[{"oa_version":"Published Version","intvolume":" 11076","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7010","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"}],"type":"conference","date_published":"2019-07-22T00:00:00Z","citation":{"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.","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."},"publication":"Advances in Microscopic Imaging II","article_processing_charge":"No","day":"22","scopus_import":"1","volume":11076,"date_updated":"2023-08-29T06:54:38Z","date_created":"2019-11-12T15:10:18Z","author":[{"full_name":"Davies, Heather S.","first_name":"Heather S.","last_name":"Davies"},{"full_name":"Baranova, Natalia S.","first_name":"Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"last_name":"El Amri","first_name":"Nouha","full_name":"El Amri, Nouha"},{"last_name":"Coche-Guérente","first_name":"Liliane","full_name":"Coche-Guérente, Liliane"},{"last_name":"Verdier","first_name":"Claude","full_name":"Verdier, Claude"},{"first_name":"Lionel","last_name":"Bureau","full_name":"Bureau, Lionel"},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."},{"last_name":"Débarre","first_name":"Delphine","full_name":"Débarre, Delphine"}],"department":[{"_id":"MaLo"}],"publisher":"SPIE","publication_status":"published","year":"2019","article_number":"110760V","language":[{"iso":"eng"}],"doi":"10.1117/12.2527058","conference":{"name":"European Conferences on Biomedical Optics","start_date":"2019-06-26","location":"Munich, Germany","end_date":"2019-06-27"},"quality_controlled":"1","isi":1,"external_id":{"isi":["000535353000023"]},"oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf","open_access":"1"}],"publication_identifier":{"issn":["1605-7422"],"isbn":["9781510628458"]},"month":"07"},{"date_updated":"2023-08-29T06:53:34Z","date_created":"2019-08-04T21:59:21Z","volume":15,"author":[{"full_name":"Khattak, Hamza K.","last_name":"Khattak","first_name":"Hamza K."},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"},{"full_name":"Slepkov, Aaron D.","first_name":"Aaron D.","last_name":"Slepkov"}],"publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"Royal Society of Chemistry","year":"2019","pmid":1,"month":"07","publication_identifier":{"eissn":["17446848"],"issn":["1744683X"]},"language":[{"iso":"eng"}],"doi":"10.1039/c9sm00756c","quality_controlled":"1","isi":1,"external_id":{"pmid":["31305853"],"isi":["000476909200002"]},"abstract":[{"text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics.","lang":"eng"}],"issue":"29","type":"journal_article","oa_version":"None","title":"Microwave induced mechanical activation of hydrogel dimers","status":"public","intvolume":" 15","_id":"6763","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2019-07-15T00:00:00Z","article_type":"original","page":"5804-5809","publication":"Soft Matter","citation":{"ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.","apa":"Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c9sm00756c","ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019.","mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:10.1039/c9sm00756c.","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c."}},{"article_number":"e1007168","file_date_updated":"2020-07-14T12:47:40Z","year":"2019","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9786"}]},"author":[{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"},{"first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"volume":15,"date_updated":"2023-08-29T07:10:06Z","date_created":"2019-08-11T21:59:19Z","publication_identifier":{"eissn":["1553-7358"]},"month":"07","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,"project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"},{"grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems"}],"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pcbi.1007168","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6784","intvolume":" 15","status":"public","ddc":["570"],"title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6803","checksum":"7ded4721b41c2a0fc66a1c634540416a","date_created":"2019-08-12T12:27:26Z","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access","file_name":"2019_PlosComputBiology_Ruess.pdf","content_type":"application/pdf","file_size":2200003,"creator":"dernst"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"02","citation":{"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.","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).","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.","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"},"publication":"PLoS Computational Biology","article_type":"original","date_published":"2019-07-02T00:00:00Z"},{"month":"08","publication_identifier":{"issn":["2041-1723"]},"external_id":{"pmid":["31375675"],"isi":["000478576500012"]},"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,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41467-019-11471-8","language":[{"iso":"eng"}],"article_number":"3480","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"year":"2019","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"author":[{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"full_name":"Xiao, G","last_name":"Xiao","first_name":"G"},{"first_name":"X","last_name":"Wang","full_name":"Wang, X"},{"full_name":"Zhang, Xixi","last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/"}]},"date_updated":"2023-08-29T07:02:44Z","date_created":"2019-08-09T08:46:26Z","volume":10,"scopus_import":"1","day":"02","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","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","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.","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","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.","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.","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019)."},"article_type":"original","date_published":"2019-08-02T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6778","status":"public","title":"Evolution of fast root gravitropism in seed plants","ddc":["580"],"intvolume":" 10","file":[{"file_size":6406141,"content_type":"application/pdf","creator":"dernst","file_name":"2019_NatureComm_Zhang.pdf","access_level":"open_access","date_created":"2019-08-12T07:09:20Z","date_updated":"2020-07-14T12:47:40Z","checksum":"d2c654fdb97f33078f606fe0c298bf6e","relation":"main_file","file_id":"6798"}],"oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1447-1460","article_type":"original","citation":{"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.","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.","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.","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.","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.","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"},"publication":"Molecular Ecology Resources","date_published":"2019-11-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"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.","lang":"eng"}],"intvolume":" 19","status":"public","title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6821","oa_version":"Submitted Version","publication_identifier":{"eissn":["1755-0998"]},"month":"11","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727","open_access":"1"}],"oa":1,"external_id":{"isi":["000480196800001"],"pmid":["31325910"]},"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.13062","department":[{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2019","volume":19,"date_created":"2019-08-18T22:00:41Z","date_updated":"2023-08-29T07:10:44Z","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."},{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"full_name":"Escobar-Camacho, Daniel","first_name":"Daniel","last_name":"Escobar-Camacho"},{"last_name":"Nandamuri","first_name":"Sri Pratima","full_name":"Nandamuri, Sri Pratima"},{"full_name":"Clark, Frances E.","first_name":"Frances E.","last_name":"Clark"},{"full_name":"Joyce, Brendan","first_name":"Brendan","last_name":"Joyce"},{"full_name":"Conte, Matthew A.","last_name":"Conte","first_name":"Matthew A."},{"full_name":"Kocher, Thomas D.","last_name":"Kocher","first_name":"Thomas D."},{"full_name":"Carleton, Karen L.","last_name":"Carleton","first_name":"Karen L."}]},{"author":[{"first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K"},{"last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"}],"volume":20,"date_updated":"2023-08-29T07:09:06Z","date_created":"2019-08-11T21:59:21Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:40Z","doi":"10.1007/s00023-019-00828-w","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":["1807.06781"],"isi":["000487036900008"]},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1424-0637"],"eissn":["1424-0661"]},"month":"10","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_AnnalesHenriPoincare_Leopold.pdf","creator":"dernst","file_size":681139,"content_type":"application/pdf","file_id":"6801","relation":"main_file","checksum":"b6dbf0d837d809293d449adf77138904","date_created":"2019-08-12T12:05:58Z","date_updated":"2020-07-14T12:47:40Z"}],"_id":"6788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","ddc":["510"],"title":"Mean-field dynamics for the Nelson model with fermions","status":"public","issue":"10","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2019-10-01T00:00:00Z","citation":{"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","ista":"Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 3471–3508.","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","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.","short":"N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508.","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."},"publication":"Annales Henri Poincare","page":"3471–3508","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"9597-9608","publication":"Ecology and Evolution","citation":{"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","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","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.","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.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","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."},"date_published":"2019-09-01T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"17","ddc":["576"],"title":"Green beards in the light of indirect genetic effects","status":"public","intvolume":" 9","_id":"6795","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"6799","checksum":"adcb70af4901977d95b8747eeee01bd7","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","access_level":"open_access","file_name":"2019_EcologyEvolution_Trubenova.pdf","file_size":2839636,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","month":"09","publication_identifier":{"eissn":["20457758"]},"quality_controlled":"1","isi":1,"project":[{"name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"external_id":{"isi":["000479973400001"]},"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":"10.1002/ece3.5484","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2019","date_created":"2019-08-11T21:59:24Z","date_updated":"2023-08-29T07:03:10Z","volume":9,"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","last_name":"Hager","first_name":"Reinmar"}]},{"abstract":[{"lang":"eng","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."}],"issue":"5","type":"journal_article","oa_version":"Preprint","_id":"6793","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"The Regge symmetry, confocal conics, and the Schläfli formula","intvolume":" 51","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","publication":"Bulletin of the London Mathematical Society","citation":{"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.","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.","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","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.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775.","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."},"article_type":"original","page":"765-775","ec_funded":1,"author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Izmestiev, Ivan","first_name":"Ivan","last_name":"Izmestiev"}],"date_updated":"2023-08-29T07:08:34Z","date_created":"2019-08-11T21:59:23Z","volume":51,"year":"2019","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"London Mathematical Society","month":"10","publication_identifier":{"issn":["00246093"],"eissn":["14692120"]},"doi":"10.1112/blms.12276","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.04929"}],"oa":1,"external_id":{"isi":["000478560200001"],"arxiv":["1903.04929"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}]},{"type":"research_data_reference","date_updated":"2023-08-29T07:10:05Z","date_created":"2021-08-06T08:23:43Z","oa_version":"Published Version","author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess","full_name":"Ruess, Jakob"},{"full_name":"Pleska, Maros","first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6784"}]},"title":"Supporting text and results","status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9786","year":"2019","day":"02","month":"07","article_processing_charge":"No","doi":"10.1371/journal.pcbi.1007168.s001","date_published":"2019-07-02T00:00:00Z","citation":{"short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","mla":"Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, 10.1371/journal.pcbi.1007168.s001."}},{"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"year":"2019","date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:17:07Z","volume":224,"author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"full_name":"Field, David","first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"related_material":{"record":[{"id":"9803","relation":"research_data","status":"public"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"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,"language":[{"iso":"eng"}],"doi":"10.1111/nph.16050","month":"11","publication_identifier":{"eissn":["1469-8137"]},"title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","ddc":["570"],"status":"public","intvolume":" 224","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6831","file":[{"date_created":"2019-08-27T12:44:54Z","date_updated":"2020-07-14T12:47:42Z","checksum":"6370e7567d96b7b562e77d8b89653f80","file_id":"6833","relation":"main_file","creator":"apreinsp","content_type":"application/pdf","file_size":2314016,"file_name":"2019_NewPhytologist_Puixeu.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","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."}],"issue":"3","article_type":"original","page":"1108-1120","publication":"New Phytologist","citation":{"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","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.","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.","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.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","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."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"}]