[{"citation":{"apa":"Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts, P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035","ieee":"D.-A. Alistarh et al., “A high-radix, low-latency optical switch for data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom, 2015, pp. 367–368.","ista":"Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special Interest Group on Data Communication, 367–368.","ama":"Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035","chicago":"Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","mla":"Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035."},"page":"367 - 368","quality_controlled":"1","doi":"10.1145/2785956.2790035","date_published":"2015-01-01T00:00:00Z","conference":{"location":"London, United Kindgdom","start_date":"2015-08-17","end_date":"2015-08-21","name":"SIGCOMM: Special Interest Group on Data Communication"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3542-3"]},"month":"01","day":"01","_id":"784","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","publication_status":"published","title":"A high-radix, low-latency optical switch for data centers","status":"public","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ballani, Hitesh","first_name":"Hitesh","last_name":"Ballani"},{"first_name":"Paolo","last_name":"Costa","full_name":"Costa, Paolo"},{"full_name":"Funnell, Adam","first_name":"Adam","last_name":"Funnell"},{"full_name":"Benjamin, Joshua","last_name":"Benjamin","first_name":"Joshua"},{"full_name":"Watts, Philip","last_name":"Watts","first_name":"Philip"},{"full_name":"Thomsen, Benn","first_name":"Benn","last_name":"Thomsen"}],"oa_version":"None","date_updated":"2023-02-23T13:18:57Z","date_created":"2018-12-11T11:48:29Z","type":"conference","publist_id":"6872","abstract":[{"text":"We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.","lang":"eng"}],"extern":"1"},{"pmid":1,"_id":"802","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","department":[{"_id":"CaHe"}],"intvolume":" 25","status":"public","publication_status":"published","title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5795-0133"},{"last_name":"Kruger","first_name":"Anke","full_name":"Kruger, Anke"},{"last_name":"Muller","first_name":"Christina","full_name":"Muller, Christina"},{"last_name":"Buettner","first_name":"Falk","full_name":"Buettner, Falk"},{"full_name":"Routier, Françoise","first_name":"Françoise","last_name":"Routier"}],"volume":25,"oa_version":"None","date_created":"2018-12-11T11:48:35Z","date_updated":"2021-01-12T08:16:33Z","type":"journal_article","publist_id":"6851","issue":"12","abstract":[{"text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.","lang":"eng"}],"external_id":{"pmid":["26306635"]},"citation":{"mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:10.1093/glycob/cwv059.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430. doi:10.1093/glycob/cwv059","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., & Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059"},"publication":"Glycobiology","page":"1423 - 1430","quality_controlled":"1","doi":"10.1093/glycob/cwv059","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"12"},{"publication":"Journal of Virology","external_id":{"pmid":["26223638"]},"citation":{"ieee":"F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20. ASM, pp. 10294–10302, 2015.","apa":"Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15","ista":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.","ama":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15","chicago":"Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology. ASM, 2015. https://doi.org/10.1128/JVI.01502-15.","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302.","mla":"Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15."},"quality_controlled":"1","page":"10294 - 10302","doi":"10.1128/JVI.01502-15","date_published":"2015-09-22T00:00:00Z","language":[{"iso":"eng"}],"month":"09","day":"22","_id":"815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","pmid":1,"publication_status":"published","status":"public","title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","publisher":"ASM","intvolume":" 89","author":[{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Schur, Florian"},{"full_name":"Dick, Robert","first_name":"Robert","last_name":"Dick"},{"last_name":"Hagen","first_name":"Wim","full_name":"Hagen, Wim"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"},{"last_name":"Briggs","first_name":"John","full_name":"Briggs, John"}],"date_updated":"2021-01-12T08:17:09Z","date_created":"2018-12-11T11:48:39Z","oa_version":"None","volume":89,"type":"journal_article","abstract":[{"text":"The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.\r\n","lang":"eng"}],"issue":"20","publist_id":"6837","extern":"1"},{"publication":"Nature","citation":{"ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508. doi:10.1038/nature13838","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., & Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838","ieee":"F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature Publishing Group, pp. 505–508, 2015.","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508.","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature13838."},"quality_controlled":0,"page":"505 - 508","date_published":"2015-01-22T00:00:00Z","doi":"10.1038/nature13838","day":"22","month":"01","_id":"814","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","year":"2015","status":"public","title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 517","author":[{"first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Florian Schur"},{"full_name":"Hagen, Wim J","last_name":"Hagen","first_name":"Wim"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"last_name":"Ruml","first_name":"Tomáš","full_name":"Ruml, Tomáš"},{"first_name":"B","last_name":"Müller","full_name":"Müller B"},{"full_name":"Kraüsslich, Hans Georg","last_name":"Kraüsslich","first_name":"Hans"},{"last_name":"Briggs","first_name":"John","full_name":"Briggs, John A"}],"date_created":"2018-12-11T11:48:39Z","date_updated":"2021-01-12T08:17:08Z","volume":517,"type":"journal_article","abstract":[{"lang":"eng","text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments."}],"issue":"7535","publist_id":"6836","extern":1},{"_id":"8242","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","publisher":"Elsevier","intvolume":" 135","author":[{"full_name":"Einhorn, Lukas","first_name":"Lukas","last_name":"Einhorn"},{"first_name":"Judit","last_name":"Fazekas","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas, Judit"},{"full_name":"Muhr, Martina","last_name":"Muhr","first_name":"Martina"},{"first_name":"Alexandra","last_name":"Schoos","full_name":"Schoos, Alexandra"},{"full_name":"Oida, Kumiko","first_name":"Kumiko","last_name":"Oida"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"last_name":"Panakova","first_name":"Lucia","full_name":"Panakova, Lucia"},{"first_name":"Krisztina","last_name":"Manzano-Szalai","full_name":"Manzano-Szalai, Krisztina"},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"}],"date_updated":"2021-01-12T08:17:42Z","date_created":"2020-08-10T11:54:09Z","volume":135,"oa_version":"None","article_number":"AB101","type":"journal_article","issue":"2","extern":"1","publication":"Journal of Allergy and Clinical Immunology","citation":{"mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.","short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101.","apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263","ieee":"L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” Journal of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015."},"article_type":"original","quality_controlled":"1","date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.jaci.2014.12.1263","language":[{"iso":"eng"}],"month":"02","day":"01","publication_identifier":{"issn":["0091-6749"]},"article_processing_charge":"No"},{"month":"04","day":"20","publication":"Bio-protocol","citation":{"ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8).","ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.","apa":"Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446","ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446","chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.","short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015)."},"quality_controlled":0,"doi":"10.21769/BioProtoc.1446","date_published":"2015-04-20T00:00:00Z","type":"journal_article","abstract":[{"text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis.","lang":"eng"}],"issue":"8","publist_id":"6816","extern":1,"_id":"832","year":"2015","acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","publication_status":"published","status":"public","title":"Real time analysis of lateral root organogenesis in arabidopsis","intvolume":" 5","publisher":"Bio-protocol LLC","author":[{"full_name":"Peter Marhavy","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"date_created":"2018-12-11T11:48:44Z","date_updated":"2021-01-12T08:18:07Z","volume":5},{"status":"public","publication_status":"published","title":"Observing the overall rocking motion of a protein in a crystal","publisher":"Springer Nature","intvolume":" 6","year":"2015","_id":"8456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:24Z","date_created":"2020-09-18T10:07:36Z","oa_version":"Published Version","volume":6,"author":[{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"full_name":"Xue, Yi","first_name":"Yi","last_name":"Xue"},{"full_name":"Coquelle, Nicolas","last_name":"Coquelle","first_name":"Nicolas"},{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Yuwen","first_name":"Tairan","full_name":"Yuwen, Tairan"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"full_name":"Mikhailovskii, Oleg","last_name":"Mikhailovskii","first_name":"Oleg"},{"full_name":"Willbold, Dieter","last_name":"Willbold","first_name":"Dieter"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"article_number":"8361","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments."}],"quality_controlled":"1","article_type":"original","publication":"Nature Communications","citation":{"ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms9361","ieee":"P. Ma et al., “Observing the overall rocking motion of a protein in a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015, doi:10.1038/ncomms9361.","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015)."},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9361","date_published":"2015-10-05T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"day":"05","month":"10","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No"},{"volume":4,"oa_version":"None","date_created":"2020-09-18T10:07:45Z","date_updated":"2021-01-12T08:19:24Z","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"publisher":"Wiley","intvolume":" 4","status":"public","title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","publication_status":"published","year":"2015","_id":"8457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"3","abstract":[{"text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1002/9780470034590.emrstm1418","date_published":"2015-09-10T00:00:00Z","page":"699-708","article_type":"original","quality_controlled":"1","citation":{"ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","apa":"Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418","chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015. https://doi.org/10.1002/9780470034590.emrstm1418.","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708."},"publication":"eMagRes","article_processing_charge":"No","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"month":"09","day":"10"},{"type":"journal_article","extern":"1","abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"issue":"2","publist_id":"6804","publication_status":"published","status":"public","title":"A model of substitution trajectories in sequence space and long-term protein evolution","intvolume":" 32","publisher":"Oxford University Press","_id":"848","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:33Z","date_created":"2018-12-11T11:48:49Z","volume":32,"oa_version":"None","author":[{"first_name":"Dinara","last_name":"Usmanova","full_name":"Usmanova, Dinara"},{"last_name":"Ferretti","first_name":"Luca","full_name":"Ferretti, Luca"},{"full_name":"Povolotskaya, Inna","first_name":"Inna","last_name":"Povolotskaya"},{"last_name":"Vlasov","first_name":"Peter","full_name":"Vlasov, Peter"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"day":"01","month":"02","quality_controlled":"1","page":"542 - 554","publication":"Molecular Biology and Evolution","citation":{"chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318.","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.","apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318"},"language":[{"iso":"eng"}],"date_published":"2015-02-01T00:00:00Z","doi":"10.1093/molbev/msu318"},{"doi":"10.1088/0951-7715/28/8/2699","date_published":"2015-06-30T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015. https://doi.org/10.1088/0951-7715/28/8/2699.","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015.","apa":"Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699"},"publication":"Nonlinearity","page":"2699-2720","quality_controlled":"1","article_type":"original","article_processing_charge":"No","publication_identifier":{"issn":["0951-7715","1361-6544"]},"day":"30","month":"06","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"author":[{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Zhang, K","first_name":"K","last_name":"Zhang"}],"volume":28,"oa_version":"None","date_updated":"2021-01-12T08:19:41Z","date_created":"2020-09-18T10:46:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8498","year":"2015","publisher":"IOP Publishing","intvolume":" 28","publication_status":"published","status":"public","title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","issue":"8","abstract":[{"lang":"eng","text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]."}],"extern":"1","type":"journal_article"},{"publication_identifier":{"issn":["1435-9855"]},"article_processing_charge":"No","month":"02","day":"05","citation":{"chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149.","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:10.4171/jems/499.","apa":"Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” Journal of the European Mathematical Society, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 2015;17(1):71-149. doi:10.4171/jems/499"},"publication":"Journal of the European Mathematical Society","page":"71-149","quality_controlled":"1","article_type":"original","date_published":"2015-02-05T00:00:00Z","doi":"10.4171/jems/499","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214","ieee":"J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214."},"publication":"Science Advances","date_published":"2015-05-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"day":"11","month":"05","date_published":"2015-05-11T00:00:00Z","doi":"10.1371/journal.pone.0125888","publication":"PLoS One","citation":{"ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888","ieee":"O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":0,"abstract":[{"text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.","lang":"eng"}],"issue":"5","publist_id":"6742","license":"https://creativecommons.org/licenses/by/4.0/","extern":1,"type":"journal_article","author":[{"last_name":"Arkhipova","first_name":"Oksana","full_name":"Arkhipova, Oksana V"},{"full_name":"Meer, Margarita V","last_name":"Meer","first_name":"Margarita"},{"last_name":"Mikoulinskaia","first_name":"Galina","full_name":"Mikoulinskaia, Galina V"},{"first_name":"Marina","last_name":"Zakharova","full_name":"Zakharova, Marina V"},{"first_name":"Alexander","last_name":"Galushko","full_name":"Galushko, Alexander S"},{"full_name":"Akimenko, Vasilii K","last_name":"Akimenko","first_name":"Vasilii"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"date_created":"2018-12-11T11:49:08Z","date_updated":"2021-01-12T08:21:48Z","volume":10,"_id":"906","year":"2015","acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","status":"public","publication_status":"published","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","publisher":"Public Library of Science","intvolume":" 10"},{"author":[{"last_name":"Lefauve","first_name":"Adrien","full_name":"Lefauve, Adrien"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"full_name":"Melet, Angélique","last_name":"Melet","first_name":"Angélique"}],"date_updated":"2022-01-24T13:45:41Z","date_created":"2021-02-15T14:21:49Z","volume":120,"year":"2015","publication_status":"published","publisher":"American Geophysical Union","extern":"1","doi":"10.1002/2014jc010598","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014JC010598"}],"quality_controlled":"1","month":"06","publication_identifier":{"issn":["2169-9275"]},"oa_version":"Published Version","_id":"9141","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"A three-dimensional map of tidal dissipation over abyssal hills","status":"public","intvolume":" 120","abstract":[{"lang":"eng","text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere."}],"issue":"7","type":"journal_article","date_published":"2015-06-08T00:00:00Z","publication":"Journal of Geophysical Research: Oceans","citation":{"ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","apa":"Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598."},"article_type":"original","page":"4760-4777","day":"08","article_processing_charge":"No"},{"file":[{"content_type":"application/pdf","file_size":7202224,"creator":"dernst","file_name":"2015_eLife_Sehring.pdf","access_level":"open_access","date_created":"2018-12-20T15:50:56Z","date_updated":"2020-07-14T12:48:15Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","relation":"main_file","file_id":"5769"}],"oa_version":"Published Version","_id":"928","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 4","ddc":["539","570"],"status":"public","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events."}],"type":"journal_article","date_published":"2015-10-21T00:00:00Z","citation":{"chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206.","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206","ieee":"I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206"},"publication":"eLife","has_accepted_license":"1","day":"21","author":[{"full_name":"Sehring, Ivonne","last_name":"Sehring","first_name":"Ivonne"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Denker","first_name":"Elsa","full_name":"Denker, Elsa"},{"full_name":"Kourakis, Matthew","last_name":"Kourakis","first_name":"Matthew"},{"last_name":"Mathiesen","first_name":"Birthe","full_name":"Mathiesen, Birthe"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"full_name":"Jiang, Di","last_name":"Jiang","first_name":"Di"}],"volume":4,"date_created":"2018-12-11T11:49:15Z","date_updated":"2021-01-12T08:21:58Z","year":"2015","publisher":"eLife Sciences Publications","publication_status":"published","publist_id":"6512","file_date_updated":"2020-07-14T12:48:15Z","extern":"1","article_number":"e09206","doi":"10.7554/eLife.09206","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"10"},{"abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 49","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","status":"public","_id":"9575","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2015-11-01T00:00:00Z","page":"181-187","article_type":"original","citation":{"chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027"},"publication":"Electronic Notes in Discrete Mathematics","extern":"1","volume":49,"date_created":"2021-06-21T06:40:34Z","date_updated":"2023-02-23T14:01:28Z","author":[{"full_name":"Krivelevich, Michael","last_name":"Krivelevich","first_name":"Michael"},{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"publisher":"Elsevier","publication_status":"published","year":"2015","publication_identifier":{"issn":["1571-0653"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1016/j.endm.2015.06.027","quality_controlled":"1","external_id":{"arxiv":["1501.04816"]},"main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"oa":1},{"doi":"10.1016/j.ijplas.2014.09.009","date_published":"2015-04-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009."},"publication":"International Journal of Plasticity","page":"1-25","article_type":"original","publication_identifier":{"issn":["0749-6419"]},"article_processing_charge":"No","month":"04","day":"01","scopus_import":"1","author":[{"first_name":"H.S.","last_name":"Leung","full_name":"Leung, H.S."},{"last_name":"Leung","first_name":"P.S.S.","full_name":"Leung, P.S.S."},{"full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"A.H.W.","last_name":"Ngan","full_name":"Ngan, A.H.W."}],"volume":67,"oa_version":"None","date_created":"2021-07-15T14:09:32Z","date_updated":"2023-02-23T14:04:28Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9673","year":"2015","intvolume":" 67","publisher":"Elsevier","status":"public","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","publication_status":"published","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}],"extern":"1","type":"journal_article"},{"article_number":"180102","extern":"1","year":"2015","publication_status":"published","publisher":"American Physical Society","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"date_created":"2021-07-19T10:07:22Z","date_updated":"2021-08-09T12:38:49Z","volume":92,"month":"11","publication_identifier":{"eissn":["1550-235X"],"issn":["1098-0121"]},"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1511.08668"]},"quality_controlled":"1","doi":"10.1103/physrevb.92.180102","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"issue":"18","_id":"9688","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Solid-liquid interfacial free energy out of equilibrium","intvolume":" 92","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Physical Review B - Condensed Matter and Materials Physics","citation":{"short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102","ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102."},"article_type":"original","date_published":"2015-11-01T00:00:00Z"},{"type":"research_data_reference","title":"Excel file containing the raw data for all figures","status":"public","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"_id":"9711","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:07:02Z","date_created":"2021-07-23T11:53:50Z","oa_version":"Published Version","author":[{"first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"full_name":"Guvenek, Aysegul","last_name":"Guvenek","first_name":"Aysegul"},{"full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal","last_name":"Ayhan"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1619"}]},"month":"11","day":"18","article_processing_charge":"No","citation":{"ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001","ieee":"G. Chevereau et al., “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, 10.1371/journal.pbio.1002299.s001.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","mla":"Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001."},"date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s001"},{"doi":"10.1111/1365-2656.12345","language":[{"iso":"eng"}],"external_id":{"pmid":["25646973"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"03","related_material":{"record":[{"id":"9720","status":"public","relation":"research_data"}]},"author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias"},{"full_name":"Caspar, Jesicca","last_name":"Caspar","first_name":"Jesicca"},{"last_name":"Theodorou","first_name":"Panagiotis","full_name":"Theodorou, Panagiotis"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"volume":84,"date_created":"2018-12-11T11:54:23Z","date_updated":"2023-02-23T14:06:09Z","pmid":1,"acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","year":"2015","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","publist_id":"5245","file_date_updated":"2020-07-14T12:45:19Z","date_published":"2015-03-03T00:00:00Z","citation":{"ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology. Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624."},"publication":"Journal of Animal Ecology","page":"615 - 624","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"03","scopus_import":"1","pubrep_id":"460","file":[{"creator":"system","content_type":"application/pdf","file_size":1823045,"access_level":"open_access","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","checksum":"542a0b9b07e78050a81b35f26f0b82da","date_created":"2018-12-12T10:18:29Z","date_updated":"2020-07-14T12:45:19Z","file_id":"5350","relation":"main_file"}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1855","intvolume":" 84","title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","ddc":["570"],"status":"public","issue":"3","abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"type":"journal_article"},{"ec_funded":1,"publist_id":"5273","date_updated":"2023-02-23T14:06:12Z","date_created":"2018-12-11T11:54:15Z","volume":370,"author":[{"last_name":"Theis","first_name":"Fabian","full_name":"Theis, Fabian"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"id":"9721","status":"public","relation":"research_data"}]},"publication_status":"published","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"year":"2015","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","pmid":1,"month":"05","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2014.0108","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"grant_number":"302004","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"},{"_id":"25E0E184-B435-11E9-9278-68D0E5697425","name":"Antnet"},{"_id":"25E24DB2-B435-11E9-9278-68D0E5697425","name":"Fellowship of Wissenschaftskolleg zu Berlin"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"external_id":{"pmid":["25870394"]},"oa":1,"abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"issue":"1669","type":"journal_article","oa_version":"Submitted Version","title":"Opposing effects of allogrooming on disease transmission in ant societies","status":"public","intvolume":" 370","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1830","day":"26","article_processing_charge":"No","scopus_import":"1","date_published":"2015-05-26T00:00:00Z","article_type":"original","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015, doi:10.1098/rstb.2014.0108.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2014.0108","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, The, 2015.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108"}},{"article_processing_charge":"No","day":"29","month":"12","doi":"10.5061/dryad.dj2bf","date_published":"2015-12-29T00:00:00Z","citation":{"mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"oa":1,"abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-07-26T09:38:36Z","date_updated":"2023-02-23T10:16:22Z","related_material":{"record":[{"id":"1830","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Theis","first_name":"Fabian","full_name":"Theis, Fabian"},{"full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"department":[{"_id":"SyCr"}],"publisher":"Dryad","status":"public","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","year":"2015","_id":"9721","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s001","citation":{"ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001."},"month":"03","day":"23","article_processing_charge":"No","author":[{"last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham E.","last_name":"Mayo","first_name":"Avraham E."},{"last_name":"Tlusty","first_name":"Tsvi","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"related_material":{"record":[{"id":"1827","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-02-23T10:16:13Z","date_created":"2021-07-26T08:35:23Z","oa_version":"Published Version","year":"2015","_id":"9718","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Supporting information text","status":"public","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","type":"research_data_reference"},{"type":"journal_article","abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}],"issue":"6","ddc":["000"],"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","status":"public","intvolume":" 10","_id":"1793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5150","relation":"main_file","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-12T10:15:30Z","checksum":"d20f26461ca575276ad3ed9ce4bfc787","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","access_level":"open_access","creator":"system","file_size":1850825,"content_type":"application/pdf"}],"pubrep_id":"454","scopus_import":1,"day":"01","has_accepted_license":"1","publication":"PLoS One","citation":{"mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015."},"date_published":"2015-06-01T00:00:00Z","article_number":"e0127657","file_date_updated":"2020-07-14T12:45:16Z","publist_id":"5318","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"year":"2015","date_updated":"2023-02-23T14:06:33Z","date_created":"2018-12-11T11:54:02Z","volume":10,"author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9737"}]},"month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0127657"},{"status":"public","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","publisher":"Public Library of Science","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"_id":"9737","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","date_created":"2021-07-28T06:20:13Z","date_updated":"2023-02-23T10:14:42Z","oa_version":"Published Version","author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1793"}]},"type":"research_data_reference","citation":{"ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001."},"doi":"10.1371/journal.pone.0127657.s001","date_published":"2015-06-01T00:00:00Z","month":"06","day":"01","article_processing_charge":"No"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5161","date_created":"2018-12-12T10:15:39Z","date_updated":"2020-07-14T12:45:17Z","checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","access_level":"open_access","file_size":1811647,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"452","intvolume":" 11","ddc":["576"],"status":"public","title":"Evolution of bow-tie architectures in biology","_id":"1827","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved."}],"type":"journal_article","date_published":"2015-03-23T00:00:00Z","citation":{"ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055."},"publication":"PLoS Computational Biology","has_accepted_license":"1","article_processing_charge":"No","day":"23","scopus_import":1,"volume":11,"date_updated":"2023-02-23T14:07:51Z","date_created":"2018-12-11T11:54:14Z","related_material":{"record":[{"id":"9718","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9773"}]},"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","year":"2015","ec_funded":1,"publist_id":"5278","file_date_updated":"2020-07-14T12:45:17Z","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1004055","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"03"},{"doi":"10.1371/journal.pone.0126907","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"05","author":[{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"id":"9772","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T11:54:07Z","date_updated":"2023-02-23T14:07:48Z","volume":10,"year":"2015","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5299","date_published":"2015-05-18T00:00:00Z","publication":"PLoS One","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"day":"18","has_accepted_license":"1","scopus_import":1,"pubrep_id":"453","file":[{"checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:09:07Z","file_id":"4730","relation":"main_file","creator":"system","file_size":2748982,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1809","ddc":["570","576"],"title":"Indirect genetic effects and the dynamics of social interactions","status":"public","intvolume":" 10","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"issue":"5","type":"journal_article"},{"day":"18","month":"05","article_processing_charge":"No","date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s003","citation":{"ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003."},"type":"research_data_reference","author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"date_created":"2021-08-05T12:55:20Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version","_id":"9772","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","title":"Description of the agent based simulations","status":"public","publisher":"Public Library of Science","department":[{"_id":"NiBa"}]},{"type":"research_data_reference","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","first_name":"Avraham E.","full_name":"Mayo, Avraham E."},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-05T12:58:07Z","date_updated":"2023-02-23T10:16:13Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9773","year":"2015","title":"Evolutionary simulation code","status":"public","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"month":"03","day":"23","article_processing_charge":"No","date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s002","citation":{"ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002."}},{"author":[{"first_name":"Ilija","last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija"},{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Raman","last_name":"Sankar","full_name":"Sankar, Raman"},{"full_name":"Walkup, Daniel","first_name":"Daniel","last_name":"Walkup"},{"full_name":"Zhou, Wenwen","first_name":"Wenwen","last_name":"Zhou"},{"full_name":"Liu, Junwei","first_name":"Junwei","last_name":"Liu"},{"full_name":"Chang, Guoqing","last_name":"Chang","first_name":"Guoqing"},{"full_name":"Wang, Yungjui","first_name":"Yungjui","last_name":"Wang"},{"last_name":"Hasan","first_name":"Md","full_name":"Hasan, Md Z"},{"full_name":"Chou, Fangcheng","last_name":"Chou","first_name":"Fangcheng"},{"first_name":"Hsin","last_name":"Lin","full_name":"Lin, Hsin"},{"first_name":"Arun","last_name":"Bansil","full_name":"Bansil, Arun"},{"first_name":"Liang","last_name":"Fu","full_name":"Fu, Liang"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"date_updated":"2021-01-12T08:22:24Z","date_created":"2018-12-11T11:49:31Z","volume":14,"_id":"981","acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","year":"2015","publication_status":"published","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","status":"public","intvolume":" 14","publisher":"Nature Publishing Group","abstract":[{"text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.","lang":"eng"}],"issue":"3","publist_id":"6419","extern":1,"type":"journal_article","doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","publication":"Nature Materials","citation":{"chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.","ieee":"I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215"},"main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"oa":1,"quality_controlled":0,"page":"318 - 324","month":"03","day":"01"},{"publisher":"American Physical Society","intvolume":" 5","status":"public","title":"Criterion for many-body localization-delocalization phase transition","publication_status":"published","year":"2015","_id":"982","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","volume":5,"date_created":"2018-12-11T11:49:32Z","date_updated":"2021-01-12T08:22:25Z","author":[{"full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"type":"journal_article","extern":1,"publist_id":"6418","issue":"4","abstract":[{"text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.","lang":"eng"}],"quality_controlled":0,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"citation":{"short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015.","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4)."},"publication":"Physical Review X","date_published":"2015-01-01T00:00:00Z","doi":"10.1103/PhysRevX.5.041047","month":"01","day":"01"},{"day":"14","date_published":"2015-09-14T00:00:00Z","page":"1017 - 1021","publication":"Nature Physics","citation":{"ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461","ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461","ieee":"A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021.","chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461."},"abstract":[{"text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"Preprint","title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","status":"public","intvolume":" 11","_id":"99","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","language":[{"iso":"eng"}],"doi":"10.1038/nphys3461","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.05155"}],"oa":1,"external_id":{"arxiv":["1501.05155"]},"extern":"1","publist_id":"7955","date_created":"2018-12-11T11:44:37Z","date_updated":"2021-01-12T08:22:28Z","volume":11,"author":[{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"last_name":"Albrecht","first_name":"S M","full_name":"Albrecht, S M"},{"full_name":"Kiršanskas, Gediminas","last_name":"Kiršanskas","first_name":"Gediminas"},{"first_name":"W","last_name":"Chang","full_name":"Chang, W"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"},{"first_name":"Peter","last_name":"Krogstrup","full_name":"Krogstrup, Peter"},{"last_name":"Jespersen","first_name":"Thomas","full_name":"Jespersen, Thomas"},{"first_name":"Jesper","last_name":"Nygård","full_name":"Nygård, Jesper"},{"last_name":"Flensberg","first_name":"Karsten","full_name":"Flensberg, Karsten"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"}],"publication_status":"published","publisher":"Nature Publishing Group","year":"2015","acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation."},{"date_published":"2015-12-21T00:00:00Z","doi":"10.1090/proc/12796","language":[{"iso":"eng"}],"citation":{"ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","apa":"Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796."},"publication":"Proceedings of the American Mathematical Society","page":"1553-1560","article_type":"letter_note","quality_controlled":"1","article_processing_charge":"No","publication_identifier":{"issn":["0002-9939","1088-6826"]},"day":"21","month":"12","author":[{"full_name":"Bounemoura, Abed","first_name":"Abed","last_name":"Bounemoura"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"}],"oa_version":"None","volume":144,"date_updated":"2021-01-12T08:19:40Z","date_created":"2020-09-18T10:46:14Z","year":"2015","_id":"8495","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Mathematical Society","intvolume":" 144","title":"A note on micro-instability for Hamiltonian systems close to integrable","status":"public","publication_status":"published","issue":"4","abstract":[{"text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.","lang":"eng"}],"extern":"1","type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"issue":"30","publist_id":"6783","extern":1,"year":"2015","_id":"866","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","publication_status":"published","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","status":"public","intvolume":" 112","publisher":"National Academy of Sciences","author":[{"first_name":"Colin","last_name":"Kretz","full_name":"Kretz, Colin A"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"full_name":"Soylemez, Onuralp","last_name":"Soylemez","first_name":"Onuralp"},{"full_name":"Yee, Andrew","first_name":"Andrew","last_name":"Yee"},{"last_name":"Desch","first_name":"Karl","full_name":"Desch, Karl C"},{"full_name":"Siemieniak, David R","last_name":"Siemieniak","first_name":"David"},{"full_name":"Tomberg, Kärt","last_name":"Tomberg","first_name":"Kärt"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov"},{"full_name":"Meng, Fan","first_name":"Fan","last_name":"Meng"},{"full_name":"Ginsburg, David B","first_name":"David","last_name":"Ginsburg"}],"date_created":"2018-12-11T11:48:55Z","date_updated":"2021-01-12T08:20:26Z","volume":112,"month":"07","day":"28","publication":"PNAS","citation":{"ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112","ieee":"C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112."},"quality_controlled":0,"page":"9328 - 9333","doi":"10.1073/pnas.1511328112","date_published":"2015-07-28T00:00:00Z"},{"extern":1,"issue":"1","publist_id":"6764","abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}],"type":"journal_article","volume":31,"date_created":"2018-12-11T11:49:01Z","date_updated":"2021-01-12T08:21:16Z","author":[{"full_name":"Kondrashov, Dmitry A","first_name":"Dmitry","last_name":"Kondrashov"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"intvolume":" 31","publisher":"Elsevier","status":"public","title":"Topological features of rugged fitness landscapes in sequence space","publication_status":"published","_id":"886","year":"2015","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","month":"01","day":"01","date_published":"2015-01-01T00:00:00Z","doi":"10.1016/j.tig.2014.09.009","page":"24 - 33","quality_controlled":0,"citation":{"ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009","apa":"Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009."},"publication":"Trends in Genetics"},{"extern":"1","pmid":1,"year":"2015","publisher":"Oxford University Press","publication_status":"published","author":[{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"first_name":"Danni","last_name":"Liu","full_name":"Liu, Danni"},{"full_name":"Legrand, Pierre","first_name":"Pierre","last_name":"Legrand"},{"full_name":"Velours, Christophe","last_name":"Velours","first_name":"Christophe"},{"full_name":"Corpet, Armelle","first_name":"Armelle","last_name":"Corpet"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"last_name":"Bakail","first_name":"May M","orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M"},{"last_name":"Moal-Raisin","first_name":"Gwenaelle","full_name":"Moal-Raisin, Gwenaelle"},{"last_name":"Guerois","first_name":"Raphael","full_name":"Guerois, Raphael"},{"full_name":"Compper, Christel","first_name":"Christel","last_name":"Compper"},{"full_name":"Besle, Arthur","last_name":"Besle","first_name":"Arthur"},{"first_name":"Berengère","last_name":"Guichard","full_name":"Guichard, Berengère"},{"full_name":"Almouzni, Genevieve","last_name":"Almouzni","first_name":"Genevieve"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"volume":43,"date_created":"2021-01-19T11:01:01Z","date_updated":"2023-02-23T13:46:50Z","publication_identifier":{"issn":["1362-4962","0305-1048"]},"month":"02","external_id":{"pmid":["25618846"]},"quality_controlled":"1","doi":"10.1093/nar/gkv021","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.","lang":"eng"}],"_id":"9017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","status":"public","oa_version":"Published Version","article_processing_charge":"No","day":"18","citation":{"ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021","ieee":"N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021.","chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021."},"publication":"Nucleic Acids Research","page":"1905-1917","article_type":"original","date_published":"2015-02-18T00:00:00Z"},{"page":"1 - 8","citation":{"ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8.","short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.","chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009."},"publication":"Applied Thermal Engineering","language":[{"iso":"eng"}],"doi":"10.1016/j.applthermaleng.2014.10.009","date_published":"2015-02-05T00:00:00Z","article_processing_charge":"No","day":"05","month":"02","intvolume":" 76","publisher":"Elsevier","publication_status":"published","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"924","year":"2015","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","volume":76,"oa_version":"None","date_updated":"2021-01-12T08:21:56Z","date_created":"2018-12-11T11:49:13Z","author":[{"full_name":"Boubaker, Riadh","last_name":"Boubaker","first_name":"Riadh"},{"last_name":"Platel","first_name":"Vincent","full_name":"Platel, Vincent"},{"first_name":"Alexis","last_name":"Bergès","full_name":"Bergès, Alexis"},{"full_name":"Bancelin, Mathieu","first_name":"Mathieu","last_name":"Bancelin"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"}],"type":"journal_article","extern":"1","publist_id":"6514","abstract":[{"lang":"eng","text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper."}]},{"article_processing_charge":"No","day":"14","month":"07","citation":{"apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112","chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112."},"publication":"PNAS","page":"8620 - 8625","date_published":"2015-07-14T00:00:00Z","doi":"10.1073/pnas.1504762112","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"6513","issue":"28","abstract":[{"lang":"eng","text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. "}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"929","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","year":"2015","intvolume":" 112","publisher":"National Academy of Sciences","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","status":"public","publication_status":"published","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"last_name":"Recho","first_name":"Pierre","full_name":"Recho, Pierre"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"},{"last_name":"Hayashi","first_name":"Shigeo","full_name":"Hayashi, Shigeo"}],"oa_version":"None","volume":112,"date_created":"2018-12-11T11:49:15Z","date_updated":"2021-01-12T08:21:59Z"},{"page":"15314 - 15319","citation":{"chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112.","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112"},"publication":"PNAS","date_published":"2015-12-15T00:00:00Z","day":"15","intvolume":" 112","status":"public","title":"Physics of active jamming during collective cellular motion in a monolayer","_id":"933","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","issue":"50","abstract":[{"lang":"eng","text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data."}],"quality_controlled":"1","external_id":{"pmid":["26627719"]},"oa":1,"main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1510973112","month":"12","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2015","volume":112,"date_updated":"2021-01-12T08:22:01Z","date_created":"2018-12-11T11:49:16Z","author":[{"first_name":"Simón","last_name":"García","full_name":"García, Simón"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"full_name":"Joanny, Jean","first_name":"Jean","last_name":"Joanny"},{"full_name":"Silberzan, Pascal","first_name":"Pascal","last_name":"Silberzan"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"extern":"1","publist_id":"6511"},{"month":"12","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["26680300"]},"language":[{"iso":"eng"}],"doi":"10.1101/gad.269902.115","extern":"1","file_date_updated":"2021-06-08T09:55:10Z","publication_status":"published","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"DaZi"}],"year":"2015","pmid":1,"date_updated":"2021-12-14T07:58:15Z","date_created":"2021-06-08T09:56:24Z","volume":29,"author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","article_type":"review","page":"2517–2531","publication":"Genes and Development","citation":{"chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115"},"date_published":"2015-12-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings."}],"issue":"24","title":"Evolution and function of genomic imprinting in plants","ddc":["570"],"status":"public","intvolume":" 29","_id":"9532","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_size":1116846,"content_type":"application/pdf","creator":"asandaue","access_level":"open_access","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","checksum":"086a88cfca4677646da26ed960cb02e9","success":1,"date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:55:10Z","relation":"main_file","file_id":"9533"}],"oa_version":"Published Version"},{"scopus_import":"1","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"article_processing_charge":"No","month":"04","day":"01","article_type":"original","quality_controlled":"1","citation":{"short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015.","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001."},"publication":"Modelling and Simulation in Materials Science and Engineering","language":[{"iso":"eng"}],"doi":"10.1088/0965-0393/23/3/035001","date_published":"2015-04-01T00:00:00Z","type":"journal_article","article_number":"035001","extern":"1","issue":"3","abstract":[{"lang":"eng","text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept."}],"publisher":"IOP Publishing","intvolume":" 23","status":"public","publication_status":"published","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","year":"2015","_id":"9684","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","volume":23,"oa_version":"None","date_created":"2021-07-19T09:11:12Z","date_updated":"2023-02-23T14:04:54Z","author":[{"last_name":"Leung","first_name":"P S S","full_name":"Leung, P S S"},{"full_name":"Leung, H S","last_name":"Leung","first_name":"H S"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"A H W","last_name":"Ngan","full_name":"Ngan, A H W"}]},{"type":"journal_article","issue":"10","abstract":[{"text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.","lang":"eng"}],"_id":"1566","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","status":"public","title":"An exploration of the universe of polyglutamine structures","ddc":["570"],"pubrep_id":"478","file":[{"creator":"system","file_size":1412511,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","checksum":"8b67d729be663bfc9af04bfd94459655","date_created":"2018-12-12T10:16:21Z","date_updated":"2020-07-14T12:45:02Z","file_id":"5207","relation":"main_file"}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"23","citation":{"short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541."},"publication":"PLoS Computational Biology","date_published":"2015-10-23T00:00:00Z","article_number":"e1004541","publist_id":"5605","file_date_updated":"2020-07-14T12:45:02Z","acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","year":"2015","publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"publication_status":"published","related_material":{"record":[{"id":"9714","status":"public","relation":"research_data"}]},"author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K","full_name":"Sikora, Mateusz K"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"last_name":"Carrión Vázquez","first_name":"Mariano","full_name":"Carrión Vázquez, Mariano"}],"volume":11,"date_created":"2018-12-11T11:52:45Z","date_updated":"2023-02-23T14:05:55Z","month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1004541","language":[{"iso":"eng"}]},{"doi":"10.1371/journal.pgen.1005639.s001","date_published":"2015-11-06T00:00:00Z","citation":{"apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001."},"article_processing_charge":"No","day":"06","month":"11","related_material":{"record":[{"id":"1666","status":"public","relation":"used_in_publication"}]},"author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","first_name":"Murat","last_name":"Tugrul","full_name":"Tugrul, Murat"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:09:08Z","date_created":"2021-07-23T12:00:37Z","year":"2015","_id":"9712","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","status":"public","title":"Other fitness models for comparison & for interacting TFBSs","type":"research_data_reference"},{"date_updated":"2023-02-23T10:04:35Z","date_created":"2021-07-23T12:05:28Z","oa_version":"Published Version","author":[{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"full_name":"Cieplak, Marek","first_name":"Marek","last_name":"Cieplak"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1566"}]},"status":"public","title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","publisher":"Public Library of Science ","department":[{"_id":"CaHe"}],"_id":"9714","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","type":"research_data_reference","date_published":"2015-10-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004541.s001","citation":{"ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , 10.1371/journal.pcbi.1004541.s001.","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:10.1371/journal.pcbi.1004541.s001","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.","mla":"Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals. Public Library of Science , 2015, doi:10.1371/journal.pcbi.1004541.s001.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015)."},"month":"10","day":"23","article_processing_charge":"No"},{"type":"research_data_reference","date_created":"2021-07-23T12:11:30Z","date_updated":"2023-02-23T10:15:25Z","oa_version":"Published Version","author":[{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"status":"public","title":"Mathematical inference of the results","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9715","year":"2015","day":"18","month":"05","article_processing_charge":"No","doi":"10.1371/journal.pone.0126907.s001","date_published":"2015-05-18T00:00:00Z","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001"}},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2014.1976","quality_controlled":"1","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"oa":1,"external_id":{"pmid":["25473011"]},"month":"01","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"date_created":"2018-12-11T11:55:06Z","date_updated":"2023-02-23T14:06:41Z","volume":282,"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"id":"9740","status":"public","relation":"research_data"}]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"SyCr"}],"acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","year":"2015","pmid":1,"publist_id":"5090","ec_funded":1,"article_number":"20141976","date_published":"2015-01-22T00:00:00Z","article_type":"original","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","citation":{"ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799. The Royal Society, 2015.","apa":"Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.1976","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:10.1098/rspb.2014.1976.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015)."},"day":"22","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","status":"public","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","intvolume":" 282","_id":"1993","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. "}],"issue":"1799","type":"journal_article"},{"abstract":[{"text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.","lang":"eng"}],"type":"research_data_reference","author":[{"full_name":"Westhus, Claudia","first_name":"Claudia","last_name":"Westhus"},{"first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Edouard","last_name":"Tourdot","full_name":"Tourdot, Edouard"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"full_name":"Doums, Claudie","first_name":"Claudie","last_name":"Doums"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"related_material":{"record":[{"id":"2161","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-02-23T10:30:52Z","date_created":"2021-07-28T08:52:53Z","oa_version":"Published Version","_id":"9742","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","publisher":"Dryad","department":[{"_id":"SyCr"}],"month":"07","day":"09","article_processing_charge":"No","date_published":"2015-07-09T00:00:00Z","doi":"10.5061/dryad.7kc79","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7kc79"}],"citation":{"chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","mla":"Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, 10.5061/dryad.7kc79.","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:10.5061/dryad.7kc79"}},{"article_processing_charge":"No","month":"11","day":"18","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s008","ieee":"G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008.","mla":"Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s008.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015)."},"doi":"10.1371/journal.pbio.1002299.s008","date_published":"2015-11-18T00:00:00Z","type":"research_data_reference","_id":"9765","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"status":"public","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1619"}]},"author":[{"first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"last_name":"Batur","first_name":"Tugce","full_name":"Batur, Tugce"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal","last_name":"Ayhan"},{"last_name":"Toprak","first_name":"Erdal","full_name":"Toprak, Erdal"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"oa_version":"Published Version","date_created":"2021-08-03T07:05:16Z","date_updated":"2023-02-23T10:07:02Z"},{"keyword":["Water Science and Technology"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"94-111","article_type":"original","citation":{"ama":"Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013","ieee":"S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” Advances in Water Resources, vol. 78, no. 4. Elsevier, pp. 94–111, 2015.","apa":"Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013","ista":"Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.","short":"S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111.","mla":"Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013.","chicago":"Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources. Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013."},"publication":"Advances in Water Resources","date_published":"2015-04-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n","lang":"eng"}],"intvolume":" 78","title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12630","oa_version":"None","publication_identifier":{"issn":["0309-1708"]},"month":"04","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.advwatres.2015.01.013","extern":"1","publisher":"Elsevier","publication_status":"published","year":"2015","volume":78,"date_created":"2023-02-20T08:16:21Z","date_updated":"2023-02-24T09:28:04Z","author":[{"full_name":"Ragettli, S.","first_name":"S.","last_name":"Ragettli"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"},{"full_name":"Immerzeel, W.W.","first_name":"W.W.","last_name":"Immerzeel"},{"full_name":"Miles, E.S.","last_name":"Miles","first_name":"E.S."},{"first_name":"L.","last_name":"Petersen","full_name":"Petersen, L."},{"full_name":"Heynen, M.","last_name":"Heynen","first_name":"M."},{"first_name":"J.M.","last_name":"Shea","full_name":"Shea, J.M."},{"full_name":"Stumm, D.","first_name":"D.","last_name":"Stumm"},{"last_name":"Joshi","first_name":"S.","full_name":"Joshi, S."},{"first_name":"A.","last_name":"Shrestha","full_name":"Shrestha, A."}]},{"type":"journal_article","abstract":[{"text":"Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation.","lang":"eng"}],"issue":"226","_id":"12628","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999","status":"public","intvolume":" 61","oa_version":"Published Version","scopus_import":"1","keyword":["Earth-Surface Processes"],"day":"01","article_processing_charge":"No","publication":"Journal of Glaciology","citation":{"mla":"Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology, vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237.","short":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386.","chicago":"Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237.","ama":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237","ista":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 61(226), 373–386.","apa":"Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., & Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog13j237","ieee":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T. Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International Glaciological Society, pp. 373–386, 2015."},"article_type":"original","page":"373-386","date_published":"2015-03-01T00:00:00Z","extern":"1","year":"2015","publication_status":"published","publisher":"International Glaciological Society","author":[{"first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"first_name":"Christa","last_name":"Stephan","full_name":"Stephan, Christa"},{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"full_name":"Herreid, Sam","last_name":"Herreid","first_name":"Sam"},{"last_name":"Immerzeel","first_name":"Walter W.","full_name":"Immerzeel, Walter W."},{"full_name":"Bolch, Tobias","last_name":"Bolch","first_name":"Tobias"}],"date_updated":"2023-02-24T09:35:21Z","date_created":"2023-02-20T08:16:11Z","volume":61,"month":"03","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.3189/2015JoG13J237","open_access":"1"}],"quality_controlled":"1","doi":"10.3189/2015jog13j237","language":[{"iso":"eng"}]}]