--- _id: '7010' abstract: - lang: eng 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. article_number: 110760V article_processing_charge: No author: - first_name: Heather S. full_name: Davies, Heather S. last_name: Davies - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Nouha full_name: El Amri, Nouha last_name: El Amri - first_name: Liliane full_name: Coche-Guérente, Liliane last_name: Coche-Guérente - first_name: Claude full_name: Verdier, Claude last_name: Verdier - first_name: Lionel full_name: Bureau, Lionel last_name: Bureau - first_name: Ralf P. full_name: Richter, Ralf P. last_name: Richter - first_name: Delphine full_name: Débarre, Delphine last_name: Débarre 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' 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. 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. 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. 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. conference: end_date: 2019-06-27 location: Munich, Germany name: European Conferences on Biomedical Optics start_date: 2019-06-26 date_created: 2019-11-12T15:10:18Z date_published: 2019-07-22T00:00:00Z date_updated: 2023-08-29T06:54:38Z day: '22' department: - _id: MaLo doi: 10.1117/12.2527058 external_id: isi: - '000535353000023' intvolume: ' 11076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf month: '07' oa: 1 oa_version: Published Version publication: Advances in Microscopic Imaging II publication_identifier: isbn: - '9781510628458' issn: - 1605-7422 publication_status: published publisher: SPIE quality_controlled: '1' scopus_import: '1' status: public title: Blood cell-vessel wall interactions probed by reflection interference contrast microscopy type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11076 year: '2019' ... --- _id: '6763' abstract: - lang: eng 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." article_processing_charge: No article_type: original author: - first_name: Hamza K. full_name: Khattak, Hamza K. last_name: Khattak - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Aaron D. full_name: Slepkov, Aaron D. last_name: Slepkov 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 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 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. 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. ista: Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809. 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. date_created: 2019-08-04T21:59:21Z date_published: 2019-07-15T00:00:00Z date_updated: 2023-08-29T06:53:34Z day: '15' department: - _id: ScWa doi: 10.1039/c9sm00756c external_id: isi: - '000476909200002' pmid: - '31305853' intvolume: ' 15' isi: 1 issue: '29' language: - iso: eng month: '07' oa_version: None page: 5804-5809 pmid: 1 publication: Soft Matter publication_identifier: eissn: - '17446848' issn: - 1744683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Microwave induced mechanical activation of hydrogel dimers type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6784' 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. article_number: e1007168 article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: 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 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 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. 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. 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. 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). date_created: 2019-08-11T21:59:19Z date_published: 2019-07-02T00:00:00Z date_updated: 2023-08-29T07:10:06Z day: '02' ddc: - '570' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007168 external_id: isi: - '000481577700032' file: - access_level: open_access checksum: 7ded4721b41c2a0fc66a1c634540416a content_type: application/pdf creator: dernst date_created: 2019-08-12T12:27:26Z date_updated: 2020-07-14T12:47:40Z file_id: '6803' file_name: 2019_PlosComputBiology_Ruess.pdf file_size: 2200003 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '7' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version 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 - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9786' relation: research_data status: public scopus_import: '1' status: public title: Molecular noise of innate immunity shapes bacteria-phage ecologies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6778' 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." article_number: '3480' article_processing_charge: No article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: G full_name: Xiao, G last_name: Xiao - first_name: X full_name: Wang, X last_name: Wang - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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. ista: Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480. 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). date_created: 2019-08-09T08:46:26Z date_published: 2019-08-02T00:00:00Z date_updated: 2023-08-29T07:02:44Z day: '02' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-019-11471-8 ec_funded: 1 external_id: isi: - '000478576500012' pmid: - '31375675' file: - access_level: open_access checksum: d2c654fdb97f33078f606fe0c298bf6e content_type: application/pdf creator: dernst date_created: 2019-08-12T07:09:20Z date_updated: 2020-07-14T12:47:40Z file_id: '6798' file_name: 2019_NatureComm_Zhang.pdf file_size: 6406141 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/ scopus_import: '1' status: public title: Evolution of fast root gravitropism in seed plants tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6821' 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. article_processing_charge: No article_type: original author: - first_name: Miranda R. full_name: Yourick, Miranda R. last_name: Yourick - first_name: Benjamin A. full_name: Sandkam, Benjamin A. last_name: Sandkam - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Daniel full_name: Escobar-Camacho, Daniel last_name: Escobar-Camacho - first_name: Sri Pratima full_name: Nandamuri, Sri Pratima last_name: Nandamuri - first_name: Frances E. full_name: Clark, Frances E. last_name: Clark - first_name: Brendan full_name: Joyce, Brendan last_name: Joyce - first_name: Matthew A. full_name: Conte, Matthew A. last_name: Conte - first_name: Thomas D. full_name: Kocher, Thomas D. last_name: Kocher - first_name: Karen L. full_name: Carleton, Karen L. last_name: Carleton 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 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. 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. 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. date_created: 2019-08-18T22:00:41Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T07:10:44Z day: '01' department: - _id: BeVi doi: 10.1111/1755-0998.13062 external_id: isi: - '000480196800001' pmid: - '31325910' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727 month: '11' oa: 1 oa_version: Submitted Version page: 1447-1460 pmid: 1 publication: Molecular Ecology Resources publication_identifier: eissn: - 1755-0998 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2019' ... --- _id: '6788' 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 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 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 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. 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. ista: Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 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. short: N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508. date_created: 2019-08-11T21:59:21Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-29T07:09:06Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00023-019-00828-w ec_funded: 1 external_id: arxiv: - '1807.06781' isi: - '000487036900008' file: - access_level: open_access checksum: b6dbf0d837d809293d449adf77138904 content_type: application/pdf creator: dernst date_created: 2019-08-12T12:05:58Z date_updated: 2020-07-14T12:47:40Z file_id: '6801' file_name: 2019_AnnalesHenriPoincare_Leopold.pdf file_size: 681139 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 3471–3508 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_identifier: eissn: - 1424-0661 issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mean-field dynamics for the Nelson model with fermions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6795' 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. article_processing_charge: No article_type: original author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager 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 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 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. 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. 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. date_created: 2019-08-11T21:59:24Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-29T07:03:10Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1002/ece3.5484 ec_funded: 1 external_id: isi: - '000479973400001' file: - access_level: open_access checksum: adcb70af4901977d95b8747eeee01bd7 content_type: application/pdf creator: dernst date_created: 2019-08-12T07:30:30Z date_updated: 2020-07-14T12:47:40Z file_id: '6799' file_name: 2019_EcologyEvolution_Trubenova.pdf file_size: 2839636 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '17' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 9597-9608 project: - _id: 25AEDD42-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '704172' name: Rate of Adaptation in Changing Environment publication: Ecology and Evolution publication_identifier: eissn: - '20457758' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Green beards in the light of indirect genetic effects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6793' 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. article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Ivan full_name: Izmestiev, Ivan last_name: Izmestiev citation: 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 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 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. 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. 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. date_created: 2019-08-11T21:59:23Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-29T07:08:34Z day: '01' department: - _id: HeEd doi: 10.1112/blms.12276 ec_funded: 1 external_id: arxiv: - '1903.04929' isi: - '000478560200001' intvolume: ' 51' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.04929 month: '10' oa: 1 oa_version: Preprint page: 765-775 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended publication: Bulletin of the London Mathematical Society publication_identifier: eissn: - '14692120' issn: - '00246093' publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: The Regge symmetry, confocal conics, and the Schläfli formula type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 51 year: '2019' ... --- _id: '9786' article_processing_charge: No author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: 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 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. 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. mla: Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001. short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019). date_created: 2021-08-06T08:23:43Z date_published: 2019-07-02T00:00:00Z date_updated: 2023-08-29T07:10:05Z day: '02' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007168.s001 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6784' relation: used_in_publication status: public status: public title: Supporting text and results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6831' 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." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David last_name: Field orcid: 0000-0002-4014-8478 - first_name: Spencer C.H. full_name: Barrett, Spencer C.H. last_name: Barrett citation: 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' 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' 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.' 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.' 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. date_created: 2019-08-25T22:00:51Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-29T07:17:07Z day: '01' ddc: - '570' department: - _id: NiBa - _id: BeVi doi: 10.1111/nph.16050 ec_funded: 1 external_id: isi: - '000481376500001' file: - access_level: open_access checksum: 6370e7567d96b7b562e77d8b89653f80 content_type: application/pdf creator: apreinsp date_created: 2019-08-27T12:44:54Z date_updated: 2020-07-14T12:47:42Z file_id: '6833' file_name: 2019_NewPhytologist_Puixeu.pdf file_size: 2314016 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 224' isi: 1 issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1108-1120 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: New Phytologist publication_identifier: eissn: - 1469-8137 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9803' relation: research_data status: public - id: '14058' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 224 year: '2019' ...