[{"date_created":"2021-07-15T14:09:32Z","doi":"10.1016/j.ijplas.2014.09.009","date_published":"2015-04-01T00:00:00Z","volume":67,"page":"1-25","language":[{"iso":"eng"}],"publication":"International Journal of Plasticity","day":"01","publication_status":"published","year":"2015","publication_identifier":{"issn":["0749-6419"]},"intvolume":" 67","month":"04","scopus_import":"1","publisher":"Elsevier","oa_version":"None","abstract":[{"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.","lang":"eng"}],"title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","article_processing_charge":"No","author":[{"last_name":"Leung","full_name":"Leung, H.S.","first_name":"H.S."},{"first_name":"P.S.S.","last_name":"Leung","full_name":"Leung, P.S.S."},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"full_name":"Ngan, A.H.W.","last_name":"Ngan","first_name":"A.H.W."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","date_updated":"2023-02-23T14:04:28Z","citation":{"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","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","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","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.","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.","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.","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."},"status":"public","article_type":"original","type":"journal_article","_id":"9673"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2015","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"01","date_created":"2021-07-19T10:07:22Z","doi":"10.1103/physrevb.92.180102","date_published":"2015-11-01T00:00:00Z","article_number":"180102","citation":{"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.","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.","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","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","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","external_id":{"arxiv":["1511.08668"]},"author":[{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"first_name":"Gareth A.","last_name":"Tribello","full_name":"Tribello, Gareth A."},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"title":"Solid-liquid interfacial free energy out of equilibrium","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.08668"}],"scopus_import":"1","intvolume":" 92","month":"11","publication_status":"published","publication_identifier":{"issn":["1098-0121"],"eissn":["1550-235X"]},"language":[{"iso":"eng"}],"volume":92,"issue":"18","_id":"9688","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-08-09T12:38:49Z","extern":"1"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"11","year":"2015","day":"18","related_material":{"record":[{"relation":"used_in_publication","id":"1619","status":"public"}]},"date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s001","date_created":"2021-07-23T11:53:50Z","_id":"9711","type":"research_data_reference","status":"public","citation":{"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.","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.","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.","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","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.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015)."},"date_updated":"2023-02-23T10:07:02Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"},{"last_name":"Batur","full_name":"Batur, Tugce","first_name":"Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"article_processing_charge":"No","title":"Excel file containing the raw data for all figures","department":[{"_id":"ToBo"}]},{"date_updated":"2023-02-23T14:06:09Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"SyCr"}],"_id":"1855","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","pubrep_id":"460","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5350","checksum":"542a0b9b07e78050a81b35f26f0b82da","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","date_created":"2018-12-12T10:18:29Z","creator":"system","file_size":1823045,"date_updated":"2020-07-14T12:45:19Z"}],"issue":"3","related_material":{"record":[{"relation":"research_data","id":"9720","status":"public"}]},"volume":84,"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 84","month":"03","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.","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.","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","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","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","external_id":{"pmid":["25646973"]},"author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Caspar","full_name":"Caspar, Jesicca","first_name":"Jesicca"},{"last_name":"Theodorou","full_name":"Theodorou, Panagiotis","first_name":"Panagiotis"},{"last_name":"Brown","full_name":"Brown, Mark","first_name":"Mark"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"publist_id":"5245","title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","year":"2015","has_accepted_license":"1","publication":"Journal of Animal Ecology","day":"03","page":"615 - 624","date_created":"2018-12-11T11:54:23Z","doi":"10.1111/1365-2656.12345","date_published":"2015-03-03T00:00:00Z","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.","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"302004","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"},{"_id":"25E24DB2-B435-11E9-9278-68D0E5697425","name":"Fellowship of Wissenschaftskolleg zu Berlin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","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","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","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.","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)."},"title":"Opposing effects of allogrooming on disease transmission in ant societies","author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"full_name":"Marr, Carsten","last_name":"Marr","first_name":"Carsten"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"5273","external_id":{"pmid":["25870394"]},"article_processing_charge":"No","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.","publisher":"Royal Society, The","quality_controlled":"1","oa":1,"day":"26","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","year":"2015","doi":"10.1098/rstb.2014.0108","date_published":"2015-05-26T00:00:00Z","date_created":"2018-12-11T11:54:15Z","_id":"1830","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-02-23T14:06:12Z","department":[{"_id":"SyCr"}],"oa_version":"Submitted Version","pmid":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."}],"month":"05","intvolume":" 370","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publication_status":"published","volume":370,"issue":"1669","related_material":{"record":[{"relation":"research_data","id":"9721","status":"public"}]},"ec_funded":1},{"date_published":"2015-12-29T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"1830","status":"public"}]},"doi":"10.5061/dryad.dj2bf","date_created":"2021-07-26T09:38:36Z","year":"2015","day":"29","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.dj2bf"}],"oa":1,"month":"12","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."}],"oa_version":"Published Version","author":[{"last_name":"Theis","full_name":"Theis, Fabian","first_name":"Fabian"},{"orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"last_name":"Marr","full_name":"Marr, Carsten","first_name":"Carsten"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","citation":{"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.","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.","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).","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.","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","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"},"date_updated":"2023-02-23T10:16:22Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9721"},{"year":"2015","day":"23","date_created":"2021-07-26T08:35:23Z","related_material":{"record":[{"status":"public","id":"1827","relation":"used_in_publication"}]},"date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s001","oa_version":"Published Version","publisher":"Public Library of Science","month":"03","citation":{"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.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001.","mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.","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","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015."},"date_updated":"2023-02-23T10:16:13Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Avraham E.","last_name":"Mayo","full_name":"Mayo, Avraham E."},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"department":[{"_id":"GaTk"}],"title":"Supporting information text","_id":"9718","type":"research_data_reference","status":"public"},{"_id":"1793","status":"public","pubrep_id":"454","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-02-23T14:06:33Z","file_date_updated":"2020-07-14T12:45:16Z","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"06","intvolume":" 10","scopus_import":1,"file":[{"file_id":"5150","checksum":"d20f26461ca575276ad3ed9ce4bfc787","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","date_created":"2018-12-12T10:15:30Z","file_size":1850825,"date_updated":"2020-07-14T12:45:16Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9737","status":"public"}]},"volume":10,"issue":"6","article_number":"e0127657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015)."},"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"},{"last_name":"Topp","full_name":"Topp, Christopher","first_name":"Christopher"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5318","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"day":"01","publication":"PLoS One","has_accepted_license":"1","year":"2015","doi":"10.1371/journal.pone.0127657","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:02Z"},{"year":"2015","day":"01","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1793"}]},"date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657.s001","date_created":"2021-07-28T06:20:13Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"06","citation":{"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.","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.","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","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","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","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."},"date_updated":"2023-02-23T10:14:42Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","_id":"9737","type":"research_data_reference","status":"public"},{"month":"03","intvolume":" 11","scopus_import":1,"oa_version":"Published Version","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."}],"volume":11,"issue":"3","related_material":{"record":[{"relation":"research_data","id":"9718","status":"public"},{"relation":"research_data","status":"public","id":"9773"}]},"ec_funded":1,"file":[{"checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_id":"5161","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","date_created":"2018-12-12T10:15:39Z","creator":"system","file_size":1811647,"date_updated":"2020-07-14T12:45:17Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"452","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1827","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"GaTk"}],"ddc":["576"],"date_updated":"2023-02-23T14:07:51Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"doi":"10.1371/journal.pcbi.1004055","date_published":"2015-03-23T00:00:00Z","date_created":"2018-12-11T11:54:14Z","day":"23","publication":"PLoS Computational Biology","has_accepted_license":"1","year":"2015","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Evolution of bow-tie architectures in biology","author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Avraham","last_name":"Mayo","full_name":"Mayo, Avraham"},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"last_name":"Alon","full_name":"Alon, Uri","first_name":"Uri"}],"publist_id":"5278","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","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.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","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.","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","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"}},{"author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"publist_id":"5299","title":"Indirect genetic effects and the dynamics of social interactions","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","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.","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.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"doi":"10.1371/journal.pone.0126907","date_published":"2015-05-18T00:00:00Z","date_created":"2018-12-11T11:54:07Z","has_accepted_license":"1","year":"2015","day":"18","publication":"PLoS One","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"453","_id":"1809","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:17Z","date_updated":"2023-02-23T14:07:48Z","ddc":["570","576"],"scopus_import":1,"month":"05","intvolume":" 10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"5","volume":10,"related_material":{"record":[{"id":"9715","status":"public","relation":"research_data"},{"id":"9772","status":"public","relation":"research_data"}]},"publication_status":"published","file":[{"file_size":2748982,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","date_created":"2018-12-12T10:09:07Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4730","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743"}],"language":[{"iso":"eng"}]},{"department":[{"_id":"NiBa"}],"title":"Description of the agent based simulations","article_processing_charge":"No","author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"last_name":"Hager","full_name":"Hager, Reinmar","first_name":"Reinmar"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","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","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 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.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003."},"date_updated":"2023-02-23T10:15:25Z","status":"public","type":"research_data_reference","_id":"9772","date_created":"2021-08-05T12:55:20Z","doi":"10.1371/journal.pone.0126907.s003","related_material":{"record":[{"relation":"used_in_publication","id":"1809","status":"public"}]},"date_published":"2015-05-18T00:00:00Z","day":"18","year":"2015","month":"05","publisher":"Public Library of Science","oa_version":"Published Version"},{"date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s002","related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-05T12:58:07Z","year":"2015","day":"23","publisher":"Public Library of Science","month":"03","oa_version":"Published Version","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"full_name":"Mayo, Avraham E.","last_name":"Mayo","first_name":"Avraham E."},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"first_name":"Uri","full_name":"Alon, Uri","last_name":"Alon"}],"article_processing_charge":"No","title":"Evolutionary simulation code","department":[{"_id":"GaTk"}],"citation":{"mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 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","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","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.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002."},"date_updated":"2023-02-23T10:16:13Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9773"},{"status":"public","type":"journal_article","_id":"981","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","author":[{"full_name":"Zeljkovic, Ilija","last_name":"Zeljkovic","first_name":"Ilija"},{"last_name":"Okada","full_name":"Okada, Yoshinori","first_name":"Yoshinori"},{"orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Raman","full_name":"Sankar, Raman","last_name":"Sankar"},{"first_name":"Daniel","last_name":"Walkup","full_name":"Walkup, Daniel"},{"first_name":"Wenwen","last_name":"Zhou","full_name":"Zhou, Wenwen"},{"full_name":"Liu, Junwei","last_name":"Liu","first_name":"Junwei"},{"full_name":"Chang, Guoqing","last_name":"Chang","first_name":"Guoqing"},{"first_name":"Yungjui","last_name":"Wang","full_name":"Wang, Yungjui"},{"last_name":"Hasan","full_name":"Hasan, Md Z","first_name":"Md"},{"full_name":"Chou, Fangcheng","last_name":"Chou","first_name":"Fangcheng"},{"first_name":"Hsin","full_name":"Lin, Hsin","last_name":"Lin"},{"last_name":"Bansil","full_name":"Bansil, Arun","first_name":"Arun"},{"first_name":"Liang","full_name":"Fu, Liang","last_name":"Fu"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"publist_id":"6419","extern":1,"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.","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.","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.","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","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","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.","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."},"date_updated":"2021-01-12T08:22:24Z","month":"03","intvolume":" 14","publisher":"Nature Publishing Group","quality_controlled":0,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"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.","abstract":[{"lang":"eng","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."}],"volume":14,"doi":"10.1038/nmat4215","issue":"3","date_published":"2015-03-01T00:00:00Z","date_created":"2018-12-11T11:49:31Z","page":"318 - 324","day":"01","publication":"Nature Materials","publication_status":"published","year":"2015"},{"_id":"982","status":"public","type":"journal_article","extern":1,"citation":{"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","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","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","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.","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.","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","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."},"date_updated":"2021-01-12T08:22:25Z","title":"Criterion for many-body localization-delocalization phase transition","author":[{"full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"full_name":"Abanin, Dmitry A","last_name":"Abanin","first_name":"Dmitry"}],"publist_id":"6418","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.","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 5","publisher":"American Physical Society","quality_controlled":0,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"day":"01","publication":"Physical Review X","publication_status":"published","year":"2015","doi":"10.1103/PhysRevX.5.041047","date_published":"2015-01-01T00:00:00Z","issue":"4","volume":5,"date_created":"2018-12-11T11:49:32Z"},{"doi":"10.1038/nphys3461","date_published":"2015-09-14T00:00:00Z","date_created":"2018-12-11T11:44:37Z","page":"1017 - 1021","day":"14","publication":"Nature Physics","year":"2015","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"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.","title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"},{"first_name":"S M","last_name":"Albrecht","full_name":"Albrecht, S M"},{"first_name":"Gediminas","last_name":"Kiršanskas","full_name":"Kiršanskas, Gediminas"},{"first_name":"W","full_name":"Chang, W","last_name":"Chang"},{"first_name":"Ferdinand","last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand"},{"last_name":"Krogstrup","full_name":"Krogstrup, Peter","first_name":"Peter"},{"first_name":"Thomas","last_name":"Jespersen","full_name":"Jespersen, Thomas"},{"last_name":"Nygård","full_name":"Nygård, Jesper","first_name":"Jesper"},{"first_name":"Karsten","last_name":"Flensberg","full_name":"Flensberg, Karsten"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"publist_id":"7955","external_id":{"arxiv":["1501.05155"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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","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.","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.","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.","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.","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."},"issue":"12","volume":11,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.05155"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"extern":"1","date_updated":"2021-01-12T08:22:28Z","status":"public","type":"journal_article","_id":"99"},{"author":[{"full_name":"Bounemoura, Abed","last_name":"Bounemoura","first_name":"Abed"},{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"article_processing_charge":"No","title":"A note on micro-instability for Hamiltonian systems close to integrable","date_updated":"2021-01-12T08:19:40Z","citation":{"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.","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.","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","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","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"letter_note","type":"journal_article","status":"public","_id":"8495","page":"1553-1560","date_published":"2015-12-21T00:00:00Z","volume":144,"doi":"10.1090/proc/12796","issue":"4","date_created":"2020-09-18T10:46:14Z","publication_identifier":{"issn":["0002-9939","1088-6826"]},"publication_status":"published","year":"2015","day":"21","language":[{"iso":"eng"}],"publication":"Proceedings of the American Mathematical Society","quality_controlled":"1","publisher":"American Mathematical Society","month":"12","intvolume":" 144","abstract":[{"lang":"eng","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."}],"oa_version":"None"},{"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","abstract":[{"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.","lang":"eng"}],"month":"07","intvolume":" 112","quality_controlled":0,"publisher":"National Academy of Sciences","day":"28","publication":"PNAS","year":"2015","publication_status":"published","issue":"30","date_published":"2015-07-28T00:00:00Z","volume":112,"doi":"10.1073/pnas.1511328112","date_created":"2018-12-11T11:48:55Z","page":"9328 - 9333","_id":"866","status":"public","type":"journal_article","extern":1,"citation":{"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.","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.","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.","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.","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","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."},"date_updated":"2021-01-12T08:20:26Z","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","author":[{"first_name":"Colin","last_name":"Kretz","full_name":"Kretz, Colin A"},{"first_name":"Manhong","full_name":"Dai, Manhong","last_name":"Dai"},{"full_name":"Soylemez, Onuralp","last_name":"Soylemez","first_name":"Onuralp"},{"first_name":"Andrew","last_name":"Yee","full_name":"Yee, Andrew"},{"full_name":"Desch, Karl C","last_name":"Desch","first_name":"Karl"},{"first_name":"David","full_name":"Siemieniak, David R","last_name":"Siemieniak"},{"first_name":"Kärt","full_name":"Tomberg, Kärt","last_name":"Tomberg"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Fan","last_name":"Meng","full_name":"Meng, Fan"},{"full_name":"Ginsburg, David B","last_name":"Ginsburg","first_name":"David"}],"publist_id":"6783"},{"type":"journal_article","status":"public","_id":"886","author":[{"first_name":"Dmitry","full_name":"Kondrashov, Dmitry A","last_name":"Kondrashov"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"publist_id":"6764","title":"Topological features of rugged fitness landscapes in sequence space","date_updated":"2021-01-12T08:21:16Z","citation":{"ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","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.","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","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","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.","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."},"extern":1,"quality_controlled":0,"publisher":"Elsevier","month":"01","intvolume":" 31","abstract":[{"lang":"eng","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."}],"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.","page":"24 - 33","doi":"10.1016/j.tig.2014.09.009","volume":31,"date_published":"2015-01-01T00:00:00Z","issue":"1","date_created":"2018-12-11T11:49:01Z","year":"2015","publication_status":"published","day":"01","publication":"Trends in Genetics"},{"citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25618846"]},"article_processing_charge":"No","author":[{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"last_name":"Liu","full_name":"Liu, Danni","first_name":"Danni"},{"last_name":"Legrand","full_name":"Legrand, Pierre","first_name":"Pierre"},{"last_name":"Velours","full_name":"Velours, Christophe","first_name":"Christophe"},{"full_name":"Corpet, Armelle","last_name":"Corpet","first_name":"Armelle"},{"last_name":"Gaubert","full_name":"Gaubert, Albane","first_name":"Albane"},{"last_name":"Bakail","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"first_name":"Gwenaelle","last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"first_name":"Christel","full_name":"Compper, Christel","last_name":"Compper"},{"first_name":"Arthur","last_name":"Besle","full_name":"Besle, Arthur"},{"first_name":"Berengère","full_name":"Guichard, Berengère","last_name":"Guichard"},{"first_name":"Genevieve","full_name":"Almouzni, Genevieve","last_name":"Almouzni"},{"last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise","first_name":"Françoise"}],"title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","quality_controlled":"1","publisher":"Oxford University Press","year":"2015","publication":"Nucleic Acids Research","day":"18","page":"1905-1917","date_created":"2021-01-19T11:01:01Z","date_published":"2015-02-18T00:00:00Z","doi":"10.1093/nar/gkv021","_id":"9017","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-23T13:46:50Z","extern":"1","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"}],"oa_version":"Published Version","pmid":1,"intvolume":" 43","month":"02","publication_status":"published","publication_identifier":{"issn":["1362-4962","0305-1048"]},"language":[{"iso":"eng"}],"volume":43,"issue":"3"},{"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."}],"acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","oa_version":"None","publisher":"Elsevier","intvolume":" 76","month":"02","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Applied Thermal Engineering","day":"05","page":"1 - 8","date_created":"2018-12-11T11:49:13Z","volume":76,"date_published":"2015-02-05T00:00:00Z","doi":"10.1016/j.applthermaleng.2014.10.009","_id":"924","type":"journal_article","status":"public","date_updated":"2021-01-12T08:21:56Z","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","short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"first_name":"Riadh","full_name":"Boubaker, Riadh","last_name":"Boubaker"},{"first_name":"Vincent","full_name":"Platel, Vincent","last_name":"Platel"},{"last_name":"Bergès","full_name":"Bergès, Alexis","first_name":"Alexis"},{"first_name":"Mathieu","last_name":"Bancelin","full_name":"Bancelin, Mathieu"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"publist_id":"6514","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop"},{"_id":"929","type":"journal_article","status":"public","citation":{"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.","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","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","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","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.","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.","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."},"date_updated":"2021-01-12T08:21:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","publist_id":"6513","author":[{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Bo","full_name":"Dong, Bo","last_name":"Dong"},{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"},{"first_name":"Shigeo","full_name":"Hayashi, Shigeo","last_name":"Hayashi"}],"title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","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. "}],"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.","oa_version":"None","publisher":"National Academy of Sciences","intvolume":" 112","month":"07","year":"2015","publication_status":"published","publication":"PNAS","language":[{"iso":"eng"}],"day":"14","page":"8620 - 8625","date_created":"2018-12-11T11:49:15Z","doi":"10.1073/pnas.1504762112","date_published":"2015-07-14T00:00:00Z","issue":"28","volume":112},{"title":"Physics of active jamming during collective cellular motion in a monolayer","author":[{"first_name":"Simón","last_name":"García","full_name":"García, Simón"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"},{"first_name":"Pascal","last_name":"Silberzan","full_name":"Silberzan, Pascal"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"publist_id":"6511","external_id":{"pmid":["26627719"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","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","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","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.","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."},"doi":"10.1073/pnas.1510973112","date_published":"2015-12-15T00:00:00Z","date_created":"2018-12-11T11:49:16Z","page":"15314 - 15319","day":"15","publication":"PNAS","year":"2015","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"extern":"1","date_updated":"2021-01-12T08:22:01Z","status":"public","type":"journal_article","_id":"933","issue":"50","volume":112,"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 112","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf"}],"pmid":1,"oa_version":"None","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."}]},{"oa":1,"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","page":"2517–2531","date_created":"2021-06-08T09:56:24Z","doi":"10.1101/gad.269902.115","date_published":"2015-12-15T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Genes and Development","day":"15","external_id":{"pmid":["26680300"]},"article_processing_charge":"No","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"title":"Evolution and function of genomic imprinting in plants","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.","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 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.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","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.","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","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"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","intvolume":" 29","month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":29,"issue":"24","publication_status":"published","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9533","checksum":"086a88cfca4677646da26ed960cb02e9","file_size":1116846,"date_updated":"2021-06-08T09:55:10Z","creator":"asandaue","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_created":"2021-06-08T09:55:10Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"review","type":"journal_article","status":"public","_id":"9532","file_date_updated":"2021-06-08T09:55:10Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:58:15Z","ddc":["570"],"extern":"1"},{"status":"public","type":"journal_article","article_type":"original","article_number":"035001","_id":"9684","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","author":[{"first_name":"P S S","last_name":"Leung","full_name":"Leung, P S S"},{"last_name":"Leung","full_name":"Leung, H S","first_name":"H S"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"A H W","full_name":"Ngan, A H W","last_name":"Ngan"}],"article_processing_charge":"No","extern":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T14:04:54Z","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).","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","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","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.","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.","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."},"month":"04","intvolume":" 23","publisher":"IOP Publishing","quality_controlled":"1","scopus_import":"1","oa_version":"None","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."}],"doi":"10.1088/0965-0393/23/3/035001","issue":"3","date_published":"2015-04-01T00:00:00Z","volume":23,"date_created":"2021-07-19T09:11:12Z","day":"01","publication":"Modelling and Simulation in Materials Science and Engineering","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"year":"2015","publication_status":"published"},{"status":"public","pubrep_id":"478","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1566","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:45:02Z","ddc":["570"],"date_updated":"2023-02-23T14:05:55Z","month":"10","intvolume":" 11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":11,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9714"}]},"issue":"10","file":[{"creator":"system","file_size":1412511,"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","date_created":"2018-12-12T10:16:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"8b67d729be663bfc9af04bfd94459655","file_id":"5207"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"e1004541","title":"An exploration of the universe of polyglutamine structures","publist_id":"5605","author":[{"first_name":"Àngel","full_name":"Gómez Sicilia, Àngel","last_name":"Gómez Sicilia"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"first_name":"Mariano","last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","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","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.","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."},"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"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. ","date_published":"2015-10-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004541","date_created":"2018-12-11T11:52:45Z","day":"23","publication":"PLoS Computational Biology","has_accepted_license":"1","year":"2015"},{"date_updated":"2023-02-23T10:09:08Z","citation":{"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.","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.","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.","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","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.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Other fitness models for comparison & for interacting TFBSs","_id":"9712","type":"research_data_reference","status":"public","year":"2015","day":"06","date_created":"2021-07-23T12:00:37Z","related_material":{"record":[{"id":"1666","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pgen.1005639.s001","date_published":"2015-11-06T00:00:00Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"11"},{"type":"research_data_reference","status":"public","_id":"9714","article_processing_charge":"No","author":[{"full_name":"Gómez Sicilia, Àngel","last_name":"Gómez Sicilia","first_name":"Àngel"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"last_name":"Cieplak","full_name":"Cieplak, Marek","first_name":"Marek"},{"first_name":"Mariano","full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez"}],"department":[{"_id":"CaHe"}],"title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","date_updated":"2023-02-23T10:04:35Z","citation":{"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.","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","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","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.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science ","month":"10","oa_version":"Published Version","date_created":"2021-07-23T12:05:28Z","date_published":"2015-10-23T00:00:00Z","related_material":{"record":[{"status":"public","id":"1566","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1004541.s001","year":"2015","day":"23"},{"year":"2015","day":"18","date_published":"2015-05-18T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1809"}]},"doi":"10.1371/journal.pone.0126907.s001","date_created":"2021-07-23T12:11:30Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"05","citation":{"ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001","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","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi: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.","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."},"date_updated":"2023-02-23T10:15:25Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Mathematical inference of the results","_id":"9715","type":"research_data_reference","status":"public"},{"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"22","year":"2015","date_created":"2018-12-11T11:55:06Z","doi":"10.1098/rspb.2014.1976","date_published":"2015-01-22T00:00:00Z","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.","oa":1,"quality_controlled":"1","publisher":"The Royal Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","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."},"title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","article_processing_charge":"No","external_id":{"pmid":["25473011"]},"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Konrad, Matthias","last_name":"Konrad"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","last_name":"Tragust"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5090","article_number":"20141976","project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"ec_funded":1,"issue":"1799","related_material":{"record":[{"relation":"research_data","status":"public","id":"9740"}]},"volume":282,"pmid":1,"oa_version":"Submitted Version","abstract":[{"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. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":" 282","month":"01","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"scopus_import":"1","date_updated":"2023-02-23T14:06:41Z","department":[{"_id":"SyCr"}],"_id":"1993","status":"public","type":"journal_article","article_type":"original"},{"date_created":"2021-07-28T08:52:53Z","date_published":"2015-07-09T00:00:00Z","related_material":{"record":[{"id":"2161","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.7kc79","year":"2015","day":"09","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.7kc79","open_access":"1"}],"publisher":"Dryad","month":"07","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Claudia","full_name":"Westhus, Claudia","last_name":"Westhus"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig"},{"full_name":"Tourdot, Edouard","last_name":"Tourdot","first_name":"Edouard"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"first_name":"Claudie","full_name":"Doums, Claudie","last_name":"Doums"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"department":[{"_id":"SyCr"}],"title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","citation":{"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","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","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","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.","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.","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.","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."},"date_updated":"2023-02-23T10:30:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9742"},{"article_processing_charge":"No","author":[{"first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","full_name":"Chevereau, Guillaume"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"},{"last_name":"Batur","full_name":"Batur, Tugce","first_name":"Tugce"},{"full_name":"Guvenek, Aysegul","last_name":"Guvenek","first_name":"Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ToBo"}],"title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","date_updated":"2023-02-23T10:07:02Z","citation":{"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.","ieee":"G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","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","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9765","date_created":"2021-08-03T07:05:16Z","date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s008","related_material":{"record":[{"relation":"used_in_publication","id":"1619","status":"public"}]},"year":"2015","day":"18","publisher":"Public Library of Science","month":"11","oa_version":"Published Version"},{"year":"2015","day":"01","publication":"Advances in Water Resources","page":"94-111","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.advwatres.2015.01.013","date_created":"2023-02-20T08:16:21Z","quality_controlled":"1","publisher":"Elsevier","citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ragettli, S.","last_name":"Ragettli","first_name":"S."},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"last_name":"Immerzeel","full_name":"Immerzeel, W.W.","first_name":"W.W."},{"last_name":"Miles","full_name":"Miles, E.S.","first_name":"E.S."},{"first_name":"L.","last_name":"Petersen","full_name":"Petersen, L."},{"last_name":"Heynen","full_name":"Heynen, M.","first_name":"M."},{"full_name":"Shea, J.M.","last_name":"Shea","first_name":"J.M."},{"last_name":"Stumm","full_name":"Stumm, D.","first_name":"D."},{"first_name":"S.","full_name":"Joshi, S.","last_name":"Joshi"},{"first_name":"A.","last_name":"Shrestha","full_name":"Shrestha, A."}],"article_processing_charge":"No","title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","publication_identifier":{"issn":["0309-1708"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":78,"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"}],"oa_version":"None","scopus_import":"1","month":"04","intvolume":" 78","date_updated":"2023-02-24T09:28:04Z","extern":"1","_id":"12630","type":"journal_article","article_type":"original","status":"public","keyword":["Water Science and Technology"]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3189/2015JoG13J237","open_access":"1"}],"month":"03","intvolume":" 61","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":61,"issue":"226","_id":"12628","type":"journal_article","article_type":"original","status":"public","keyword":["Earth-Surface Processes"],"date_updated":"2023-02-24T09:35:21Z","extern":"1","quality_controlled":"1","publisher":"International Glaciological Society","oa":1,"year":"2015","day":"01","publication":"Journal of Glaciology","page":"373-386","doi":"10.3189/2015jog13j237","date_published":"2015-03-01T00:00:00Z","date_created":"2023-02-20T08:16:11Z","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.","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.","short":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"full_name":"Stephan, Christa","last_name":"Stephan","first_name":"Christa"},{"full_name":"Miles, Evan","last_name":"Miles","first_name":"Evan"},{"full_name":"Herreid, Sam","last_name":"Herreid","first_name":"Sam"},{"first_name":"Walter W.","full_name":"Immerzeel, Walter W.","last_name":"Immerzeel"},{"last_name":"Bolch","full_name":"Bolch, Tobias","first_name":"Tobias"}],"article_processing_charge":"No","title":"Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999"},{"date_updated":"2023-02-24T09:16:26Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"status":"public","_id":"12631","volume":120,"issue":"8","publication_status":"published","publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 120","month":"04","abstract":[{"lang":"eng","text":"Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Ayala","full_name":"Ayala, A.","first_name":"A."},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"first_name":"J. M.","full_name":"Shea, J. M.","last_name":"Shea"}],"title":"Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming","citation":{"mla":"Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.","ama":"Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137","apa":"Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137","ieee":"A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015.","short":"A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.","chicago":"Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137.","ista":"Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3139-3157","date_created":"2023-02-20T08:16:28Z","date_published":"2015-04-18T00:00:00Z","doi":"10.1002/2015jd023137","year":"2015","publication":"Journal of Geophysical Research: Atmospheres","day":"18","quality_controlled":"1","publisher":"American Geophysical Union"},{"extern":"1","date_updated":"2023-02-24T09:30:42Z","_id":"12629","status":"public","keyword":["Water Science and Technology","Development"],"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1360-0648"],"issn":["0790-0627"]},"publication_status":"published","volume":31,"issue":"2","oa_version":"Published Version","abstract":[{"text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region.","lang":"eng"}],"month":"04","intvolume":" 31","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1080/07900627.2015.1020417","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417.","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417","ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.","short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200.","chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.","ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200."},"title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","author":[{"first_name":"J.M.","full_name":"Shea, J.M.","last_name":"Shea"},{"full_name":"Wagnon, P.","last_name":"Wagnon","first_name":"P."},{"last_name":"Immerzeel","full_name":"Immerzeel, W.W.","first_name":"W.W."},{"last_name":"Biron","full_name":"Biron, R.","first_name":"R."},{"last_name":"Brun","full_name":"Brun, F.","first_name":"F."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"}],"article_processing_charge":"No","day":"18","publication":"International Journal of Water Resources Development","year":"2015","doi":"10.1080/07900627.2015.1020417","date_published":"2015-04-18T00:00:00Z","date_created":"2023-02-20T08:16:17Z","page":"174-200","publisher":"Taylor & Francis","quality_controlled":"1","oa":1},{"title":"Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya","author":[{"last_name":"Steiner","full_name":"Steiner, Jakob F.","first_name":"Jakob F."},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"full_name":"Immerzeel, Walter W.","last_name":"Immerzeel","first_name":"Walter W."},{"full_name":"Reid, Tim D.","last_name":"Reid","first_name":"Tim D."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194","apa":"Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194","short":"J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907.","ieee":"J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015.","mla":"Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.","ista":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907.","chicago":"Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194."},"doi":"10.3189/2015jog14j194","date_published":"2015-07-01T00:00:00Z","date_created":"2023-02-20T08:16:01Z","page":"889-907","day":"01","publication":"Journal of Glaciology","year":"2015","publisher":"International Glaciological Society","quality_controlled":"1","oa":1,"extern":"1","date_updated":"2023-02-24T09:43:14Z","status":"public","type":"journal_article","article_type":"original","_id":"12626","volume":61,"issue":"229","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"publication_status":"published","month":"07","intvolume":" 61","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG14J194"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%."}]},{"oa":1,"quality_controlled":"1","publisher":"International Glaciological Society","date_created":"2023-02-20T08:16:06Z","doi":"10.3189/2015jog14j227","date_published":"2015-05-01T00:00:00Z","page":"524-536","publication":"Journal of Glaciology","day":"01","year":"2015","title":"Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014","article_processing_charge":"No","author":[{"first_name":"Sam","full_name":"Herreid, Sam","last_name":"Herreid"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"first_name":"Alvaro","full_name":"Ayala, Alvaro","last_name":"Ayala"},{"first_name":"Anna","last_name":"Chesnokova","full_name":"Chesnokova, Anna"},{"last_name":"Kienholz","full_name":"Kienholz, Christian","first_name":"Christian"},{"full_name":"Shea, Joseph","last_name":"Shea","first_name":"Joseph"},{"last_name":"Shrestha","full_name":"Shrestha, Arun","first_name":"Arun"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227.","apa":"Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227","ama":"Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227","short":"S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536.","ieee":"S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015.","chicago":"Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227.","ista":"Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536."},"intvolume":" 61","month":"05","main_file_link":[{"url":"https://doi.org/10.3189/2015JoG14J227","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known.","lang":"eng"}],"volume":61,"issue":"227","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"status":"public","article_type":"original","type":"journal_article","_id":"12627","extern":"1","date_updated":"2023-02-24T09:40:30Z"},{"ec_funded":1,"issue":"27","volume":54,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/","open_access":"1"}],"scopus_import":"1","intvolume":" 54","month":"06","abstract":[{"lang":"eng","text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed."}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"MiSi"}],"date_updated":"2023-03-30T11:32:57Z","type":"journal_article","status":"public","_id":"1618","page":"4163 - 4166","date_created":"2018-12-11T11:53:03Z","doi":"10.1021/acs.biochem.5b00560","date_published":"2015-06-26T00:00:00Z","year":"2015","publication":"Biochemistry","day":"26","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","external_id":{"pmid":["26115234"]},"article_processing_charge":"No","publist_id":"5548","author":[{"first_name":"Christopher","full_name":"Veldkamp, Christopher","last_name":"Veldkamp"},{"id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Kiermaier","orcid":"0000-0001-6165-5738","full_name":"Kiermaier, Eva"},{"last_name":"Gabel Eissens","full_name":"Gabel Eissens, Skylar","first_name":"Skylar"},{"first_name":"Miranda","last_name":"Gillitzer","full_name":"Gillitzer, Miranda"},{"full_name":"Lippner, David","last_name":"Lippner","first_name":"David"},{"first_name":"Frank","last_name":"Disilvio","full_name":"Disilvio, Frank"},{"full_name":"Mueller, Casey","last_name":"Mueller","first_name":"Casey"},{"first_name":"Paeton","last_name":"Wantuch","full_name":"Wantuch, Paeton"},{"last_name":"Chaffee","full_name":"Chaffee, Gary","first_name":"Gary"},{"full_name":"Famiglietti, Michael","last_name":"Famiglietti","first_name":"Michael"},{"first_name":"Danielle","full_name":"Zgoba, Danielle","last_name":"Zgoba"},{"full_name":"Bailey, Asha","last_name":"Bailey","first_name":"Asha"},{"first_name":"Yaya","full_name":"Bah, Yaya","last_name":"Bah"},{"first_name":"Samantha","last_name":"Engebretson","full_name":"Engebretson, Samantha"},{"last_name":"Graupner","full_name":"Graupner, David","first_name":"David"},{"last_name":"Lackner","full_name":"Lackner, Emily","first_name":"Emily"},{"last_name":"Larosa","full_name":"Larosa, Vincent","first_name":"Vincent"},{"last_name":"Medeiros","full_name":"Medeiros, Tysha","first_name":"Tysha"},{"first_name":"Michael","last_name":"Olson","full_name":"Olson, Michael"},{"last_name":"Phillips","full_name":"Phillips, Andrew","first_name":"Andrew"},{"last_name":"Pyles","full_name":"Pyles, Harley","first_name":"Harley"},{"last_name":"Richard","full_name":"Richard, Amanda","first_name":"Amanda"},{"full_name":"Schoeller, Scott","last_name":"Schoeller","first_name":"Scott"},{"first_name":"Boris","full_name":"Touzeau, Boris","last_name":"Touzeau"},{"first_name":"Larry","full_name":"Williams, Larry","last_name":"Williams"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Peterson","full_name":"Peterson, Francis","first_name":"Francis"}],"title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","citation":{"mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560","ieee":"C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}]},{"acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","oa":1,"quality_controlled":"1","publisher":"MIT Press","year":"2015","has_accepted_license":"1","publication":"Proceedings of the 13th European Conference on Artificial Life","day":"01","page":"78","date_created":"2023-04-30T22:01:07Z","date_published":"2015-07-01T00:00:00Z","doi":"10.7551/978-0-262-33027-5-ch018","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eckehard","last_name":"Olbrich","full_name":"Olbrich, Eckehard"}],"title":"Quantifying self-organizing behavior of autonomous robots","oa_version":"Published Version","scopus_import":"1","month":"07","publication_status":"published","publication_identifier":{"isbn":["9780262330275"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2015_ECAL_Martius.pdf","date_created":"2023-05-02T07:02:59Z","creator":"dernst","file_size":1674241,"date_updated":"2023-05-02T07:02:59Z","success":1,"file_id":"12882","checksum":"880eabe59c9df12f06a882aa1bc4e600","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"_id":"12881","conference":{"start_date":"2015-07-20","location":"York, United Kingdom","end_date":"2015-07-24","name":"ECAL: European Conference on Artificial Life"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","date_updated":"2023-05-02T07:06:21Z","ddc":["000"],"file_date_updated":"2023-05-02T07:02:59Z","department":[{"_id":"ChLa"}]},{"title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","external_id":{"pmid":["26063389"]},"article_processing_charge":"No","author":[{"full_name":"Johnson, Kaeli C.M.","last_name":"Johnson","first_name":"Kaeli C.M."},{"first_name":"Shitou","full_name":"Xia, Shitou","last_name":"Xia"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"last_name":"Li","full_name":"Li, Xin","first_name":"Xin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","apa":"Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087."},"date_created":"2023-01-16T09:20:22Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1093/pcp/pcv087","page":"1616-1623","publication":"Plant and Cell Physiology","year":"2015","quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","department":[{"_id":"XiFe"}],"extern":"1","date_updated":"2023-05-08T11:03:23Z","keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"status":"public","type":"journal_article","article_type":"original","_id":"12196","volume":56,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0032-0781","1471-9053"]},"intvolume":" 56","month":"08","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity."}]},{"publisher":"Springer Nature","quality_controlled":"1","day":"23","publication":"Nature Nanotechnology","year":"2015","doi":"10.1038/nnano.2015.256","date_published":"2015-11-23T00:00:00Z","date_created":"2023-08-01T09:44:04Z","page":"82-88","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda, Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256.","ista":"Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK, Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.","mla":"Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature, 2015, pp. 82–88, doi:10.1038/nnano.2015.256.","short":"H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K. Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.","ieee":"H. Zhao et al., “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11. Springer Nature, pp. 82–88, 2015.","ama":"Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 2015;11:82-88. doi:10.1038/nnano.2015.256","apa":"Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D., … Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256"},"title":"Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks","author":[{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"last_name":"Sen","full_name":"Sen, Soumyo","first_name":"Soumyo"},{"first_name":"T.","full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao"},{"last_name":"Sawczyk","full_name":"Sawczyk, Michał","first_name":"Michał"},{"last_name":"Kučanda","full_name":"Kučanda, Kristina","first_name":"Kristina"},{"first_name":"Debasish","last_name":"Manna","full_name":"Manna, Debasish"},{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"full_name":"Lee, Ji-Woong","last_name":"Lee","first_name":"Ji-Woong"},{"first_name":"Petr","last_name":"Král","full_name":"Král, Petr"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["26595335"]},"article_processing_charge":"No","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution."}],"month":"11","intvolume":" 11","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"publication_status":"published","volume":11,"_id":"13392","status":"public","keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-08-07T12:55:46Z"},{"doi":"10.1038/nchem.2303","date_published":"2015-07-20T00:00:00Z","date_created":"2023-08-01T09:44:33Z","page":"646-652","day":"20","publication":"Nature Chemistry","year":"2015","publisher":"Springer Nature","quality_controlled":"1","title":"Light-controlled self-assembly of non-photoresponsive nanoparticles","author":[{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"first_name":"Dipak","full_name":"Samanta, Dipak","last_name":"Samanta"},{"full_name":"Leizrowice, Ron","last_name":"Leizrowice","first_name":"Ron"},{"last_name":"Margulis","full_name":"Margulis, Baruch","first_name":"Baruch"},{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"full_name":"Börner, Martin","last_name":"Börner","first_name":"Martin"},{"full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao","first_name":"T."},{"full_name":"Manna, Debasish","last_name":"Manna","first_name":"Debasish"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"article_processing_charge":"No","external_id":{"pmid":["26201741"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 7, 646–652.","chicago":"Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao, Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.","ama":"Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303","apa":"Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner, M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303","ieee":"P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652, 2015.","short":"P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T. Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.","mla":"Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52, doi:10.1038/nchem.2303."},"volume":7,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"publication_status":"published","month":"07","intvolume":" 7","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time."}],"extern":"1","date_updated":"2023-08-07T13:00:15Z","status":"public","keyword":["General Chemical Engineering","General Chemistry"],"type":"journal_article","article_type":"original","_id":"13394"},{"title":"Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes","article_processing_charge":"No","external_id":{"pmid":["25959725"]},"author":[{"first_name":"Debasish","last_name":"Manna","full_name":"Manna, Debasish"},{"first_name":"Thumu","full_name":"Udayabhaskararao, Thumu","last_name":"Udayabhaskararao"},{"first_name":"Hui","full_name":"Zhao, Hui","last_name":"Zhao"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.","short":"D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397.","apa":"Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419","ama":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419","mla":"Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.","ista":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 54(42), 12394–12397.","chicago":"Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419."},"date_created":"2023-08-01T09:44:19Z","doi":"10.1002/anie.201502419","date_published":"2015-10-01T00:00:00Z","page":"12394-12397","publication":"Angewandte Chemie International Edition","day":"01","year":"2015","quality_controlled":"1","publisher":"Wiley","extern":"1","date_updated":"2023-08-07T12:58:29Z","keyword":["General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"original","_id":"13393","volume":54,"issue":"42","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"intvolume":" 54","month":"10","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light."}]},{"status":"public","keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"type":"journal_article","article_type":"original","_id":"13395","extern":"1","date_updated":"2023-08-07T13:01:53Z","month":"11","intvolume":" 51","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1039/C4CC08541H","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate."}],"volume":51,"issue":"11","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"publication_status":"published","title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","author":[{"last_name":"Lee","full_name":"Lee, Ji-Woong","first_name":"Ji-Woong"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["25417754"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.","ista":"Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.","mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h.","ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” Chemical Communications, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 2015;51(11):2036-2039. doi:10.1039/c4cc08541h","apa":"Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h"},"publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"date_published":"2015-11-18T00:00:00Z","doi":"10.1039/c4cc08541h","date_created":"2023-08-01T09:44:48Z","page":"2036-2039","day":"18","publication":"Chemical Communications","year":"2015"},{"article_processing_charge":"No","external_id":{"pmid":["25544061"]},"author":[{"first_name":"Thomas","last_name":"Moldt","full_name":"Moldt, Thomas"},{"last_name":"Brete","full_name":"Brete, Daniel","first_name":"Daniel"},{"first_name":"Daniel","full_name":"Przyrembel, Daniel","last_name":"Przyrembel"},{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"full_name":"Goldman, Joel R.","last_name":"Goldman","first_name":"Joel R."},{"first_name":"Pintu K.","full_name":"Kundu, Pintu K.","last_name":"Kundu"},{"full_name":"Gahl, Cornelius","last_name":"Gahl","first_name":"Cornelius"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"},{"last_name":"Weinelt","full_name":"Weinelt, Martin","first_name":"Martin"}],"title":"Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature","citation":{"ista":"Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.","chicago":"Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman, Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.","short":"T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl, R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.","ieee":"T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015.","apa":"Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K., … Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. American Chemical Society. https://doi.org/10.1021/la504291n","ama":"Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057. doi:10.1021/la504291n","mla":"Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1048-1057","date_created":"2023-08-01T09:45:02Z","date_published":"2015-01-27T00:00:00Z","doi":"10.1021/la504291n","year":"2015","publication":"Langmuir","day":"27","publisher":"American Chemical Society","quality_controlled":"1","date_updated":"2023-08-07T13:05:04Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"status":"public","_id":"13396","volume":31,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0743-7463"],"eissn":["1520-5827"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 31","month":"01","abstract":[{"text":"Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs.","lang":"eng"}],"pmid":1,"oa_version":"None"},{"citation":{"chicago":"Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.","ista":"Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421.","mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:10.1039/c4fd00265b.","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b","apa":"Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b","short":"G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.","ieee":"G. Singh et al., “Magnetic field-induced self-assembly of iron oxide nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Singh, Gurvinder","last_name":"Singh","first_name":"Gurvinder"},{"first_name":"Henry","full_name":"Chan, Henry","last_name":"Chan"},{"full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao","first_name":"T."},{"first_name":"Elijah","full_name":"Gelman, Elijah","last_name":"Gelman"},{"full_name":"Peddis, Davide","last_name":"Peddis","first_name":"Davide"},{"full_name":"Baskin, Artem","last_name":"Baskin","first_name":"Artem"},{"last_name":"Leitus","full_name":"Leitus, Gregory","first_name":"Gregory"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"article_processing_charge":"No","external_id":{"pmid":["25920522"]},"title":"Magnetic field-induced self-assembly of iron oxide nanocubes","year":"2015","day":"02","publication":"Faraday Discussions","page":"403-421","date_published":"2015-01-02T00:00:00Z","doi":"10.1039/c4fd00265b","date_created":"2023-08-01T09:45:17Z","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"date_updated":"2023-08-07T13:06:23Z","extern":"1","_id":"13397","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry"],"publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":181,"abstract":[{"lang":"eng","text":"Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C4FD00265B"}],"month":"01","intvolume":" 181"},{"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 181","month":"07","publication_status":"published","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"language":[{"iso":"eng"}],"volume":181,"_id":"13398","article_type":"letter_note","type":"journal_article","keyword":["Physical and Theoretical Chemistry"],"status":"public","date_updated":"2023-08-08T07:16:20Z","extern":"1","publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2015","publication":"Faraday Discussions","day":"07","page":"463-479","date_created":"2023-08-01T09:45:29Z","date_published":"2015-07-07T00:00:00Z","doi":"10.1039/c5fd90041g","citation":{"chicago":"Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.","ista":"Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M, Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly process: General discussion. Faraday Discussions. 181, 463–479.","mla":"Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:10.1039/c5fd90041g.","ama":"Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g","apa":"Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g","short":"Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa, P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R. Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B. Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R. Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.","ieee":"Y. Sun et al., “Field-assisted self-assembly process: General discussion,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26149295"]},"article_processing_charge":"No","author":[{"first_name":"Yugang","last_name":"Sun","full_name":"Sun, Yugang"},{"last_name":"Scarabelli","full_name":"Scarabelli, Leonardo","first_name":"Leonardo"},{"full_name":"Kotov, Nicholas","last_name":"Kotov","first_name":"Nicholas"},{"first_name":"Moritz","full_name":"Tebbe, Moritz","last_name":"Tebbe"},{"first_name":"Xiao-Min","last_name":"Lin","full_name":"Lin, Xiao-Min"},{"last_name":"Brullot","full_name":"Brullot, Ward","first_name":"Ward"},{"first_name":"Lucio","full_name":"Isa, Lucio","last_name":"Isa"},{"last_name":"Schurtenberger","full_name":"Schurtenberger, Peter","first_name":"Peter"},{"full_name":"Moehwald, Helmuth","last_name":"Moehwald","first_name":"Helmuth"},{"full_name":"Fedin, Igor","last_name":"Fedin","first_name":"Igor"},{"first_name":"Orlin","full_name":"Velev, Orlin","last_name":"Velev"},{"last_name":"Faivre","full_name":"Faivre, Damien","first_name":"Damien"},{"last_name":"Sorensen","full_name":"Sorensen, Christopher","first_name":"Christopher"},{"last_name":"Perzynski","full_name":"Perzynski, Régine","first_name":"Régine"},{"first_name":"Munish","last_name":"Chanana","full_name":"Chanana, Munish"},{"last_name":"Li","full_name":"Li, Zhihai","first_name":"Zhihai"},{"first_name":"Fernando","last_name":"Bresme","full_name":"Bresme, Fernando"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"last_name":"Firlar","full_name":"Firlar, Emre","first_name":"Emre"},{"last_name":"Schiffrin","full_name":"Schiffrin, David","first_name":"David"},{"first_name":"Joao Batista","full_name":"Souza Junior, Joao Batista","last_name":"Souza Junior"},{"first_name":"Andreas","full_name":"Fery, Andreas","last_name":"Fery"},{"last_name":"Shevchenko","full_name":"Shevchenko, Elena","first_name":"Elena"},{"full_name":"Tarhan, Ozgur","last_name":"Tarhan","first_name":"Ozgur"},{"full_name":"Alivisatos, Armand Paul","last_name":"Alivisatos","first_name":"Armand Paul"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"first_name":"Suvojit","full_name":"Ghosh, Suvojit","last_name":"Ghosh"}],"title":"Field-assisted self-assembly process: General discussion"},{"date_updated":"2023-08-22T08:56:34Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Atomic and Molecular Physics","and Optics"],"status":"public","_id":"14017","issue":"2","volume":91,"publication_status":"published","publication_identifier":{"eissn":["1094-1622"],"issn":["1050-2947"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.03933"}],"scopus_import":"1","intvolume":" 91","month":"02","abstract":[{"lang":"eng","text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results."}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"arxiv":["1504.03933"]},"author":[{"first_name":"Song Bin","full_name":"Zhang, Song Bin","last_name":"Zhang"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"first_name":"Peter M.","full_name":"Kraus, Peter M.","last_name":"Kraus"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"},{"last_name":"Rohringer","full_name":"Rohringer, Nina","first_name":"Nina"}],"title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","citation":{"mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421.","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.91.023421","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” Physical Review A, vol. 91, no. 2. American Physical Society, 2015.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015).","chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.","ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"023421","date_created":"2023-08-10T06:38:10Z","doi":"10.1103/physreva.91.023421","date_published":"2015-02-19T00:00:00Z","year":"2015","publication":"Physical Review A","day":"19","oa":1,"publisher":"American Physical Society","quality_controlled":"1"},{"date_updated":"2023-08-22T08:52:56Z","extern":"1","article_type":"original","type":"journal_article","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"status":"public","_id":"14016","volume":6,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"scopus_import":"1","intvolume":" 6","month":"05","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"oa_version":"Published Version","pmid":1,"article_processing_charge":"No","external_id":{"pmid":["25940229"]},"author":[{"last_name":"Kraus","full_name":"Kraus, P. M.","first_name":"P. M."},{"first_name":"O. I.","last_name":"Tolstikhin","full_name":"Tolstikhin, O. I."},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"full_name":"Rupenyan, A.","last_name":"Rupenyan","first_name":"A."},{"first_name":"J.","full_name":"Schneider, J.","last_name":"Schneider"},{"first_name":"C. Z.","last_name":"Bisgaard","full_name":"Bisgaard, C. Z."},{"full_name":"Morishita, T.","last_name":"Morishita","first_name":"T."},{"first_name":"F.","last_name":"Jensen","full_name":"Jensen, F."},{"last_name":"Madsen","full_name":"Madsen, L. B.","first_name":"L. B."},{"full_name":"Wörner, H. J.","last_name":"Wörner","first_name":"H. J."}],"title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","citation":{"mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039.","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","ieee":"P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015.","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.","ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"7039","date_created":"2023-08-10T06:38:01Z","doi":"10.1038/ncomms8039","date_published":"2015-05-05T00:00:00Z","year":"2015","publication":"Nature Communications","day":"05","oa":1,"publisher":"Springer Nature","quality_controlled":"1"}]