[{"external_id":{"isi":["000428234100005"]},"department":[{"_id":"MaJö"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"410","language":[{"iso":"eng"}],"publication_status":"published","ddc":["571","572"],"file_date_updated":"2020-07-14T12:46:23Z","article_processing_charge":"No","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"pubrep_id":"994","year":"2018","type":"journal_article","isi":1,"scopus_import":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"7419","doi":"10.1038/s41598-018-23247-z","quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Scientific Reports","intvolume":"         8","issue":"1","oa":1,"author":[{"last_name":"Masís","first_name":"Javier","full_name":"Masís, Javier"},{"full_name":"Mankus, David","last_name":"Mankus","first_name":"David"},{"full_name":"Wolff, Steffen","last_name":"Wolff","first_name":"Steffen"},{"last_name":"Guitchounts","first_name":"Grigori","full_name":"Guitchounts, Grigori"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","article_number":"5184","status":"public","day":"26","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-23247-z\">10.1038/s41598-018-23247-z</a>","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” <i>Scientific Reports</i>, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-23247-z\">10.1038/s41598-018-23247-z</a>.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-23247-z\">https://doi.org/10.1038/s41598-018-23247-z</a>.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., &#38; Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-23247-z\">https://doi.org/10.1038/s41598-018-23247-z</a>","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018."},"file":[{"date_created":"2018-12-12T10:10:42Z","file_size":2359430,"relation":"main_file","file_id":"4831","creator":"system","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","date_updated":"2020-07-14T12:46:23Z","checksum":"653fcb852f899c75b00ceee2a670d738"}],"date_updated":"2023-09-08T11:48:39Z","date_created":"2018-12-11T11:46:19Z","date_published":"2018-03-26T00:00:00Z","month":"03","has_accepted_license":"1","volume":8},{"language":[{"iso":"eng"}],"_id":"411","publication_status":"published","series_title":"MIMB","publication":"Root Development. Methods and Protocols","intvolume":"      1761","department":[{"_id":"JiFr"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","page":"131 - 143","publisher":"Springer","status":"public","abstract":[{"lang":"eng","text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins."}],"title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia","author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","year":"2018","scopus_import":1,"date_updated":"2021-01-12T07:54:34Z","editor":[{"full_name":"Ristova, Daniela","first_name":"Daniela","last_name":"Ristova"},{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"}],"day":"11","citation":{"apa":"Karampelias, M., Tejos, R., Friml, J., &#38; Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In D. Ristova &#38; E. Barbez (Eds.), <i>Root Development. Methods and Protocols</i> (Vol. 1761, pp. 131–143). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_10\">https://doi.org/10.1007/978-1-4939-7747-5_10</a>","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia,” in <i>Root Development. Methods and Protocols</i>, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. <i>Root Development. Methods and Protocols</i>. Vol 1761. MIMB. Springer; 2018:131-143. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_10\">10.1007/978-1-4939-7747-5_10</a>","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” <i>Root Development. Methods and Protocols</i>, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_10\">10.1007/978-1-4939-7747-5_10</a>.","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” In <i>Root Development. Methods and Protocols</i>, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_10\">https://doi.org/10.1007/978-1-4939-7747-5_10</a>."},"doi":"10.1007/978-1-4939-7747-5_10","publist_id":"7418","volume":1761,"month":"03","date_published":"2018-03-11T00:00:00Z","date_created":"2018-12-11T11:46:20Z","oa_version":"None"},{"issue":"3","publication":"The Plant Cell","intvolume":"        30","page":"700 - 716","quality_controlled":"1","publisher":"American Society of Plant Biologists","status":"public","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula","last_name":"Kania","first_name":"Urszula"},{"first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"oa":1,"related_material":{"record":[{"id":"6269","relation":"dissertation_contains","status":"public"}]},"date_updated":"2025-05-07T11:12:27Z","citation":{"short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., &#38; Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” <i>The Plant Cell</i>, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. <i>The Plant Cell</i>. 2018;30(3):700-716. doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:<a href=\"https://doi.org/10.1105/tpc.17.00785\">10.1105/tpc.17.00785</a>.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2018. <a href=\"https://doi.org/10.1105/tpc.17.00785\">https://doi.org/10.1105/tpc.17.00785</a>."},"day":"09","file":[{"date_created":"2022-05-23T09:12:38Z","file_size":4407538,"file_id":"11406","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PlantCell_Adamowski.pdf","success":1,"date_updated":"2022-05-23T09:12:38Z","checksum":"4e165e653b67d3f0684697f21aace5a1"}],"volume":30,"article_type":"original","has_accepted_license":"1","month":"04","date_created":"2018-12-11T11:46:20Z","date_published":"2018-04-09T00:00:00Z","_id":"412","language":[{"iso":"eng"}],"ddc":["580"],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300"}],"external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana."}],"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","article_processing_charge":"No","file_date_updated":"2022-05-23T09:12:38Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"year":"2018","type":"journal_article","isi":1,"scopus_import":"1","publist_id":"7417","doi":"10.1105/tpc.17.00785","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"oa_version":"Published Version"},{"scopus_import":"1","type":"journal_article","isi":1,"year":"2018","pmid":1,"oa_version":"Published Version","doi":"10.1073/pnas.1713501115","publist_id":"7416","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"SyCr"}],"external_id":{"isi":["000427245400069"],"pmid":["29463746"]},"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071"}],"publication_status":"published","_id":"413","language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"abstract":[{"text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.","lang":"eng"}],"date_updated":"2023-09-08T13:22:21Z","day":"13","citation":{"ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. <i>PNAS</i>. 2018;115(11):2782-2787. doi:<a href=\"https://doi.org/10.1073/pnas.1713501115\">10.1073/pnas.1713501115</a>","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” <i>PNAS</i>, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:<a href=\"https://doi.org/10.1073/pnas.1713501115\">10.1073/pnas.1713501115</a>.","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713501115\">https://doi.org/10.1073/pnas.1713501115</a>.","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., &#38; Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713501115\">https://doi.org/10.1073/pnas.1713501115</a>","ieee":"M. Konrad <i>et al.</i>, “Ants avoid superinfections by performing risk-adjusted sanitary care,” <i>PNAS</i>, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018."},"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/"}]},"month":"03","date_created":"2018-12-11T11:46:20Z","date_published":"2018-03-13T00:00:00Z","volume":115,"intvolume":"       115","publication":"PNAS","publisher":"National Academy of Sciences","page":"2782 - 2787","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746","open_access":"1"}],"quality_controlled":"1","issue":"11","author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher"},{"full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","last_name":"Metzler","first_name":"Sina"},{"first_name":"Katharina","last_name":"Seif","full_name":"Seif, Katharina","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"oa":1,"status":"public","title":"Ants avoid superinfections by performing risk-adjusted sanitary care"},{"month":"03","date_published":"2018-03-14T00:00:00Z","date_created":"2018-12-11T11:46:21Z","article_type":"original","volume":148,"date_updated":"2024-02-28T13:01:59Z","day":"14","citation":{"apa":"Rzadkowski, W., &#38; Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5017591\">https://doi.org/10.1063/1.5017591</a>","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” <i>The Journal of Chemical Physics</i>, vol. 148, no. 10. AIP Publishing, 2018.","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2018. <a href=\"https://doi.org/10.1063/1.5017591\">https://doi.org/10.1063/1.5017591</a>.","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. <i>The Journal of Chemical Physics</i>. 2018;148(10). doi:<a href=\"https://doi.org/10.1063/1.5017591\">10.1063/1.5017591</a>","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” <i>The Journal of Chemical Physics</i>, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:<a href=\"https://doi.org/10.1063/1.5017591\">10.1063/1.5017591</a>."},"related_material":{"record":[{"id":"10759","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Wojciech","last_name":"Rzadkowski","orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87","full_name":"Rzadkowski, Wojciech"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"oa":1,"status":"public","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","article_number":"104307","publication":"The Journal of Chemical Physics","intvolume":"       148","main_file_link":[{"url":"https://arxiv.org/abs/1711.09904","open_access":"1"}],"quality_controlled":"1","publisher":"AIP Publishing","issue":"10","oa_version":"Preprint","publist_id":"7408","doi":"10.1063/1.5017591","isi":1,"type":"journal_article","year":"2018","arxiv":1,"scopus_import":"1","acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","article_processing_charge":"No","ec_funded":1,"abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"external_id":{"arxiv":["1711.09904"],"isi":["000427517200065"]},"language":[{"iso":"eng"}],"_id":"415","publication_status":"published"},{"date_created":"2018-12-11T11:46:22Z","date_published":"2018-10-16T00:00:00Z","month":"10","volume":121,"citation":{"chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.121.165301\">https://doi.org/10.1103/PhysRevLett.121.165301</a>.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. <i>Physical Review Letters</i>. 2018;121(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.165301\">10.1103/PhysRevLett.121.165301</a>","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” <i>Physical Review Letters</i>, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.165301\">10.1103/PhysRevLett.121.165301</a>.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Bighin, G., Tscherbul, T., &#38; Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.121.165301\">https://doi.org/10.1103/PhysRevLett.121.165301</a>","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” <i>Physical Review Letters</i>, vol. 121, no. 16. American Physical Society, 2018."},"day":"16","date_updated":"2024-02-28T13:14:53Z","oa":1,"author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo"},{"last_name":"Tscherbul","first_name":"Timur","full_name":"Tscherbul, Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"}],"article_number":"165301","title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","status":"public","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"quality_controlled":"1","intvolume":"       121","publication":"Physical Review Letters","issue":"16","oa_version":"Preprint","publist_id":"8025","doi":"10.1103/PhysRevLett.121.165301","scopus_import":"1","type":"journal_article","year":"2018","arxiv":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. "}],"external_id":{"arxiv":["1803.07990"]},"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"_id":"417"},{"department":[{"_id":"HaJa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571","570"],"publication_status":"published","_id":"418","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-07-14T12:46:24Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion."}],"pubrep_id":"913","type":"dissertation","year":"2018","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"supervisor":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"publist_id":"7405","doi":"10.15479/AT:ISTA:th_913","publisher":"Institute of Science and Technology Austria","page":"107","oa":1,"author":[{"first_name":"Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"}],"title":"Optical and optogenetic control of proliferation and survival ","status":"public","file":[{"date_updated":"2020-07-14T12:46:24Z","file_name":"2018_THESIS_Gschaider-Reichhart_source.docx","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","relation":"source_file","creator":"dernst","file_id":"6222","file_size":7012495,"date_created":"2019-04-05T09:28:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"content_type":"application/pdf","access_level":"open_access","file_size":6355280,"creator":"dernst","relation":"main_file","file_id":"6223","date_created":"2019-04-05T09:28:03Z","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","date_updated":"2020-07-14T12:46:24Z","file_name":"2018_THESIS_Gschaider-Reichhart.pdf"}],"day":"08","citation":{"chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">https://doi.org/10.15479/AT:ISTA:th_913</a>.","ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">10.15479/AT:ISTA:th_913</a>","mla":"Gschaider-Reichhart, Eva. <i>Optical and Optogenetic Control of Proliferation and Survival </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">10.15479/AT:ISTA:th_913</a>.","apa":"Gschaider-Reichhart, E. (2018). <i>Optical and optogenetic control of proliferation and survival </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">https://doi.org/10.15479/AT:ISTA:th_913</a>","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018."},"date_updated":"2023-09-22T09:20:10Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"1441","status":"public"},{"status":"public","id":"1678","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2084"},{"status":"public","id":"1028","relation":"part_of_dissertation"}]},"date_published":"2018-01-08T00:00:00Z","date_created":"2018-12-11T11:46:22Z","month":"01","has_accepted_license":"1","degree_awarded":"PhD"},{"date_created":"2018-12-11T11:46:22Z","date_published":"2018-03-19T00:00:00Z","month":"03","has_accepted_license":"1","article_type":"review","volume":2,"file":[{"date_created":"2019-11-19T08:19:51Z","file_size":598033,"file_id":"7052","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_NatureHumanBeh_Hilbe.pdf","date_updated":"2020-07-14T12:46:25Z","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb"}],"citation":{"apa":"Hilbe, C., Chatterjee, K., &#38; Nowak, M. (2018). Partners and rivals in direct reciprocity. <i>Nature Human Behaviour</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41562-018-0320-9\">https://doi.org/10.1038/s41562-018-0320-9</a>","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” <i>Nature Human Behaviour</i>, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. <i>Nature Human Behaviour</i>. 2018;2:469–477. doi:<a href=\"https://doi.org/10.1038/s41562-018-0320-9\">10.1038/s41562-018-0320-9</a>","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” <i>Nature Human Behaviour</i>, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:<a href=\"https://doi.org/10.1038/s41562-018-0320-9\">10.1038/s41562-018-0320-9</a>.","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” <i>Nature Human Behaviour</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41562-018-0320-9\">https://doi.org/10.1038/s41562-018-0320-9</a>."},"day":"19","date_updated":"2023-09-13T09:38:54Z","related_material":{"link":[{"url":"http://doi.org/10.1038/s41562-018-0342-3","relation":"erratum"}]},"oa":1,"author":[{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"title":"Partners and rivals in direct reciprocity","status":"public","publisher":"Nature Publishing Group","quality_controlled":"1","page":"469–477","intvolume":"         2","publication":"Nature Human Behaviour","oa_version":"Submitted Version","doi":"10.1038/s41562-018-0320-9","publist_id":"7404","scopus_import":"1","year":"2018","type":"journal_article","isi":1,"file_date_updated":"2020-07-14T12:46:25Z","article_processing_charge":"No","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"ec_funded":1,"external_id":{"isi":["000446612000016"]},"project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"department":[{"_id":"KrCh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"publication_status":"published","_id":"419","language":[{"iso":"eng"}]},{"publist_id":"8012","doi":"10.1093/jxb/ery281","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","scopus_import":"1","type":"journal_article","year":"2018","isi":1,"abstract":[{"lang":"eng","text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield."}],"acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:25Z","ddc":["575"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"42","department":[{"_id":"EvBe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000448163900015"]},"volume":69,"has_accepted_license":"1","month":"07","date_created":"2018-12-11T11:44:19Z","date_published":"2018-07-26T00:00:00Z","date_updated":"2023-09-11T12:52:03Z","file":[{"creator":"dernst","relation":"main_file","file_id":"5691","file_size":1292128,"date_created":"2018-12-17T10:44:16Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","file_name":"2018_JournalExperimBotany_Cucinotta.pdf","checksum":"ca3b6711040b1662488aeb3d1f961f13"}],"citation":{"apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., &#38; Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery281\">https://doi.org/10.1093/jxb/ery281</a>","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery281\">https://doi.org/10.1093/jxb/ery281</a>.","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. <i>Journal of Experimental Botany</i>. 2018;69(21):5169-5176. doi:<a href=\"https://doi.org/10.1093/jxb/ery281\">10.1093/jxb/ery281</a>","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:<a href=\"https://doi.org/10.1093/jxb/ery281\">10.1093/jxb/ery281</a>."},"day":"26","status":"public","title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","author":[{"full_name":"Cucinotta, Mara","first_name":"Mara","last_name":"Cucinotta"},{"full_name":"Manrique, Silvia","first_name":"Silvia","last_name":"Manrique"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","first_name":"Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}],"oa":1,"issue":"21","intvolume":"        69","publication":"Journal of Experimental Botany","publisher":"Oxford University Press","page":"5169 - 5176","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"article_processing_charge":"No","publication_status":"published","_id":"420","language":[{"iso":"eng"}],"external_id":{"isi":["000438217300007"]},"department":[{"_id":"MiLe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1142/S0217979218400222","publist_id":"7402","oa_version":"Preprint","scopus_import":"1","isi":1,"type":"journal_article","year":"2018","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","status":"public","oa":1,"author":[{"last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"}],"issue":"17","publisher":"World Scientific Publishing","page":"1840022","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"quality_controlled":"1","intvolume":"        32","publication":"International Journal of Modern Physics B","volume":32,"date_published":"2018-07-10T00:00:00Z","date_created":"2018-12-11T11:46:22Z","month":"07","day":"10","citation":{"ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” <i>International Journal of Modern Physics B</i>, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","apa":"Bighin, G., &#38; Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. <i>International Journal of Modern Physics B</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0217979218400222\">https://doi.org/10.1142/S0217979218400222</a>","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” <i>International Journal of Modern Physics B</i>. World Scientific Publishing, 2018. <a href=\"https://doi.org/10.1142/S0217979218400222\">https://doi.org/10.1142/S0217979218400222</a>.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” <i>International Journal of Modern Physics B</i>, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:<a href=\"https://doi.org/10.1142/S0217979218400222\">10.1142/S0217979218400222</a>.","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. <i>International Journal of Modern Physics B</i>. 2018;32(17):1840022. doi:<a href=\"https://doi.org/10.1142/S0217979218400222\">10.1142/S0217979218400222</a>","ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022."},"date_updated":"2023-09-18T08:09:59Z"},{"oa":1,"author":[{"first_name":"Kinjal","last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Claude-Edouard B","full_name":"Hannezo, Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"page":"968 - 977","quality_controlled":"1","publisher":"Biophysical Society","publication":"Biophysical Journal","intvolume":"       114","issue":"4","date_created":"2018-12-11T11:46:23Z","date_published":"2018-02-27T00:00:00Z","month":"02","volume":114,"citation":{"chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>. Biophysical Society, 2018. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. 2018;114(4):968-977. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","apa":"Dasbiswas, K., Hannezo, E. B., &#38; Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” <i>Biophysical Journal</i>, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018."},"day":"27","date_updated":"2023-09-19T10:13:55Z","article_processing_charge":"No","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"EdHa"}],"_id":"421","language":[{"iso":"eng"}],"publication_status":"published","oa_version":"Submitted Version","doi":"10.1016/j.bpj.2017.12.022","publist_id":"7403","year":"2018","type":"journal_article","isi":1,"arxiv":1,"scopus_import":"1"},{"department":[{"_id":"BjHo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin"}],"external_id":{"isi":["000433113900004"]},"language":[{"iso":"eng"}],"_id":"422","ddc":["530"],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2020-07-14T12:46:25Z","ec_funded":1,"abstract":[{"text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle.","lang":"eng"}],"isi":1,"year":"2018","type":"journal_article","scopus_import":"1","oa_version":"Published Version","doi":"10.1007/s10494-018-9896-4","publist_id":"7401","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Flow Turbulence and Combustion","intvolume":"       100","quality_controlled":"1","page":"919 - 942","publisher":"Springer","issue":"4","author":[{"first_name":"Jakob","last_name":"Kühnen","orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob"},{"first_name":"Davide","last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schaner","first_name":"Markus","full_name":"Schaner, Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"oa":1,"status":"public","title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","date_updated":"2024-03-25T23:30:20Z","citation":{"chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. 2018;100(4):919-942. doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>.","apa":"Kühnen, J., Scarselli, D., Schaner, M., &#38; Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. Springer. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4. Springer, pp. 919–942, 2018."},"day":"01","file":[{"checksum":"d7c0bade150faabca150b0a9986e60ca","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","date_updated":"2020-07-14T12:46:25Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-17T15:52:37Z","file_size":2210020,"creator":"dernst","file_id":"5717","relation":"main_file"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7258"}]},"month":"01","date_created":"2018-12-11T11:46:23Z","date_published":"2018-01-01T00:00:00Z","volume":100,"has_accepted_license":"1"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.32035","publist_id":"7400","oa_version":"Published Version","year":"2018","type":"journal_article","isi":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","article_processing_charge":"No","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","_id":"423","language":[{"iso":"eng"}],"publication_status":"published","ddc":["576"],"project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"external_id":{"isi":["000431035800001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","volume":7,"date_created":"2018-12-11T11:46:23Z","date_published":"2018-03-09T00:00:00Z","month":"03","related_material":{"record":[{"id":"9840","relation":"research_data","status":"public"}]},"day":"09","citation":{"ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>."},"file":[{"file_size":3533881,"creator":"dernst","file_id":"5689","relation":"main_file","date_created":"2018-12-17T10:36:07Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","file_name":"2018_eLife_Payne.pdf","checksum":"447cf6e680bdc3c01062a8737d876569"}],"date_updated":"2023-09-11T12:49:17Z","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","article_number":"e32035","status":"public","oa":1,"author":[{"first_name":"Pavel","last_name":"Payne","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612"}],"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","intvolume":"         7"},{"day":"01","citation":{"short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","apa":"Matoušek, J., Sedgwick, E., Tancer, M., &#38; Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” <i>Journal of the ACM</i>, vol. 65, no. 1. ACM, 2018.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. 2018;65(1). doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>, vol. 65, no. 1, 5, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>."},"date_updated":"2023-09-11T13:38:49Z","related_material":{"record":[{"status":"public","id":"2157","relation":"earlier_version"}]},"date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:46:24Z","month":"01","article_type":"original","volume":65,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"publisher":"ACM","publication":"Journal of the ACM","intvolume":"        65","issue":"1","oa":1,"author":[{"full_name":"Matoušek, Jiří","first_name":"Jiří","last_name":"Matoušek"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"Embeddability in the 3-Sphere is decidable","article_number":"5","status":"public","type":"journal_article","arxiv":1,"isi":1,"year":"2018","scopus_import":"1","oa_version":"Preprint","publist_id":"7398","doi":"10.1145/3078632","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"external_id":{"isi":["000425685900006"],"arxiv":["1402.0815"]},"department":[{"_id":"UlWa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"425","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","abstract":[{"text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X.","lang":"eng"}],"ec_funded":1},{"date_updated":"2023-09-12T07:43:26Z","day":"01","citation":{"ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” <i>Journal of Insect Physiology</i>, vol. 107. Elsevier, pp. 284–290, 2018.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","apa":"Metzler, S., Schrempf, A., &#38; Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>, vol. 107, Elsevier, 2018, pp. 284–90, doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>.","ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. 2018;107:284-290. doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>."},"volume":107,"month":"05","date_published":"2018-05-01T00:00:00Z","date_created":"2018-12-11T11:46:25Z","publication":"Journal of Insect Physiology","intvolume":"       107","quality_controlled":"1","page":"284-290","publisher":"Elsevier","status":"public","title":"Individual- and ejaculate-specific sperm traits in ant males","author":[{"first_name":"Sina","last_name":"Metzler","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schrempf, Alexandra","first_name":"Alexandra","last_name":"Schrempf"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"type":"journal_article","year":"2018","isi":1,"scopus_import":"1","publist_id":"7397","doi":"10.1016/j.jinsphys.2017.12.003","oa_version":"None","language":[{"iso":"eng"}],"_id":"426","publication_status":"published","department":[{"_id":"SyCr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000434751100034"]},"abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","article_processing_charge":"No"},{"status":"public","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","article_number":"022510","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"full_name":"Loureiro, Ulisses","first_name":"Ulisses","last_name":"Loureiro"},{"last_name":"Safari","first_name":"Laleh","full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"},{"full_name":"Indelicato, Paul","first_name":"Paul","last_name":"Indelicato"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"}],"oa":1,"issue":"2","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","intvolume":"        97","main_file_link":[{"url":"https://arxiv.org/abs/1802.07920","open_access":"1"}],"quality_controlled":"1","publisher":"American Physical Society","volume":97,"article_type":"original","month":"02","date_published":"2018-02-21T00:00:00Z","date_created":"2018-12-11T11:46:25Z","date_updated":"2023-09-15T12:09:35Z","day":"21","citation":{"mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">10.1103/PhysRevA.97.022510</a>.","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2018;97(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">10.1103/PhysRevA.97.022510</a>","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions.  Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">https://doi.org/10.1103/PhysRevA.97.022510</a>.","ieee":"P. Amaro <i>et al.</i>, “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 2. American Physical Society, 2018.","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., &#38; Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">https://doi.org/10.1103/PhysRevA.97.022510</a>","short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos,  Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018)."},"ec_funded":1,"abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"article_processing_charge":"No","acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","language":[{"iso":"eng"}],"_id":"427","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiLe"}],"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"external_id":{"arxiv":["1802.07920"],"isi":["000425601000004"]},"publist_id":"7396","doi":"10.1103/PhysRevA.97.022510","oa_version":"Preprint","year":"2018","isi":1,"arxiv":1,"type":"journal_article","scopus_import":"1"},{"quality_controlled":"1","page":" 3716 - 3721","publisher":"National Academy of Sciences","publication":"PNAS","intvolume":"       115","issue":"14","oa":1,"author":[{"last_name":"Salanenka","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge"},{"last_name":"Löfke","first_name":"Christian","full_name":"Löfke, Christian"},{"full_name":"Tabata, Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","last_name":"Tabata","first_name":"Kaori"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"}],"title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","status":"public","day":"03","citation":{"mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>PNAS</i>, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>.","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>PNAS</i>. 2018;115(14):3716-3721. doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>.","ieee":"Y. Salanenka <i>et al.</i>, “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” <i>PNAS</i>, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., &#38; Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>"},"file":[{"checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","date_updated":"2020-07-14T12:46:26Z","file_name":"2018_PNAS_Salanenka.pdf","content_type":"application/pdf","access_level":"open_access","file_size":1924101,"file_id":"5700","creator":"dernst","relation":"main_file","date_created":"2018-12-17T12:30:14Z"}],"date_updated":"2025-05-07T11:12:27Z","date_created":"2018-12-11T11:46:25Z","date_published":"2018-04-03T00:00:00Z","month":"04","has_accepted_license":"1","volume":115,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"external_id":{"isi":["000429012500073"]},"department":[{"_id":"JiFr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"428","language":[{"iso":"eng"}],"publication_status":"published","ddc":["580"],"file_date_updated":"2020-07-14T12:46:26Z","article_processing_charge":"No","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"ec_funded":1,"type":"journal_article","year":"2018","isi":1,"scopus_import":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publist_id":"7395","doi":"10.1073/pnas.1721760115"},{"publisher":"National Academy of Sciences","quality_controlled":"1","page":"10690 - 10695","intvolume":"       115","publication":"PNAS","issue":"42","oa":1,"author":[{"last_name":"Rybicki","orcid":"0000-0002-6432-6646","first_name":"Joel","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"last_name":"Anttila","first_name":"Jani","full_name":"Anttila, Jani"}],"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","status":"public","file":[{"file_size":4070777,"relation":"main_file","creator":"dernst","file_id":"6258","date_created":"2019-04-09T08:02:50Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:26Z","file_name":"2018_PNAS_Rybicki.pdf","checksum":"df7ac544a587c06b75692653b9fabd18"}],"day":"02","citation":{"ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” <i>PNAS</i>, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","apa":"Rybicki, J., Kisdi, E., &#38; Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>PNAS</i>, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>PNAS</i>. 2018;115(42):10690-10695. doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>."},"date_updated":"2023-09-13T08:57:38Z","date_created":"2018-12-11T11:44:19Z","date_published":"2018-10-02T00:00:00Z","month":"10","has_accepted_license":"1","volume":115,"external_id":{"isi":["000447491300057"]},"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"department":[{"_id":"DaAl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570","577"],"publication_status":"published","_id":"43","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:26Z","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"ec_funded":1,"pubrep_id":"1063","scopus_import":"1","year":"2018","isi":1,"type":"journal_article","oa_version":"Submitted Version","publist_id":"8011","doi":"10.1073/pnas.1721061115"},{"year":"2018","isi":1,"type":"journal_article","scopus_import":"1","pubrep_id":"1012","publist_id":"7393","doi":"10.1534/genetics.118.300786","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","_id":"430","language":[{"iso":"eng"}],"publication_status":"published","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"external_id":{"isi":["000429094400005"]},"abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:26Z","date_updated":"2023-09-19T10:17:30Z","citation":{"short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","apa":"Novembre, J., &#38; Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” <i>Genetics</i>, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. 2018;208(4):1351-1355. doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>."},"day":"01","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:12:40Z","creator":"system","file_id":"4958","relation":"main_file","file_size":500129,"checksum":"3d838dc285df394376555b794b6a5ad1","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_updated":"2020-07-14T12:46:26Z"}],"volume":208,"has_accepted_license":"1","month":"04","date_created":"2018-12-11T11:46:26Z","date_published":"2018-04-01T00:00:00Z","issue":"4","publication":"Genetics","intvolume":"       208","page":"1351 - 1355","quality_controlled":"1","publisher":"Genetics Society of America","status":"public","title":"Tread lightly interpreting polygenic tests of selection","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"oa":1},{"oa_version":"Submitted Version","publist_id":"7390","doi":"10.1007/978-3-319-73915-1_14","type":"conference","arxiv":1,"year":"2018","scopus_import":1,"alternative_title":["LNCS"],"abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"external_id":{"arxiv":["1708.08037"]},"department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"433","publication_status":"published","date_published":"2018-01-21T00:00:00Z","date_created":"2018-12-11T11:46:27Z","month":"01","volume":10692,"citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>.","mla":"Fulek, Radoslav, and János Pach. <i>Thrackles: An Improved Upper Bound</i>. Vol. 10692, Springer, 2018, pp. 160–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","apa":"Fulek, R., &#38; Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>"},"day":"21","date_updated":"2023-08-24T14:39:32Z","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","location":"Boston, MA, United States","start_date":"201-09-25","end_date":"2017-09-27"},"related_material":{"record":[{"status":"public","relation":"later_version","id":"5857"}]},"oa":1,"author":[{"orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"title":"Thrackles: An improved upper bound","status":"public","page":"160 - 166","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"quality_controlled":"1","publisher":"Springer","intvolume":"     10692"}]