[{"oa":1,"day":"07","doi":"10.1016/j.molp.2016.08.010","year":"2016","page":"1504 - 1519","acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","scopus_import":1,"publication":"Molecular Plant","publist_id":"6213","intvolume":" 9","citation":{"short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., & Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010"},"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:37Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","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)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["581"],"publication_status":"published","abstract":[{"text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors","lang":"eng"}],"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","file_date_updated":"2018-12-12T10:13:22Z","date_published":"2016-11-07T00:00:00Z","publisher":"Cell Press","_id":"1145","type":"journal_article","date_created":"2018-12-11T11:50:23Z","status":"public","pubrep_id":"746","ec_funded":1,"oa_version":"Published Version","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"file":[{"file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","date_created":"2018-12-12T10:13:22Z","date_updated":"2018-12-12T10:13:22Z","content_type":"application/pdf","access_level":"open_access","file_size":5005876,"file_id":"5004","creator":"system","relation":"main_file"}],"issue":"11","month":"11","has_accepted_license":"1","volume":9,"language":[{"iso":"eng"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:38Z","citation":{"ieee":"J. Balla et al., “Auxin flow mediated competition between axillary buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., & Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep35955","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 2016;6. doi:10.1038/srep35955","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature Publishing Group, 2016, doi:10.1038/srep35955.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016)."},"file_date_updated":"2018-12-12T10:09:28Z","date_published":"2016-11-08T00:00:00Z","publisher":"Nature Publishing Group","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","publication_status":"published","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"ddc":["581"],"acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","year":"2016","doi":"10.1038/srep35955","day":"08","oa":1,"publist_id":"6211","intvolume":" 6","publication":"Scientific Reports","scopus_import":1,"author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"full_name":"Medved'Ová, Zuzana","last_name":"Medved'Ová","first_name":"Zuzana"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"first_name":"Natálie","last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Reinöhl, Vilém","last_name":"Reinöhl","first_name":"Vilém"},{"first_name":"Stanislav","last_name":"Procházka","full_name":"Procházka, Stanislav"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":6,"has_accepted_license":"1","month":"11","file":[{"file_id":"4752","creator":"system","access_level":"open_access","file_size":1587544,"relation":"main_file","file_name":"IST-2017-745-v1+1_srep35955.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:09:28Z","date_updated":"2018-12-12T10:09:28Z"}],"article_number":"35955","status":"public","date_created":"2018-12-11T11:50:24Z","type":"journal_article","_id":"1147","pubrep_id":"745"},{"oa":1,"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","page":"2286 - 2296","year":"2016","doi":"10.1101/gad.285361.116","day":"15","scopus_import":1,"publist_id":"6207","intvolume":" 30","publication":"Genes and Development","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:39Z","citation":{"ieee":"S. Simonini et al., “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 2016;30(20):2286-2296. doi:10.1101/gad.285361.116","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.285361.116.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296."},"external_id":{"pmid":["27898393"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.","lang":"eng"}],"ddc":["570"],"pmid":1,"file_date_updated":"2019-01-25T09:32:55Z","date_published":"2016-10-15T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","date_created":"2018-12-11T11:50:25Z","_id":"1151","type":"journal_article","status":"public","quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"last_name":"Deb","first_name":"Joyita","full_name":"Deb, Joyita"},{"full_name":"Moubayidin, Laila","first_name":"Laila","last_name":"Moubayidin"},{"full_name":"Stephenson, Pauline","last_name":"Stephenson","first_name":"Pauline"},{"full_name":"Valluru, Manoj","last_name":"Valluru","first_name":"Manoj"},{"last_name":"Freire Rios","first_name":"Alejandra","full_name":"Freire Rios, Alejandra"},{"full_name":"Sorefan, Karim","first_name":"Karim","last_name":"Sorefan"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Östergaard","first_name":"Lars","full_name":"Östergaard, Lars"}],"has_accepted_license":"1","month":"10","file":[{"file_size":1419263,"access_level":"open_access","creator":"dernst","file_id":"5882","relation":"main_file","success":1,"file_name":"2016_GeneDev_Simonini.pdf","date_updated":"2019-01-25T09:32:55Z","date_created":"2019-01-25T09:32:55Z","content_type":"application/pdf"}],"issue":"20","language":[{"iso":"eng"}],"volume":30},{"scopus_import":1,"publist_id":"6205","intvolume":" 28","publication":"Plant Cell","oa":1,"acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","day":"01","page":"2464 - 2477","doi":"10.1105/tpc.15.00569","year":"2016","publication_status":"published","abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"publisher":"American Society of Plant Biologists","date_published":"2016-10-01T00:00:00Z","title":"A model of differential growth guided apical hook formation in plants","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:40Z","citation":{"mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"date_created":"2018-12-11T11:50:26Z","type":"journal_article","_id":"1153","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"status":"public","month":"10","issue":"10","language":[{"iso":"eng"}],"volume":28,"project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"quality_controlled":"1","oa_version":"Submitted Version","author":[{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"full_name":"Gallemí, Marçal","last_name":"Gallemí","first_name":"Marçal"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"first_name":"Richard","last_name":"Smith","full_name":"Smith, Richard"},{"full_name":"Inze, Dirk","first_name":"Dirk","last_name":"Inze"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Przemysław","last_name":"Prusinkiewicz","full_name":"Prusinkiewicz, Przemysław"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}]},{"oa":1,"acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","year":"2016","doi":"10.1038/srep36440","day":"07","scopus_import":1,"publist_id":"6204","intvolume":" 6","publication":"Scientific Reports","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"date_updated":"2021-01-12T06:48:41Z","citation":{"mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol. 6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","ieee":"J. Schwarz et al., “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep36440","chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 2016;6. doi:10.1038/srep36440","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"ddc":["579"],"publisher":"Nature Publishing Group","file_date_updated":"2018-12-12T10:09:32Z","date_published":"2016-11-07T00:00:00Z","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","date_created":"2018-12-11T11:50:27Z","_id":"1154","type":"journal_article","status":"public","pubrep_id":"744","ec_funded":1,"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"},{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz"},{"full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika","last_name":"Bierbaum"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"first_name":"Tino","last_name":"Frank","full_name":"Frank, Tino"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"},{"full_name":"Tay, Savaş","last_name":"Tay","first_name":"Savaş"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Mehling","orcid":"0000-0001-8599-1226","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","full_name":"Mehling, Matthias"}],"month":"11","has_accepted_license":"1","article_number":"36440","file":[{"file_name":"IST-2017-744-v1+1_srep36440.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:09:32Z","date_updated":"2018-12-12T10:09:32Z","file_id":"4756","creator":"system","access_level":"open_access","file_size":2353456,"relation":"main_file"}],"language":[{"iso":"eng"}],"volume":6},{"scopus_import":1,"publication":"Annals of Applied Probability","intvolume":" 26","publist_id":"6201","oa":1,"doi":"10.1214/16-AAP1193","day":"15","page":"3786 - 3839","year":"2016","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","abstract":[{"text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.","lang":"eng"}],"publication_status":"published","title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","date_published":"2016-12-15T00:00:00Z","publisher":"Institute of Mathematical Statistics","citation":{"apa":"Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 2016;26(6):3786-3839. doi:10.1214/16-AAP1193","ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” Annals of Applied Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:10.1214/16-AAP1193."},"date_updated":"2021-01-12T06:48:43Z","department":[{"_id":"LaEr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"_id":"1157","type":"journal_article","date_created":"2018-12-11T11:50:27Z","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.4979"}],"issue":"6","month":"12","volume":26,"language":[{"iso":"eng"}],"oa_version":"Preprint","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"first_name":"Ji","last_name":"Lee","full_name":"Lee, Ji"},{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}]},{"publication_status":"published","abstract":[{"text":"We present new results from the widest narrow-band survey search for Lyα emitters at z = 5.7, just after reionization. We survey a total of 7 deg2 spread over the COSMOS, UDS and SA22 fields. We find over 11 000 line emitters, out of which 514 are robust Lyα candidates at z = 5.7 within a volume of 6.3 × 106 Mpc3. Our Lyα emitters span a wide range in Lyα luminosities, from faint to bright (LLyα ∼ 1042.5–44 erg s−1) and rest-frame equivalent widths (EW0 ∼ 25–1000 Å) in a single, homogeneous data set. By combining all our fields, we find that the faint end slope of the z = 5.7 Lyα luminosity function is very steep, with α=−2.3+0.4−0.3. We also present an updated z = 6.6 Lyα luminosity function, based on comparable volumes and obtained with the same methods, which we directly compare with that at z = 5.7. We find a significant decline of the number density of faint Lyα emitters from z = 5.7 to 6.6 (by 0.5 ± 0.1 dex), but no evolution at the bright end/no evolution in L*. Faint Lyα emitters at z = 6.6 show much more extended haloes than those at z = 5.7, suggesting that neutral Hydrogen plays an important role, increasing the scattering and leading to observations missing faint Lyα emission within the epoch of reionization. Altogether, our results suggest that we are observing patchy reionization which happens first around the brightest Lyα emitters, allowing the number densities of those sources to remain unaffected by the increase of neutral Hydrogen fraction from z ∼ 5 to 7.","lang":"eng"}],"title":"The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization","publisher":"Oxford University Press","date_published":"2016-12-01T00:00:00Z","citation":{"ama":"Santos S, Sobral D, Matthee JJ. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. Monthly Notices of the Royal Astronomical Society. 2016;463(2):1678-1691. doi:10.1093/mnras/stw2076","ista":"Santos S, Sobral D, Matthee JJ. 2016. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. Monthly Notices of the Royal Astronomical Society. 463(2), 1678–1691.","chicago":"Santos, Sérgio, David Sobral, and Jorryt J Matthee. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw2076.","apa":"Santos, S., Sobral, D., & Matthee, J. J. (2016). The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2076","ieee":"S. Santos, D. Sobral, and J. J. Matthee, “The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization,” Monthly Notices of the Royal Astronomical Society, vol. 463, no. 2. Oxford University Press, pp. 1678–1691, 2016.","mla":"Santos, Sérgio, et al. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” Monthly Notices of the Royal Astronomical Society, vol. 463, no. 2, Oxford University Press, 2016, pp. 1678–91, doi:10.1093/mnras/stw2076.","short":"S. Santos, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 463 (2016) 1678–1691."},"extern":"1","date_updated":"2022-08-19T08:09:54Z","external_id":{"arxiv":["1606.07435"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift","galaxies: luminosity function","mass function","cosmology: observations","dark ages","reionization","first stars"],"publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"intvolume":" 463","oa":1,"day":"01","page":"1678-1691","doi":"10.1093/mnras/stw2076","year":"2016","acknowledgement":"We thank the anonymous referee for useful and constructive comments and suggestions which greatly improved the quality and clarity of our work. The authors acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. SS and DS acknowledge funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). SS also acknowledges support from FCT through the research grants UID/FIS/04434/2013 and PTDC/FIS-AST/2194/2012. JM acknowledges a Huygens PhD fellowship from Leiden University. Based on observations with the Subaru Telescope (Program IDs: S05B-027, S06A-025, S06B-010, S07A-013, S07B-008, S08B-008, S09A-017, S14A-086). Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. We are grateful to the CFHTLS, COSMOS-UltraVISTA, UKIDSS, SXDF and COSMOS survey teams. Without these legacy surveys, this research would have been impossible. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Mauna Kea has always had within the indigenous Hawaiian community. We are most fortunate to have the opportunity to conduct and explore observations from this mountain. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY, PYFITS, MATPLOTLIB, SCIPY and ASTROPY (Astropy Collaboration et al.","issue":"2","month":"12","volume":463,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","author":[{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"}],"article_type":"original","type":"journal_article","_id":"11574","date_created":"2022-07-13T10:08:20Z","status":"public","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07435"}]},{"author":[{"full_name":"Lagos, Claudia del P.","last_name":"Lagos","first_name":"Claudia del P."},{"last_name":"Theuns","first_name":"Tom","full_name":"Theuns, Tom"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"},{"full_name":"Furlong, Michelle","last_name":"Furlong","first_name":"Michelle"},{"first_name":"Richard G.","last_name":"Bower","full_name":"Bower, Richard G."},{"last_name":"Schaller","first_name":"Matthieu","full_name":"Schaller, Matthieu"},{"full_name":"Crain, Robert A.","last_name":"Crain","first_name":"Robert A."},{"full_name":"Trayford, James W.","last_name":"Trayford","first_name":"James W."},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"}],"oa_version":"Preprint","quality_controlled":"1","article_processing_charge":"No","volume":459,"language":[{"iso":"eng"}],"issue":"3","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1510.08067","open_access":"1"}],"status":"public","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"_id":"11575","type":"journal_article","article_type":"original","date_created":"2022-07-13T10:21:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1510.08067"]},"citation":{"ama":"Lagos C del P, Theuns T, Schaye J, et al. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal Astronomical Society. 2016;459(3):2632-2650. doi:10.1093/mnras/stw717","ista":"Lagos C del P, Theuns T, Schaye J, Furlong M, Bower RG, Schaller M, Crain RA, Trayford JW, Matthee JJ. 2016. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal Astronomical Society. 459(3), 2632–2650.","chicago":"Lagos, Claudia del P., Tom Theuns, Joop Schaye, Michelle Furlong, Richard G. Bower, Matthieu Schaller, Robert A. Crain, James W. Trayford, and Jorryt J Matthee. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw717.","apa":"Lagos, C. del P., Theuns, T., Schaye, J., Furlong, M., Bower, R. G., Schaller, M., … Matthee, J. J. (2016). The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw717","ieee":"C. del P. Lagos et al., “The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations,” Monthly Notices of the Royal Astronomical Society, vol. 459, no. 3. Oxford University Press, pp. 2632–2650, 2016.","mla":"Lagos, Claudia del P., et al. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” Monthly Notices of the Royal Astronomical Society, vol. 459, no. 3, Oxford University Press, 2016, pp. 2632–50, doi:10.1093/mnras/stw717.","short":"C. del P. Lagos, T. Theuns, J. Schaye, M. Furlong, R.G. Bower, M. Schaller, R.A. Crain, J.W. Trayford, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 459 (2016) 2632–2650."},"date_updated":"2022-08-19T08:12:07Z","extern":"1","title":"The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations","date_published":"2016-07-01T00:00:00Z","publisher":"Oxford University Press","abstract":[{"text":"We investigate correlations between different physical properties of star-forming galaxies in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE) cosmological hydrodynamical simulation suite over the redshift range 0 ≤ z ≤ 4.5. A principal component analysis reveals that neutral gas fraction (fgas,neutral), stellar mass (Mstellar) and star formation rate (SFR) account for most of the variance seen in the population, with galaxies tracing a two-dimensional, nearly flat, surface in the three-dimensional space of fgas, neutral–Mstellar–SFR with little scatter. The location of this plane varies little with redshift, whereas galaxies themselves move along the plane as their fgas, neutral and SFR drop with redshift. The positions of galaxies along the plane are highly correlated with gas metallicity. The metallicity can therefore be robustly predicted from fgas, neutral, or from the Mstellar and SFR. We argue that the appearance of this ‘Fundamental Plane of star formation’ is a consequence of self-regulation, with the plane's curvature set by the dependence of the SFR on gas density and metallicity. We analyse a large compilation of observations spanning the redshift range 0 ≲ z ≲ 3, and find that such a plane is also present in the data. The properties of the observed Fundamental Plane of star formation are in good agreement with EAGLE's predictions.","lang":"eng"}],"publication_status":"published","year":"2016","doi":"10.1093/mnras/stw717","day":"01","page":"2632-2650","acknowledgement":"We thank Luca Cortese, Matt Bothwell, Paola Santini and Tim Davis for providing observational data sets, and Aaron Robotham, Luca Cortese and Barbara Catinella for useful discussions. CdPL is funded by a Discovery Early Career Researcher Award (DE150100618). CdPL also thanks the MERAC Foundation for a Postdoctoral Research Award. This work used the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure. Support was also received via the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office ([AP P7/08 CHARM]), the National Science Foundation under grant no. NSF PHY11-25915, and the UK Science and Technology Facilities Council (grant numbers ST/F001166/1 and ST/I000976/1) via rolling and consolidating grants awarded to the ICC. The research was supported in part by the European Research Council under the European Union‘s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 278594-GasAroundGalaxies.","oa":1,"publication":"Monthly Notices of the Royal Astronomical Society","intvolume":" 459","arxiv":1,"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics stars: formation","ISM: evolution","galaxies: evolution","galaxies: formation","galaxies: ISM"]},{"date_created":"2022-07-13T12:50:36Z","article_type":"original","type":"journal_article","_id":"11576","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"main_file_link":[{"url":"https://arxiv.org/abs/1601.02266","open_access":"1"}],"status":"public","month":"04","issue":"2","language":[{"iso":"eng"}],"volume":457,"article_processing_charge":"No","quality_controlled":"1","oa_version":"Preprint","author":[{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"last_name":"Kohn","first_name":"Saul A.","full_name":"Kohn, Saul A."},{"full_name":"Best, Philip N.","last_name":"Best","first_name":"Philip N."},{"last_name":"Smail","first_name":"Ian","full_name":"Smail, Ian"},{"full_name":"Harrison, Chris M.","last_name":"Harrison","first_name":"Chris M."},{"last_name":"Stott","first_name":"John","full_name":"Stott, John"},{"last_name":"Calhau","first_name":"João","full_name":"Calhau, João"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations"],"scopus_import":"1","arxiv":1,"intvolume":" 457","publication":"Monthly Notices of the Royal Astronomical Society","oa":1,"acknowledgement":"The authors would like to thank the anonymous reviewer for the many helpful comments and suggestions which greatly improved the clarity and quality of this work. DS and SAK acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEst-OE/FIS/UI2751/2014. Part of this project was undertaken during the inaugural Leiden/ESA Astrophysics Program for Summer Students (LEAPS). IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. CH acknowledges support from STFC. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 087.A-0337 and ID 089.A-0965. Also based on data from the Telescopio Nazionale Galileo, with time awarded through OPTICON programmes 2011A/026 and 2012A020 and the William Herschel Telescope under programme W12BN007. The William Herschel Telescope is operated on the island of La Palma by the Isaac Newton Group in the Spanish\r\nObservatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. The authors wish to thank all the help given by the telescope staff from all the observatories used in this study: ESO staff in La Silla, and the TNG and WHT staff in La Palma. This publication makes use of data products from the Two Micron All-Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation.","doi":"10.1093/mnras/stw022","page":"1739-1752","year":"2016","day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"We use new near-infrared spectroscopic observations to investigate the nature and evolution of the most luminous Hα emitters at z ∼ 0.8–2.23, which evolve strongly in number density over this period, and compare them to more typical Hα emitters. We study 59 luminous Hα emitters with LHα > L∗Hα, roughly equally split per redshift slice at z ∼ 0.8, 1.47 and 2.23 from the HiZELS and CF-HiZELS surveys. We find that, overall, 30 ± 8 per cent are active galactic nuclei [AGNs; 80 ± 30 per cent of these AGNs are broad-line AGNs, BL-AGNs], and we find little to no evolution in the AGN fraction with redshift, within the errors. However, the AGN fraction increases strongly with Hα luminosity and correlates best with LHα/L∗Hα(z). While LHα ≤ L∗Hα(z) Hα emitters are largely dominated by star-forming galaxies (>80 per cent), the most luminous Hα emitters (LHα>10L∗Hα(z)) at any cosmic time are essentially all BL-AGN. Using our AGN-decontaminated sample of luminous star-forming galaxies, and integrating down to a fixed Hα luminosity, we find a factor of ∼1300 evolution in the star formation rate density from z = 0 to 2.23. This is much stronger than the evolution from typical Hα star-forming galaxies and in line with the evolution seen for constant luminosity cuts used to select ‘ultraluminous’ infrared galaxies and/or sub-millimetre galaxies. By taking into account the evolution in the typical Hα luminosity, we show that the most strongly star-forming Hα-selected galaxies at any epoch (LHα>L∗Hα(z)) contribute the same fractional amount of ≈15 per cent to the total star formation rate density, at least up to z = 2.23."}],"date_published":"2016-04-01T00:00:00Z","publisher":"Oxford University Press","title":"The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies","extern":"1","date_updated":"2022-08-19T08:15:21Z","citation":{"short":"D. Sobral, S.A. Kohn, P.N. Best, I. Smail, C.M. Harrison, J. Stott, J. Calhau, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 457 (2016) 1739–1752.","mla":"Sobral, David, et al. “The Most Luminous H α Emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and Star-Forming Galaxies.” Monthly Notices of the Royal Astronomical Society, vol. 457, no. 2, Oxford University Press, 2016, pp. 1739–52, doi:10.1093/mnras/stw022.","apa":"Sobral, D., Kohn, S. A., Best, P. N., Smail, I., Harrison, C. M., Stott, J., … Matthee, J. J. (2016). The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw022","ista":"Sobral D, Kohn SA, Best PN, Smail I, Harrison CM, Stott J, Calhau J, Matthee JJ. 2016. The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical Society. 457(2), 1739–1752.","chicago":"Sobral, David, Saul A. Kohn, Philip N. Best, Ian Smail, Chris M. Harrison, John Stott, João Calhau, and Jorryt J Matthee. “The Most Luminous H α Emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and Star-Forming Galaxies.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw022.","ama":"Sobral D, Kohn SA, Best PN, et al. The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical Society. 2016;457(2):1739-1752. doi:10.1093/mnras/stw022","ieee":"D. Sobral et al., “The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies,” Monthly Notices of the Royal Astronomical Society, vol. 457, no. 2. Oxford University Press, pp. 1739–1752, 2016."},"external_id":{"arxiv":["1601.02266"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","abstract":[{"text":"We present the first results from our CAlibrating LYMan α with Hα (CALYMHA) pilot survey at the Isaac Newton Telescope. We measure Lyα emission for 488 Hα selected galaxies at z = 2.23 from High-z Emission Line Survey in the COSMOS and UDS fields with a specially designed narrow-band filter (λc = 3918 Å, Δλ = 52 Å). We find 17 dual Hα-Lyα emitters [fLyα > 5 × 10−17 erg s−1 cm−2, of which five are X-ray active galactic nuclei (AGN)]. For star-forming galaxies, we find a range of Lyα escape fractions (fesc, measured with 3 arcsec apertures) from 2 to 30 per cent. These galaxies have masses from 3 × 108 M⊙ to 1011 M⊙ and dust attenuations E(B − V) = 0–0.5. Using stacking, we measure a median escape fraction of 1.6 ± 0.5 per cent (4.0 ± 1.0 per cent without correcting Hα for dust), but show that this depends on galaxy properties. The stacked fesc tends to decrease with increasing star formation rate and dust attenuation. However, at the highest masses and dust attenuations, we detect individual galaxies with fesc much higher than the typical values from stacking, indicating significant scatter in the values of fesc. Relations between fesc and UV slope are bimodal, with high fesc for either the bluest or reddest galaxies. We speculate that this bimodality and large scatter in the values of fesc is due to additional physical mechanisms such as outflows facilitating fesc for dusty/massive systems. Lyα is significantly more extended than Hα and the UV. fesc continues to increase up to at least 20 kpc (3σ, 40 kpc [2σ]) for typical star-forming galaxies and thus the aperture is the most important predictor of fesc.","lang":"eng"}],"title":"The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23","date_published":"2016-05-01T00:00:00Z","publisher":"Oxford University Press","citation":{"short":"J.J. Matthee, D. Sobral, I. Oteo, P. Best, I. Smail, H. Röttgering, A. Paulino-Afonso, Monthly Notices of the Royal Astronomical Society 458 (2016) 449–467.","mla":"Matthee, Jorryt J., et al. “The CALYMHA Survey: Lyα Escape Fraction and Its Dependence on Galaxy Properties at z = 2.23.” Monthly Notices of the Royal Astronomical Society, vol. 458, no. 1, Oxford University Press, 2016, pp. 449–67, doi:10.1093/mnras/stw322.","apa":"Matthee, J. J., Sobral, D., Oteo, I., Best, P., Smail, I., Röttgering, H., & Paulino-Afonso, A. (2016). The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw322","ama":"Matthee JJ, Sobral D, Oteo I, et al. The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. Monthly Notices of the Royal Astronomical Society. 2016;458(1):449-467. doi:10.1093/mnras/stw322","chicago":"Matthee, Jorryt J, David Sobral, Iván Oteo, Philip Best, Ian Smail, Huub Röttgering, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Escape Fraction and Its Dependence on Galaxy Properties at z = 2.23.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw322.","ista":"Matthee JJ, Sobral D, Oteo I, Best P, Smail I, Röttgering H, Paulino-Afonso A. 2016. The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23. Monthly Notices of the Royal Astronomical Society. 458(1), 449–467.","ieee":"J. J. Matthee et al., “The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties at z = 2.23,” Monthly Notices of the Royal Astronomical Society, vol. 458, no. 1. Oxford University Press, pp. 449–467, 2016."},"extern":"1","date_updated":"2022-08-19T08:17:19Z","external_id":{"arxiv":["1602.02756"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM"],"scopus_import":"1","publication":"Monthly Notices of the Royal Astronomical Society","arxiv":1,"intvolume":" 458","oa":1,"page":"449-467","year":"2016","doi":"10.1093/mnras/stw322","day":"01","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions which have improved the quality of this work. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS and JM acknowledge financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, and DS from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEst-OE/FIS/UI2751/2014. IO acknowledges support from the European Research Council (ERC) in the form of Advanced Investigator Programme, COSMICISM, 321302. HR acknowledges support from the ERC Advanced Investigator programme NewClusters 321271. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. APA acknowledges support from the Fundac¸ao para a Ciencia e para a Tecnologia (FCT) through the Fellowship SFRH/BD/52706/2014.\r\nBased on observations made with the Isaac Newton Telescope (proposals 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118) operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrof´ısica de Canarias. We acknowledge the tremendous work that has been done by both COSMOS and UKIDSS UDS/SXDF teams in assembling such large, state-ofthe-art multi-wavelength data sets over such wide areas, as those have been crucial for the results presented in this paper. The sample of HAEs is publicly available from Sobral et al. (2013).\r\nWe have benefited greatly from the publically available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the imaging tools SEXTRACTOR, SWARP and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010) and the TOPCAT analysis program (Taylor 2005).","issue":"1","month":"05","volume":458,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","author":[{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J"},{"full_name":"Sobral, David","first_name":"David","last_name":"Sobral"},{"full_name":"Oteo, Iván","first_name":"Iván","last_name":"Oteo"},{"last_name":"Best","first_name":"Philip","full_name":"Best, Philip"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"full_name":"Röttgering, Huub","first_name":"Huub","last_name":"Röttgering"},{"last_name":"Paulino-Afonso","first_name":"Ana","full_name":"Paulino-Afonso, Ana"}],"article_type":"original","type":"journal_article","_id":"11578","date_created":"2022-07-14T08:51:37Z","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1602.02756","open_access":"1"}]},{"intvolume":" 14","publist_id":"6200","publication":"PLoS Biology","related_material":{"record":[{"relation":"research_data","id":"9862","status":"public"},{"relation":"research_data","id":"9863","status":"public"}]},"scopus_import":1,"acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","day":"27","doi":"10.1371/journal.pbio.2000234","year":"2016","oa":1,"file_date_updated":"2020-07-14T12:44:36Z","date_published":"2016-12-27T00:00:00Z","publisher":"Public Library of Science","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","abstract":[{"text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.","lang":"eng"}],"publication_status":"published","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T14:11:16Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234"},"pubrep_id":"742","status":"public","date_created":"2018-12-11T11:50:28Z","_id":"1158","type":"journal_article","language":[{"iso":"eng"}],"volume":14,"has_accepted_license":"1","month":"12","issue":"12","article_number":"e2000234","file":[{"relation":"main_file","file_size":2494348,"access_level":"open_access","creator":"system","checksum":"2bab63b068a9840efd532b9ae583f9bb","file_id":"5164","date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-12T10:15:42Z","content_type":"application/pdf","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf"}],"author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"quality_controlled":"1","oa_version":"Published Version"},{"citation":{"mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801, Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36","ista":"Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 468–481."},"department":[{"_id":"UlWa"}],"date_updated":"2023-02-23T10:05:57Z","alternative_title":["LNCS"],"external_id":{"arxiv":["1608.08662"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing."}],"title":"Hanani-Tutte for radial planarity II","publisher":"Springer","date_published":"2016-12-08T00:00:00Z","oa":1,"day":"08","page":"468 - 481","doi":"10.1007/978-3-319-50106-2_36","year":"2016","scopus_import":1,"related_material":{"record":[{"relation":"later_version","id":"1113","status":"public"},{"status":"public","relation":"earlier_version","id":"1595"}]},"arxiv":1,"publist_id":"6193","intvolume":" 9801","oa_version":"Preprint","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"},{"full_name":"Pelsmajer, Michael","last_name":"Pelsmajer","first_name":"Michael"},{"full_name":"Schaefer, Marcus","first_name":"Marcus","last_name":"Schaefer"}],"month":"12","volume":9801,"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"conference","_id":"1164","date_created":"2018-12-11T11:50:29Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08662"}],"status":"public","conference":{"start_date":"2016-09-19","end_date":"2016-09-21","name":"GD: Graph Drawing and Network Visualization","location":"Athens, Greece"},"ec_funded":1},{"conference":{"end_date":"2016-09-21","start_date":"2016-09-19","name":"GD: Graph Drawing and Network Visualization","location":"Athens, Greece"},"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"status":"public","date_created":"2018-12-11T11:50:30Z","type":"conference","_id":"1165","language":[{"iso":"eng"}],"volume":"9801 ","month":"12","author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Preprint","publist_id":"6192","scopus_import":1,"related_material":{"record":[{"status":"public","id":"794","relation":"later_version"}]},"acknowledgement":"R. Fulek—The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions that helped to improve the presentation of the result.","doi":"10.1007/978-3-319-50106-2_8","day":"08","year":"2016","page":"94 - 106","oa":1,"publisher":"Springer","date_published":"2016-12-08T00:00:00Z","title":"C-planarity of embedded cyclic c-graphs","publication_status":"published","abstract":[{"lang":"eng","text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle."}],"alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"date_updated":"2023-09-27T12:14:48Z","citation":{"ama":"Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer; 2016:94-106. doi:10.1007/978-3-319-50106-2_8","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106.","apa":"Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp. 94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","mla":"Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801, Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8."}},{"file_date_updated":"2020-07-14T12:44:37Z","date_published":"2016-12-09T00:00:00Z","publisher":"Public Library of Science","title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","publication_status":"published","abstract":[{"text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K > 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task.","lang":"eng"}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"AnKi"}],"date_updated":"2023-02-23T14:11:22Z","citation":{"ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” PLoS Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.","ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218","ista":"Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 12(12), e1005218.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218.","apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218","mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016)."},"publist_id":"6190","intvolume":" 12","publication":"PLoS Computational Biology","scopus_import":"1","related_material":{"record":[{"status":"public","id":"9866","relation":"research_data"}]},"acknowledgement":"MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107. BW was supported by the Scottish Government/Royal Society of Edinburgh Personal Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading the manuscript.","doi":"10.1371/journal.pcbi.1005218","day":"09","year":"2016","oa":1,"language":[{"iso":"eng"}],"volume":12,"article_processing_charge":"No","month":"12","has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:12:08Z","date_updated":"2020-07-14T12:44:37Z","content_type":"application/pdf","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","relation":"main_file","access_level":"open_access","file_size":3822299,"checksum":"84f44ae92866c52ff1ca8a574558dca7","file_id":"4926","creator":"system"}],"article_number":"e1005218","issue":"12","author":[{"first_name":"Marcin P","last_name":"Zagórski","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej","last_name":"Wacław"}],"quality_controlled":"1","oa_version":"Published Version","pubrep_id":"740","status":"public","date_created":"2018-12-11T11:50:30Z","type":"journal_article","_id":"1167"},{"oa":1,"doi":"10.1038/srep38840","year":"2016","day":"19","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","scopus_import":1,"publication":"Scientific Reports","intvolume":" 6","publist_id":"6183","citation":{"short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."},"date_updated":"2021-01-12T06:48:50Z","department":[{"_id":"NiBa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["576"],"abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"publication_status":"published","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","date_published":"2016-12-19T00:00:00Z","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","_id":"1172","date_created":"2018-12-11T11:50:32Z","status":"public","pubrep_id":"737","oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barma","first_name":"Mustansir","full_name":"Barma, Mustansir"},{"full_name":"Rao, Madan","first_name":"Madan","last_name":"Rao"}],"file":[{"file_name":"IST-2017-737-v1+1_srep38840.pdf","date_created":"2018-12-12T10:12:56Z","date_updated":"2020-07-14T12:44:37Z","content_type":"application/pdf","access_level":"open_access","file_size":760967,"file_id":"4977","checksum":"cb378732da885ea4959ec5b845fb6e52","creator":"system","relation":"main_file"}],"article_number":"38840","month":"12","has_accepted_license":"1","volume":6,"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"date_published":"2016-04-01T00:00:00Z","publisher":"Springer","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","volume":74,"month":"04","publication_status":"published","abstract":[{"text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.","lang":"eng"}],"issue":"4","author":[{"first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Chatterjee, Sanjit","first_name":"Sanjit","last_name":"Chatterjee"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"quality_controlled":"1","date_updated":"2021-01-12T06:48:52Z","citation":{"ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-9997-6.","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362. doi:10.1007/s00453-015-9997-6","apa":"Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-9997-6","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.","short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362."},"oa_version":"Submitted Version","publist_id":"6177","intvolume":" 74","publication":"Algorithmica","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","doi":"10.1007/s00453-015-9997-6","status":"public","day":"01","year":"2016","main_file_link":[{"url":"http://eprint.iacr.org/2013/651","open_access":"1"}],"page":"1321 - 1362","date_created":"2018-12-11T11:50:33Z","oa":1,"_id":"1177","type":"journal_article"},{"alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:48:53Z","citation":{"ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","apa":"Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203, doi:10.1007/978-3-662-53641-4_8.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203."},"date_published":"2016-10-22T00:00:00Z","publisher":"Springer","title":"Pseudoentropy: Lower-bounds for chain rules and transformations","publication_status":"published","abstract":[{"text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.","lang":"eng"}],"acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","page":"183 - 203","doi":"10.1007/978-3-662-53641-4_8","year":"2016","day":"22","oa":1,"publist_id":"6175","intvolume":" 9985","scopus_import":1,"author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"full_name":"Maciej, Skorski","first_name":"Skorski","last_name":"Maciej"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"volume":9985,"month":"10","main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"status":"public","date_created":"2018-12-11T11:50:34Z","type":"conference","_id":"1179","conference":{"location":"Beijing, China","name":"TCC: Theory of Cryptography Conference","end_date":"2016-11-03","start_date":"2016-10-31"},"ec_funded":1},{"title":"Are lock free concurrent algorithms practically wait free ","publisher":"ACM","date_published":"2016-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. Although obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most nonblocking commercial code is only lock-free. This article suggests a simple solution to this problem.We show that for a large class of lock-free algorithms, under scheduling conditions that approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can continue to design simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes to the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1 but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst-case adversary, in a stochastic model capturing their expected asymptotic behavior."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1311.3200"]},"citation":{"ieee":"D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent algorithms practically wait free ,” Journal of the ACM, vol. 63, no. 4. ACM, 2016.","ama":"Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms practically wait free . Journal of the ACM. 2016;63(4). doi:10.1145/2903136","chicago":"Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free Concurrent Algorithms Practically Wait Free .” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2903136.","ista":"Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms practically wait free . Journal of the ACM. 63(4).","apa":"Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2016). Are lock free concurrent algorithms practically wait free . Journal of the ACM. ACM. https://doi.org/10.1145/2903136","mla":"Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically Wait Free .” Journal of the ACM, vol. 63, no. 4, ACM, 2016, doi:10.1145/2903136.","short":"D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016)."},"date_updated":"2023-02-23T13:19:04Z","extern":"1","publication":"Journal of the ACM","intvolume":" 63","arxiv":1,"publist_id":"6870","year":"2016","doi":"10.1145/2903136","day":"01","acknowledgement":"Part of this work was performed while the first author was a postdoctoral associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations. The second author was supported in part by ISF grant 1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926, IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923, and by equipment grants from Intel Corporation.","oa":1,"article_processing_charge":"No","volume":63,"language":[{"iso":"eng"}],"issue":"4","month":"09","author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Censor Hillel, Keren","first_name":"Keren","last_name":"Censor Hillel"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"oa_version":"Preprint","quality_controlled":"1","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3200"}],"_id":"786","type":"journal_article","date_created":"2018-12-11T11:48:29Z"},{"month":"04","has_accepted_license":"1","file":[{"content_type":"application/pdf","date_created":"2020-07-09T09:57:04Z","date_updated":"2020-07-14T12:48:08Z","file_name":"2016_Neuron_Barron.pdf","relation":"main_file","checksum":"9ce7a1c64986dce0435c070285a7ef9b","file_id":"8104","creator":"cziletti","access_level":"open_access","file_size":5334136}],"issue":"1","language":[{"iso":"eng"}],"volume":90,"article_processing_charge":"No","quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Barron, H.C.","first_name":"H.C.","last_name":"Barron"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181"},{"full_name":"Emir, U.E.","first_name":"U.E.","last_name":"Emir"},{"full_name":"Makin, T.R.","last_name":"Makin","first_name":"T.R."},{"last_name":"O’Shea","first_name":"J.","full_name":"O’Shea, J."},{"full_name":"Clare, S.","last_name":"Clare","first_name":"S."},{"full_name":"Jbabdi, S.","last_name":"Jbabdi","first_name":"S."},{"last_name":"Dolan","first_name":"R.J.","full_name":"Dolan, R.J."},{"first_name":"T.E.J.","last_name":"Behrens","full_name":"Behrens, T.E.J."}],"date_created":"2020-06-25T13:05:33Z","article_type":"original","_id":"8020","type":"journal_article","status":"public","publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Balance of cortical excitation and inhibition (EI) is thought to be disrupted in several neuropsychiatric conditions, yet it is not clear how it is maintained in the healthy human brain. When EI balance is disturbed during learning and memory in animal models, it can be restabilized via formation of inhibitory replicas of newly formed excitatory connections. Here we assess evidence for such selective inhibitory rebalancing in humans. Using fMRI repetition suppression we measure newly formed cortical associations in the human brain. We show that expression of these associations reduces over time despite persistence in behavior, consistent with inhibitory rebalancing. To test this, we modulated excitation/inhibition balance with transcranial direct current stimulation (tDCS). Using ultra-high-field (7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations to be re-expressed. This suggests that in humans associative memories are stored in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory connections are unmasked."}],"ddc":["570"],"pmid":1,"publisher":"Elsevier","date_published":"2016-04-06T00:00:00Z","file_date_updated":"2020-07-14T12:48:08Z","title":"Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories","extern":"1","date_updated":"2021-01-12T08:16:34Z","citation":{"short":"H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.","mla":"Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” Neuron, vol. 90, no. 1, Elsevier, 2016, pp. 191–203, doi:10.1016/j.neuron.2016.02.031.","ieee":"H. C. Barron et al., “Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories,” Neuron, vol. 90, no. 1. Elsevier, pp. 191–203, 2016.","apa":"Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare, S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.02.031","ista":"Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. Neuron. 90(1), 191–203.","ama":"Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories. Neuron. 2016;90(1):191-203. doi:10.1016/j.neuron.2016.02.031","chicago":"Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.” Neuron. Elsevier, 2016. https://doi.org/10.1016/j.neuron.2016.02.031."},"external_id":{"pmid":["26996082"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 90","publication":"Neuron","oa":1,"day":"06","page":"191-203","year":"2016","doi":"10.1016/j.neuron.2016.02.031"},{"author":[{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius"},{"full_name":"Hostettler, Rafael","last_name":"Hostettler","first_name":"Rafael"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"volume":28,"article_processing_charge":"No","language":[{"iso":"eng"}],"file":[{"file_name":"2016_ProcALIFE_Martius.pdf","content_type":"application/pdf","date_created":"2020-07-06T12:59:09Z","date_updated":"2020-07-14T12:48:09Z","file_id":"8096","checksum":"cff63e7a4b8ac466ba51a9c84153a940","creator":"cziletti","access_level":"open_access","file_size":678670,"relation":"main_file"}],"month":"09","has_accepted_license":"1","status":"public","publication_identifier":{"isbn":["9780262339360"]},"_id":"8094","type":"conference","date_created":"2020-07-05T22:00:47Z","conference":{"end_date":"2016-07-08","start_date":"2016-07-04","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","location":"Cancun, Mexico"},"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference 2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In Proceedings of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029."},"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2021-01-12T08:16:53Z","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","file_date_updated":"2020-07-14T12:48:09Z","date_published":"2016-09-01T00:00:00Z","publisher":"MIT Press","ddc":["610"],"publication_status":"published","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"day":"01","year":"2016","page":"142-143","doi":"10.7551/978-0-262-33936-0-ch029","oa":1,"publication":"Proceedings of the Artificial Life Conference 2016","intvolume":" 28","scopus_import":1}]