8782"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000482426800017"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/joa.13001"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance."}],"_id":"6855","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","ddc":["576"],"status":"public","oa_version":"Published Version","file":[{"date_created":"2019-09-09T07:22:12Z","date_updated":"2020-07-14T12:47:42Z","checksum":"23d3978cf4739a89ce2c3e779f9305ca","file_id":"6862","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":411491,"file_name":"2019_AnnualReview_Sella.pdf","access_level":"open_access"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"05","citation":{"short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493.","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.","chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.","apa":"Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316","ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493."},"publication":"Annual Review of Genomics and Human Genetics","page":"461-493","date_published":"2019-07-05T00:00:00Z","file_date_updated":"2020-07-14T12:47:42Z","pmid":1,"year":"2019","publisher":"Annual Reviews","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Sella, Guy","last_name":"Sella","first_name":"Guy"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":20,"date_created":"2019-09-07T14:28:29Z","date_updated":"2023-08-29T07:49:38Z","publication_identifier":{"issn":["1527-8204"],"eissn":["1545-293X"]},"month":"07","external_id":{"isi":["000485148400020"],"pmid":["31283361"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1146/annurev-genom-083115-022316","language":[{"iso":"eng"}]},{"scopus_import":"1","article_processing_charge":"No","day":"13","citation":{"chicago":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab190d.","mla":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063101, IOP Publishing, 2019, doi:10.1088/1742-5468/ab190d.","short":"K. Mysliwy, M. Napiórkowski, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","ista":"Mysliwy K, Napiórkowski M. 2019. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063101.","ieee":"K. Mysliwy and M. Napiórkowski, “Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.","apa":"Mysliwy, K., & Napiórkowski, M. (2019). Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab190d","ama":"Mysliwy K, Napiórkowski M. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab190d"},"publication":"Journal of Statistical Mechanics: Theory and Experiment","date_published":"2019-06-13T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We discuss thermodynamic properties of harmonically trapped\r\nimperfect quantum gases. The spatial inhomogeneity of these systems imposes\r\na redefinition of the mean-field interparticle potential energy as compared\r\nto the homogeneous case. In our approach, it takes the form a\r\n2N2 ωd, where\r\nN is the number of particles, ω—the harmonic trap frequency, d—system’s\r\ndimensionality, and a is a parameter characterizing the interparticle interaction.\r\nWe provide arguments that this model corresponds to the limiting case of\r\na long-ranged interparticle potential of vanishingly small amplitude. This\r\nconclusion is drawn from a computation similar to the well-known Kac scaling\r\nprocedure, which is presented here in a form adapted to the case of an isotropic\r\nharmonic trap. We show that within the model, the imperfect gas of trapped\r\nrepulsive bosons undergoes the Bose–Einstein condensation provided d > 1.\r\nThe main result of our analysis is that in d = 1 the gas of attractive imperfect\r\nfermions with a = −aF < 0 is thermodynamically equivalent to the gas of\r\nrepulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill\r\nthe relation aB + aF = \u001f. This result supplements similar recent conclusion\r\nabout thermodynamic equivalence of two-dimensional (2D) uniform imperfect\r\nrepulsive Bose and attractive Fermi gases."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6840","intvolume":" 2019","title":"Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps","status":"public","oa_version":"Preprint","publication_identifier":{"eissn":["1742-5468"]},"month":"06","oa":1,"external_id":{"arxiv":["1810.02209"],"isi":["000471650100001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1810.02209","open_access":"1"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1088/1742-5468/ab190d","language":[{"iso":"eng"}],"article_number":"063101","ec_funded":1,"year":"2019","publisher":"IOP Publishing","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Napiórkowski, Marek","last_name":"Napiórkowski","first_name":"Marek"}],"volume":2019,"date_updated":"2023-08-29T07:19:13Z","date_created":"2019-09-01T22:00:59Z"},{"date_published":"2019-12-15T00:00:00Z","citation":{"ista":"Gehér GP, Titkos T, Virosztek D. 2019. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 480(2), 123435.","apa":"Gehér, G. P., Titkos, T., & Virosztek, D. (2019). On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. Elsevier. https://doi.org/10.1016/j.jmaa.2019.123435","ieee":"G. P. Gehér, T. Titkos, and D. Virosztek, “On isometric embeddings of Wasserstein spaces – the discrete case,” Journal of Mathematical Analysis and Applications, vol. 480, no. 2. Elsevier, 2019.","ama":"Gehér GP, Titkos T, Virosztek D. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 2019;480(2). doi:10.1016/j.jmaa.2019.123435","chicago":"Gehér, György Pál, Tamás Titkos, and Daniel Virosztek. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis and Applications. Elsevier, 2019. https://doi.org/10.1016/j.jmaa.2019.123435.","mla":"Gehér, György Pál, et al. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis and Applications, vol. 480, no. 2, 123435, Elsevier, 2019, doi:10.1016/j.jmaa.2019.123435.","short":"G.P. Gehér, T. Titkos, D. Virosztek, Journal of Mathematical Analysis and Applications 480 (2019)."},"publication":"Journal of Mathematical Analysis and Applications","article_type":"original","article_processing_charge":"No","day":"15","scopus_import":"1","oa_version":"Preprint","_id":"6843","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 480","title":"On isometric embeddings of Wasserstein spaces – the discrete case","status":"public","issue":"2","abstract":[{"lang":"eng","text":"The aim of this short paper is to offer a complete characterization of all (not necessarily surjective) isometric embeddings of the Wasserstein space Wp(X), where S is a countable discrete metric space and 0
Bulletin Des Sciences Mathematiques. Elsevier. https://doi.org/10.1016/j.bulsci.2019.102794","ieee":"K. N. Destagnol and E. Sofos, “Rational points and prime values of polynomials in moderately many variables,” Bulletin des Sciences Mathematiques, vol. 156, no. 11. Elsevier, 2019.","ista":"Destagnol KN, Sofos E. 2019. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 156(11), 102794.","ama":"Destagnol KN, Sofos E. Rational points and prime values of polynomials in moderately many variables. Bulletin des Sciences Mathematiques. 2019;156(11). doi:10.1016/j.bulsci.2019.102794","chicago":"Destagnol, Kevin N, and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques. Elsevier, 2019. https://doi.org/10.1016/j.bulsci.2019.102794.","short":"K.N. Destagnol, E. Sofos, Bulletin Des Sciences Mathematiques 156 (2019).","mla":"Destagnol, Kevin N., and Efthymios Sofos. “Rational Points and Prime Values of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques, vol. 156, no. 11, 102794, Elsevier, 2019, doi:10.1016/j.bulsci.2019.102794."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"02","citation":{"ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-48930-7","ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","ieee":"M. Fenu et al., “A novel magnet-based scratch method for standardisation of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019.","apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7","mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:10.1038/s41598-019-48930-7.","short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7."},"publication":"Scientific Reports","date_published":"2019-09-02T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories.","lang":"eng"}],"_id":"6867","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","title":"A novel magnet-based scratch method for standardisation of wound-healing assays","ddc":["570"],"status":"public","file":[{"file_id":"6879","relation":"main_file","date_created":"2019-09-16T12:42:40Z","date_updated":"2020-07-14T12:47:42Z","checksum":"9cfd986d4108e288cc72276ef047ab0c","file_name":"2019_ScientificReports_Fenu.pdf","access_level":"open_access","creator":"dernst","file_size":3523795,"content_type":"application/pdf"}],"oa_version":"Published Version","publication_identifier":{"eissn":["20452322"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31477739"],"isi":["000483697800007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-019-48930-7","language":[{"iso":"eng"}],"article_number":"12625","file_date_updated":"2020-07-14T12:47:42Z","pmid":1,"year":"2019","department":[{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Fenu, M.","first_name":"M.","last_name":"Fenu"},{"full_name":"Bettermann, T.","first_name":"T.","last_name":"Bettermann"},{"last_name":"Vogl","first_name":"C.","full_name":"Vogl, C."},{"full_name":"Darwish-Miranda, Nasser","orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","last_name":"Darwish-Miranda","first_name":"Nasser"},{"first_name":"J.","last_name":"Schramel","full_name":"Schramel, J."},{"full_name":"Jenner, F.","last_name":"Jenner","first_name":"F."},{"first_name":"I.","last_name":"Ribitsch","full_name":"Ribitsch, I."}],"volume":9,"date_created":"2019-09-15T22:00:42Z","date_updated":"2023-08-29T07:55:15Z"},{"publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","volume":6,"date_updated":"2023-08-29T07:51:09Z","date_created":"2019-09-07T14:43:02Z","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-10-02T09:16:44Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"language":[{"iso":"eng"}],"doi":"10.1093/nsr/nwy113","publication_identifier":{"issn":["2095-5138"],"eissn":["2053-714X"]},"month":"03","intvolume":" 6","ddc":["570"],"status":"public","title":"Is speciation driven by cycles of mixing and isolation?","_id":"6858","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8595","checksum":"571d60fa21a568607d1fd04e119da88c","success":1,"date_created":"2020-10-02T09:16:44Z","date_updated":"2020-10-02T09:16:44Z","access_level":"open_access","file_name":"2019_NSR_Barton.pdf","file_size":106463,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","issue":"2","page":"291-292","article_type":"review","citation":{"chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113"},"publication":"National Science Review","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"article_type":"original","publication":"eLife","citation":{"chicago":"Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber, Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42766.","short":"N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger, M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019).","mla":"Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” ELife, vol. 8, e42766, eLife Sciences Publications, 2019, doi:10.7554/eLife.42766.","ieee":"N. Byczkowicz et al., “HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger, J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42766","ista":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 8, e42766.","ama":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 2019;8. doi:10.7554/eLife.42766"},"date_published":"2019-09-09T00:00:00Z","scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons","ddc":["570"],"intvolume":" 8","_id":"6868","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"c350b7861ef0fb537cae8a3232aec016","date_created":"2019-09-16T13:14:33Z","date_updated":"2020-07-14T12:47:42Z","relation":"main_file","file_id":"6880","file_size":4008137,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_eLife_Byczkowicz.pdf"}],"type":"journal_article","abstract":[{"text":"Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential\r\nand are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain.","lang":"eng"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485663900001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.42766","month":"09","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"eLife Sciences Publications","year":"2019","date_updated":"2023-08-30T06:17:06Z","date_created":"2019-09-15T22:00:43Z","volume":8,"author":[{"full_name":"Byczkowicz, Niklas","first_name":"Niklas","last_name":"Byczkowicz"},{"last_name":"Eshra","first_name":"Abdelmoneim","full_name":"Eshra, Abdelmoneim"},{"first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Trevisiol, Andrea","first_name":"Andrea","last_name":"Trevisiol"},{"first_name":"Johannes","last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes"},{"full_name":"Kole, Maarten Hp","last_name":"Kole","first_name":"Maarten Hp"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hallermann, Stefan","last_name":"Hallermann","first_name":"Stefan"}],"article_number":"e42766","file_date_updated":"2020-07-14T12:47:42Z"},{"date_published":"2019-09-12T00:00:00Z","article_type":"original","publication":"Development","citation":{"ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” Development, vol. 146, no. 17. The Company of Biologists, 2019.","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., & Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. The Company of Biologists. https://doi.org/10.1242/dev.175919","ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 2019;146(17). doi:10.1242/dev.175919","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.175919.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:10.1242/dev.175919."},"day":"12","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","status":"public","intvolume":" 146","_id":"6897","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins.","lang":"eng"}],"issue":"17","type":"journal_article","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1242/dev.175919","quality_controlled":"1","isi":1,"project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"external_id":{"pmid":["31391194"],"isi":["000486297400011"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.175919"}],"oa":1,"month":"09","publication_identifier":{"eissn":["14779129"]},"date_created":"2019-09-22T22:00:36Z","date_updated":"2023-08-30T06:19:04Z","volume":146,"author":[{"full_name":"Zhu, Qiang","last_name":"Zhu","first_name":"Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marçal","last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","full_name":"Gallemi, Marçal"},{"first_name":"Jiří","last_name":"Pospíšil","full_name":"Pospíšil, Jiří"},{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"The Company of Biologists","year":"2019","acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","pmid":1,"ec_funded":1,"article_number":"dev175919"},{"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","_id":"9731","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","oa_version":"Published Version","date_created":"2021-07-27T14:09:11Z","date_updated":"2023-08-30T06:20:21Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"author":[{"full_name":"Sigalova, Olga","first_name":"Olga","last_name":"Sigalova"},{"first_name":"Andrei","last_name":"Chaplin","full_name":"Chaplin, Andrei"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Shelyakin, Pavel","first_name":"Pavel","last_name":"Shelyakin"},{"full_name":"Filaretov, Vsevolod","last_name":"Filaretov","first_name":"Vsevolod"},{"full_name":"Akkuratov, Evgeny","last_name":"Akkuratov","first_name":"Evgeny"},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"type":"research_data_reference","abstract":[{"text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"citation":{"mla":"Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1","ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1.","ieee":"O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1"},"oa":1,"doi":"10.6084/m9.figshare.9808772.v1","date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","month":"09","day":"12"},{"oa_version":"Published Version","date_created":"2021-08-06T07:59:56Z","date_updated":"2023-08-30T06:20:21Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","_id":"9783","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","abstract":[{"lang":"eng","text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)"}],"type":"research_data_reference","doi":"10.6084/m9.figshare.9808760.v1","date_published":"2019-09-12T00:00:00Z","oa":1,"citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1","ieee":"O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.","mla":"Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808760.v1"}],"article_processing_charge":"No","month":"09","day":"12"},{"doi":"10.6084/m9.figshare.9808850.v1","date_published":"2019-09-12T00:00:00Z","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808850.v1","ieee":"O. M. 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(CSV 24 kb)","lang":"eng"}],"type":"research_data_reference"},{"date_published":"2019-09-11T00:00:00Z","page":"4113","publication":"Nature communications","citation":{"chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:10.1038/s41467-019-12068-x.","ieee":"D. Bornhorst et al., “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x","ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113.","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x"},"day":"11","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_name":"2019_Nature_Bornhorst.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":3905793,"file_id":"6926","relation":"main_file","date_created":"2019-10-01T11:18:50Z","date_updated":"2020-07-14T12:47:44Z","checksum":"62c2512712e16d27c1797d318d14ba9f"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6899","abstract":[{"lang":"eng","text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-12068-x","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"month":"09","publication_identifier":{"eissn":["20411723"]},"date_created":"2019-09-22T22:00:37Z","date_updated":"2023-08-30T06:21:23Z","volume":10,"author":[{"first_name":"Dorothee","last_name":"Bornhorst","full_name":"Bornhorst, Dorothee"},{"full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng"},{"full_name":"Nakajima, Hiroyuki","first_name":"Hiroyuki","last_name":"Nakajima"},{"first_name":"Chaitanya","last_name":"Dingare","full_name":"Dingare, Chaitanya"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"last_name":"Lecaudey","first_name":"Virginie","full_name":"Lecaudey, Virginie"},{"first_name":"Naoki","last_name":"Mochizuki","full_name":"Mochizuki, Naoki"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yelon, Deborah","first_name":"Deborah","last_name":"Yelon"},{"full_name":"Abdelilah-Seyfried, Salim","first_name":"Salim","last_name":"Abdelilah-Seyfried"}],"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:44Z"},{"title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","ddc":["570"],"status":"public","intvolume":" 20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6898","oa_version":"Published Version","file":[{"file_size":4157175,"content_type":"application/pdf","creator":"kschuh","file_name":"2019_BioMed_Sigalova.pdf","access_level":"open_access","date_created":"2019-10-01T10:33:17Z","date_updated":"2020-07-14T12:47:44Z","checksum":"b798773c5823012d31c812c9f7975da2","relation":"main_file","file_id":"6924"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity."}],"issue":"1","publication":"BMC Genomics","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central, 2019. https://doi.org/10.1186/s12864-019-6059-5.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics, vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.","ieee":"O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” BMC Genomics, vol. 20, no. 1. BioMed Central, 2019.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5"},"date_published":"2019-09-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"FyKo"}],"year":"2019","date_created":"2019-09-22T22:00:36Z","date_updated":"2023-08-30T06:20:22Z","volume":20,"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9731"},{"status":"public","relation":"research_data","id":"9783"},{"id":"9890","relation":"research_data","status":"public"},{"id":"9892","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9893"},{"id":"9894","relation":"research_data","status":"public"},{"id":"9895","relation":"research_data","status":"public"},{"id":"9896","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9897"},{"status":"public","relation":"research_data","id":"9898"},{"id":"9899","status":"public","relation":"research_data"},{"id":"9900","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9901"}]},"article_number":"710","file_date_updated":"2020-07-14T12:47:44Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000485256100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s12864-019-6059-5","month":"09","publication_identifier":{"eissn":["14712164"]}},{"citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.","mla":"Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1","ieee":"O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808859.v1","open_access":"1"}],"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808859.v1","day":"12","month":"09","article_processing_charge":"No","_id":"9898","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-12T08:10:23Z","date_updated":"2023-08-30T06:20:22Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)"}]}]