[{"year":"2013","extern":"1","author":[{"full_name":"Immerzeel, W. W.","first_name":"W. W.","last_name":"Immerzeel"},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"full_name":"Bierkens, M. F. P.","first_name":"M. F. P.","last_name":"Bierkens"}],"quality_controlled":"1","citation":{"chicago":"Immerzeel, W. W., Francesca Pellicciotti, and M. F. P. Bierkens. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” <i>Nature Geoscience</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/ngeo1896\">https://doi.org/10.1038/ngeo1896</a>.","short":"W.W. Immerzeel, F. Pellicciotti, M.F.P. Bierkens, Nature Geoscience 6 (2013) 742–745.","ista":"Immerzeel WW, Pellicciotti F, Bierkens MFP. 2013. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience. 6(9), 742–745.","ama":"Immerzeel WW, Pellicciotti F, Bierkens MFP. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. <i>Nature Geoscience</i>. 2013;6(9):742-745. doi:<a href=\"https://doi.org/10.1038/ngeo1896\">10.1038/ngeo1896</a>","ieee":"W. W. Immerzeel, F. Pellicciotti, and M. F. P. Bierkens, “Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds,” <i>Nature Geoscience</i>, vol. 6, no. 9. Springer Nature, pp. 742–745, 2013.","apa":"Immerzeel, W. W., Pellicciotti, F., &#38; Bierkens, M. F. P. (2013). Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. <i>Nature Geoscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ngeo1896\">https://doi.org/10.1038/ngeo1896</a>","mla":"Immerzeel, W. W., et al. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” <i>Nature Geoscience</i>, vol. 6, no. 9, Springer Nature, 2013, pp. 742–45, doi:<a href=\"https://doi.org/10.1038/ngeo1896\">10.1038/ngeo1896</a>."},"abstract":[{"text":"Greater Himalayan glaciers are retreating and losing mass at rates comparable to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes and their associated hydrological impacts are scarce, oversimplify glacier dynamics or include a limited number of climate models6,7,8,9. Here, we use results from the latest ensemble of climate models in combination with a high-resolution glacio-hydrological model to assess the hydrological impact of climate change on two climatically contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds that drain into the Indus and Ganges rivers, respectively. We show that the largest uncertainty in future runoff is a result of variations in projected precipitation between climate models. In both watersheds, strong, but highly variable, increases in future runoff are projected and, despite the different characteristics of the watersheds, their responses are surprisingly similar. In both cases, glaciers will recede but net glacier melt runoff is on a rising limb at least until 2050. In combination with a positive change in precipitation, water availability during this century is not likely to decline. We conclude that river basins that depend on monsoon rains and glacier melt will continue to sustain the increasing water demands expected in these areas10.","lang":"eng"}],"publication_status":"published","_id":"12640","publication":"Nature Geoscience","title":"Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds","article_type":"letter_note","publisher":"Springer Nature","issue":"9","volume":6,"status":"public","month":"09","date_created":"2023-02-20T08:17:17Z","intvolume":"         6","day":"13","oa_version":"None","type":"journal_article","date_updated":"2023-02-21T10:46:37Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/ngeo1896","language":[{"iso":"eng"}],"page":"742-745","keyword":["General Earth and Planetary Sciences"],"date_published":"2013-09-13T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1752-0908"],"issn":["1752-0894"]}},{"issue":"63","volume":54,"publisher":"International Glaciological Society","article_type":"original","intvolume":"        54","status":"public","month":"08","date_created":"2023-02-20T08:17:21Z","quality_controlled":"1","extern":"1","author":[{"full_name":"Heynen, Martin","first_name":"Martin","last_name":"Heynen"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca"},{"full_name":"Carenzo, Marco","first_name":"Marco","last_name":"Carenzo"}],"main_file_link":[{"url":"https://doi.org/10.3189/2013aog63a537","open_access":"1"}],"citation":{"apa":"Heynen, M., Pellicciotti, F., &#38; Carenzo, M. (2013). Parameter sensitivity of a distributed enhanced temperature-index melt model. <i>Annals of Glaciology</i>. International Glaciological Society. <a href=\"https://doi.org/10.3189/2013aog63a537\">https://doi.org/10.3189/2013aog63a537</a>","mla":"Heynen, Martin, et al. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” <i>Annals of Glaciology</i>, vol. 54, no. 63, International Glaciological Society, 2013, pp. 311–21, doi:<a href=\"https://doi.org/10.3189/2013aog63a537\">10.3189/2013aog63a537</a>.","ista":"Heynen M, Pellicciotti F, Carenzo M. 2013. Parameter sensitivity of a distributed enhanced temperature-index melt model. Annals of Glaciology. 54(63), 311–321.","chicago":"Heynen, Martin, Francesca Pellicciotti, and Marco Carenzo. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” <i>Annals of Glaciology</i>. International Glaciological Society, 2013. <a href=\"https://doi.org/10.3189/2013aog63a537\">https://doi.org/10.3189/2013aog63a537</a>.","short":"M. Heynen, F. Pellicciotti, M. Carenzo, Annals of Glaciology 54 (2013) 311–321.","ieee":"M. Heynen, F. Pellicciotti, and M. Carenzo, “Parameter sensitivity of a distributed enhanced temperature-index melt model,” <i>Annals of Glaciology</i>, vol. 54, no. 63. International Glaciological Society, pp. 311–321, 2013.","ama":"Heynen M, Pellicciotti F, Carenzo M. Parameter sensitivity of a distributed enhanced temperature-index melt model. <i>Annals of Glaciology</i>. 2013;54(63):311-321. doi:<a href=\"https://doi.org/10.3189/2013aog63a537\">10.3189/2013aog63a537</a>"},"year":"2013","_id":"12641","oa":1,"publication":"Annals of Glaciology","title":"Parameter sensitivity of a distributed enhanced temperature-index melt model","abstract":[{"text":"We investigate the sensitivity of a distributed enhanced temperature-index (ETI) melt model, in order to understand which parameters have the largest influence on model outputs and thus need to be accurately known. We use melt and meteorological data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity analysis is conducted in a systematic way in terms of parameters and the different conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined. The sensitivity of total melt to changes in individual parameters is calculated using a local method around the optimal value of the parameters. We verify that the parameters are optimal at the distributed scale and assess the model uncertainty induced by uncertainty in the parameters using a Monte Carlo technique. Model sensitivity to parameters is consistent across melt seasons, glaciers, different conditions and the daily statistics examined. The parameters to which the model is most sensitive are the shortwave-radiation factor, the temperature lapse rate for extrapolation of air temperature, the albedo parameters, the temperature threshold and the cloud transmittance factor parameters. A parameter uncertainty of 5% results in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland.","lang":"eng"}],"publication_status":"published","page":"311-321","date_published":"2013-08-01T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1727-5644"],"issn":["0260-3055"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","date_updated":"2023-02-21T10:43:42Z","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3189/2013aog63a537"},{"publisher":"International Glaciological Society","article_type":"original","issue":"63","volume":54,"status":"public","month":"08","date_created":"2023-02-20T08:17:29Z","intvolume":"        54","year":"2013","extern":"1","author":[{"last_name":"Petersen","first_name":"Lene","full_name":"Petersen, Lene"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"},{"full_name":"Juszak, Inge","first_name":"Inge","last_name":"Juszak"},{"last_name":"Carenzo","first_name":"Marco","full_name":"Carenzo, Marco"},{"last_name":"Brock","first_name":"Ben","full_name":"Brock, Ben"}],"quality_controlled":"1","citation":{"ista":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. 2013. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. Annals of Glaciology. 54(63), 120–130.","chicago":"Petersen, Lene, Francesca Pellicciotti, Inge Juszak, Marco Carenzo, and Ben Brock. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” <i>Annals of Glaciology</i>. International Glaciological Society, 2013. <a href=\"https://doi.org/10.3189/2013aog63a477\">https://doi.org/10.3189/2013aog63a477</a>.","short":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, B. Brock, Annals of Glaciology 54 (2013) 120–130.","ieee":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, and B. Brock, “Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative,” <i>Annals of Glaciology</i>, vol. 54, no. 63. International Glaciological Society, pp. 120–130, 2013.","ama":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. <i>Annals of Glaciology</i>. 2013;54(63):120-130. doi:<a href=\"https://doi.org/10.3189/2013aog63a477\">10.3189/2013aog63a477</a>","apa":"Petersen, L., Pellicciotti, F., Juszak, I., Carenzo, M., &#38; Brock, B. (2013). Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. <i>Annals of Glaciology</i>. International Glaciological Society. <a href=\"https://doi.org/10.3189/2013aog63a477\">https://doi.org/10.3189/2013aog63a477</a>","mla":"Petersen, Lene, et al. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” <i>Annals of Glaciology</i>, vol. 54, no. 63, International Glaciological Society, 2013, pp. 120–30, doi:<a href=\"https://doi.org/10.3189/2013aog63a477\">10.3189/2013aog63a477</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2013aog63a477"}],"abstract":[{"text":"Near-surface air temperature, typically measured at a height of 2 m, is the most important control on the energy exchange and the melt rate at a snow or ice surface. It is distributed in a simplistic manner in most glacier melt models by using constant linear lapse rates, which poorly represent the actual spatial and temporal variability of air temperature. In this paper, we test a simple thermodynamic model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset of air temperature measurements from along the flowline of Haut Glacier d’Arolla, Switzerland. The unmodified model performs little better than assuming a constant linear lapse rate. When modified to allow the ratio of the boundary layer height to the bulk heat transfer coefficient to vary along the flowline, the model matches measured air temperatures better, and a further reduction of the root-mean-square error is obtained, although there is still considerable scope for improvement. The modified model is shown to perform best under conditions favourable to the development of katabatic winds – few clouds, positive ambient air temperature, limited influence of synoptic or valley winds and a long fetch – but its performance is poor under cloudy conditions.","lang":"eng"}],"publication_status":"published","_id":"12642","oa":1,"publication":"Annals of Glaciology","title":"Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative","page":"120-130","keyword":["Earth-Surface Processes"],"date_published":"2013-08-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0260-3055"],"eissn":["1727-5644"]},"day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2023-02-21T10:18:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","doi":"10.3189/2013aog63a477","language":[{"iso":"eng"}]},{"abstract":[{"text":"Parameterizations of incoming longwave radiation are increasingly receiving attention for both low and high elevation glacierized sites. In this paper, we test 13 clear-sky parameterizations combined with seven cloud corrections for all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also analyze the four seasons separately and conduct a cross-validation to test the parameters’ robustness. The best parameterization is the one by Dilley and O'Brien, B for clear-sky conditions combined with Unsworth and Monteith cloud correction. This model is also the most robust when tested in cross-validation. When validated at different sites in the southern Alps of Switzerland and north-western Italian Alps, all parameterizations show a substantial decrease in performance, except for one site, thus suggesting that it is important to recalibrate parameterizations of incoming longwave radiation for different locations. We argue that this is due to differences in the structure of the atmosphere at the sites. We also quantify the effect that the incoming longwave radiation parameterizations have on energy-balance melt modeling, and show that recalibration of model parameters is needed. Using parameters from other sites leads to a significant underestimation of melt and to an error that is larger than that associated with using different parameterizations. Once recalibrated, however, the parameters of most models seem to be stable over seasons and years at the location on Haut Glacier d'Arolla.","lang":"eng"}],"publication_status":"published","publication":"Journal of Geophysical Research: Atmospheres","title":"A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability","_id":"12643","oa":1,"year":"2013","citation":{"mla":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 118, no. 8, American Geophysical Union, 2013, pp. 3066–84, doi:<a href=\"https://doi.org/10.1002/jgrd.50277\">10.1002/jgrd.50277</a>.","apa":"Juszak, I., &#38; Pellicciotti, F. (2013). A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/jgrd.50277\">https://doi.org/10.1002/jgrd.50277</a>","ieee":"I. Juszak and F. Pellicciotti, “A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 118, no. 8. American Geophysical Union, pp. 3066–3084, 2013.","ama":"Juszak I, Pellicciotti F. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. <i>Journal of Geophysical Research: Atmospheres</i>. 2013;118(8):3066-3084. doi:<a href=\"https://doi.org/10.1002/jgrd.50277\">10.1002/jgrd.50277</a>","short":"I. Juszak, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 118 (2013) 3066–3084.","chicago":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2013. <a href=\"https://doi.org/10.1002/jgrd.50277\">https://doi.org/10.1002/jgrd.50277</a>.","ista":"Juszak I, Pellicciotti F. 2013. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. Journal of Geophysical Research: Atmospheres. 118(8), 3066–3084."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/jgrd.50277"}],"quality_controlled":"1","author":[{"full_name":"Juszak, I.","first_name":"I.","last_name":"Juszak"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti"}],"extern":"1","month":"04","date_created":"2023-02-20T08:17:34Z","status":"public","intvolume":"       118","article_type":"original","publisher":"American Geophysical Union","issue":"8","volume":118,"doi":"10.1002/jgrd.50277","language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2023-02-21T10:10:46Z","type":"journal_article","day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["2169-897X"]},"keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"date_published":"2013-04-27T00:00:00Z","page":"3066-3084"},{"date_created":"2018-12-11T11:51:16Z","month":"01","status":"public","intvolume":"        33","publist_id":"5967","publisher":"Society for Neuroscience","date_published":"2013-01-01T00:00:00Z","issue":"34","volume":33,"page":"13927 - 13934","acknowledgement":"This work was supported by the Max Planck Society. ","publication_status":"published","abstract":[{"text":"When confronted with a large-field stimulus rotating around the vertical body axis, flies display a following behavior called &quot;optomotor response.&quot; As neural control elements, the large tangential horizontal system (HS) cells of the lobula plate have been prime candidates for long. Here, we applied optogenetic stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize interference of the optical activation of channelrhodopsin-2 with the visual perception of the flies, we used a bistable variant called ChR2-C128S. By applying pulses of blue and yellow light, we first demonstrate electrophysiologically that lobula plate tangential cells can be activated and deactivated repeatedly with no evident change in depolarization strength over trials. We next show that selective optogenetic activation of HS cells elicits robust yaw head movements and yaw turning responses in fixed and tethered flying flies, respectively.","lang":"eng"}],"title":"Optogenetic control of fly optomotor responses","publication":"Journal of Neuroscience","doi":"10.1523/JNEUROSCI.0340-13.2013","_id":"1304","type":"journal_article","date_updated":"2021-01-12T06:49:45Z","day":"01","year":"2013","citation":{"ista":"Haikala V, Jösch MA, Borst A, Mauss A. 2013. Optogenetic control of fly optomotor responses. Journal of Neuroscience. 33(34), 13927–13934.","chicago":"Haikala, Väinö, Maximilian A Jösch, Alexander Borst, and Alex Mauss. “Optogenetic Control of Fly Optomotor Responses.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2013. <a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">https://doi.org/10.1523/JNEUROSCI.0340-13.2013</a>.","short":"V. Haikala, M.A. Jösch, A. Borst, A. Mauss, Journal of Neuroscience 33 (2013) 13927–13934.","ama":"Haikala V, Jösch MA, Borst A, Mauss A. Optogenetic control of fly optomotor responses. <i>Journal of Neuroscience</i>. 2013;33(34):13927-13934. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">10.1523/JNEUROSCI.0340-13.2013</a>","ieee":"V. Haikala, M. A. Jösch, A. Borst, and A. Mauss, “Optogenetic control of fly optomotor responses,” <i>Journal of Neuroscience</i>, vol. 33, no. 34. Society for Neuroscience, pp. 13927–13934, 2013.","apa":"Haikala, V., Jösch, M. A., Borst, A., &#38; Mauss, A. (2013). Optogenetic control of fly optomotor responses. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">https://doi.org/10.1523/JNEUROSCI.0340-13.2013</a>","mla":"Haikala, Väinö, et al. “Optogenetic Control of Fly Optomotor Responses.” <i>Journal of Neuroscience</i>, vol. 33, no. 34, Society for Neuroscience, 2013, pp. 13927–34, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0340-13.2013\">10.1523/JNEUROSCI.0340-13.2013</a>."},"author":[{"full_name":"Haikala, Väinö","first_name":"Väinö","last_name":"Haikala"},{"last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Maximilian Jösch"},{"last_name":"Borst","first_name":"Alexander","full_name":"Borst, Alexander"},{"last_name":"Mauss","first_name":"Alex","full_name":"Mauss, Alex S"}],"quality_controlled":0,"extern":1},{"doi":"10.1523/JNEUROSCI.3374-12.2013","_id":"1305","title":"Functional specialization of parallel motion detection circuits in the fly","publication":"Journal of Neuroscience","publication_status":"published","abstract":[{"lang":"eng","text":"In the fly Drosophila melanogaster, photoreceptor input to motion vision is split into two parallel pathways as represented by first-order interneurons L1 and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways are functionally specialized remains controversial. One study (Eichner et al., 2011) proposed that the L1-pathway evaluates only sequences of brightness increments (ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF). Another study (Clark et al., 2011) proposed that each of the two pathways evaluates both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded from motionsensitive neurons in flies in which the output from either L1 or L2 was genetically blocked. We found that blocking L1 abolishes ON-ON responses but leaves OFF-OFF responses intact. The opposite was true, when the output from L2 was blocked. We conclude that the L1 and L2 pathways are functionally specialized to detect ON-ON and OFF-OFF sequences, respectively."}],"acknowledgement":"This work was supported by the Max-Planck-Society and the SFB 870 of the Deutsche Forschungsgemeinschaft.","extern":1,"quality_controlled":0,"author":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Maximilian Jösch","last_name":"Jösch","first_name":"Maximilian A"},{"first_name":"Franz","last_name":"Weber","full_name":"Weber, Franz"},{"first_name":"Hubert","last_name":"Eichner","full_name":"Eichner, Hubert"},{"full_name":"Borst, Alexander","last_name":"Borst","first_name":"Alexander"}],"citation":{"apa":"Jösch, M. A., Weber, F., Eichner, H., &#38; Borst, A. (2013). Functional specialization of parallel motion detection circuits in the fly. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">https://doi.org/10.1523/JNEUROSCI.3374-12.2013</a>","mla":"Jösch, Maximilian A., et al. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” <i>Journal of Neuroscience</i>, vol. 33, no. 3, Society for Neuroscience, 2013, pp. 902–05, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">10.1523/JNEUROSCI.3374-12.2013</a>.","ista":"Jösch MA, Weber F, Eichner H, Borst A. 2013. Functional specialization of parallel motion detection circuits in the fly. Journal of Neuroscience. 33(3), 902–905.","chicago":"Jösch, Maximilian A, Franz Weber, Hubert Eichner, and Alexander Borst. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2013. <a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">https://doi.org/10.1523/JNEUROSCI.3374-12.2013</a>.","short":"M.A. Jösch, F. Weber, H. Eichner, A. Borst, Journal of Neuroscience 33 (2013) 902–905.","ieee":"M. A. Jösch, F. Weber, H. Eichner, and A. Borst, “Functional specialization of parallel motion detection circuits in the fly,” <i>Journal of Neuroscience</i>, vol. 33, no. 3. Society for Neuroscience, pp. 902–905, 2013.","ama":"Jösch MA, Weber F, Eichner H, Borst A. Functional specialization of parallel motion detection circuits in the fly. <i>Journal of Neuroscience</i>. 2013;33(3):902-905. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3374-12.2013\">10.1523/JNEUROSCI.3374-12.2013</a>"},"day":"16","year":"2013","type":"journal_article","date_updated":"2021-01-12T06:49:45Z","publist_id":"5968","intvolume":"        33","status":"public","date_created":"2018-12-11T11:51:16Z","month":"01","volume":33,"page":"902 - 905","issue":"3","date_published":"2013-01-16T00:00:00Z","publisher":"Society for Neuroscience"},{"date_created":"2018-12-11T11:51:17Z","month":"11","status":"public","intvolume":"        38","publist_id":"5962","publisher":"Taylor & Francis","date_published":"2013-11-01T00:00:00Z","page":"2004 - 2047","issue":"11","volume":38,"publication_status":"published","abstract":[{"text":"We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator.","lang":"eng"}],"publication":"Communications in Partial Differential Equations","title":"Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models","doi":"10.1080/03605302.2013.823548","_id":"1307","type":"journal_article","date_updated":"2021-01-12T06:49:46Z","day":"01","year":"2013","citation":{"mla":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” <i>Communications in Partial Differential Equations</i>, vol. 38, no. 11, Taylor &#38; Francis, 2013, pp. 2004–47, doi:<a href=\"https://doi.org/10.1080/03605302.2013.823548\">10.1080/03605302.2013.823548</a>.","apa":"Fischer, J. L. (2013). Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/03605302.2013.823548\">https://doi.org/10.1080/03605302.2013.823548</a>","chicago":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.1080/03605302.2013.823548\">https://doi.org/10.1080/03605302.2013.823548</a>.","short":"J.L. Fischer, Communications in Partial Differential Equations 38 (2013) 2004–2047.","ista":"Fischer JL. 2013. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. Communications in Partial Differential Equations. 38(11), 2004–2047.","ama":"Fischer JL. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. <i>Communications in Partial Differential Equations</i>. 2013;38(11):2004-2047. doi:<a href=\"https://doi.org/10.1080/03605302.2013.823548\">10.1080/03605302.2013.823548</a>","ieee":"J. L. Fischer, “Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models,” <i>Communications in Partial Differential Equations</i>, vol. 38, no. 11. Taylor &#38; Francis, pp. 2004–2047, 2013."},"extern":1,"author":[{"first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":0},{"month":"01","date_created":"2018-12-11T11:51:17Z","status":"public","intvolume":"        45","publist_id":"5963","publisher":"Society for Industrial and Applied Mathematics ","date_published":"2013-01-01T00:00:00Z","page":"1585 - 1615","volume":45,"issue":"3","abstract":[{"lang":"eng","text":"We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions."}],"publication_status":"published","publication":"SIAM Journal on Mathematical Analysis","title":"Advection-driven support shrinking in a chemotaxis model with degenerate mobility","_id":"1308","doi":"10.1137/120874291","type":"journal_article","date_updated":"2021-01-12T06:49:46Z","year":"2013","day":"01","citation":{"ista":"Fischer JL. 2013. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. SIAM Journal on Mathematical Analysis. 45(3), 1585–1615.","short":"J.L. Fischer, SIAM Journal on Mathematical Analysis 45 (2013) 1585–1615.","chicago":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics , 2013. <a href=\"https://doi.org/10.1137/120874291\">https://doi.org/10.1137/120874291</a>.","ieee":"J. L. Fischer, “Advection-driven support shrinking in a chemotaxis model with degenerate mobility,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 3. Society for Industrial and Applied Mathematics , pp. 1585–1615, 2013.","ama":"Fischer JL. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. <i>SIAM Journal on Mathematical Analysis</i>. 2013;45(3):1585-1615. doi:<a href=\"https://doi.org/10.1137/120874291\">10.1137/120874291</a>","mla":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 45, no. 3, Society for Industrial and Applied Mathematics , 2013, pp. 1585–615, doi:<a href=\"https://doi.org/10.1137/120874291\">10.1137/120874291</a>.","apa":"Fischer, J. L. (2013). Advection-driven support shrinking in a chemotaxis model with degenerate mobility. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/120874291\">https://doi.org/10.1137/120874291</a>"},"quality_controlled":0,"extern":1,"author":[{"first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Julian Fischer","orcid":"0000-0002-0479-558X"}]},{"day":"15","year":"2013","type":"journal_article","date_updated":"2021-01-12T06:49:47Z","author":[{"orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer"}],"extern":1,"quality_controlled":0,"citation":{"ama":"Fischer JL. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. <i>Journal of Differential Equations</i>. 2013;255(10):3127-3149. doi:<a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">10.1016/j.jde.2013.07.028</a>","ieee":"J. L. Fischer, “Optimal lower bounds on asymptotic support propagation rates for the thin-film equation,” <i>Journal of Differential Equations</i>, vol. 255, no. 10. Academic Press, pp. 3127–3149, 2013.","ista":"Fischer JL. 2013. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. Journal of Differential Equations. 255(10), 3127–3149.","short":"J.L. Fischer, Journal of Differential Equations 255 (2013) 3127–3149.","chicago":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” <i>Journal of Differential Equations</i>. Academic Press, 2013. <a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">https://doi.org/10.1016/j.jde.2013.07.028</a>.","apa":"Fischer, J. L. (2013). Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. <i>Journal of Differential Equations</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">https://doi.org/10.1016/j.jde.2013.07.028</a>","mla":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” <i>Journal of Differential Equations</i>, vol. 255, no. 10, Academic Press, 2013, pp. 3127–49, doi:<a href=\"https://doi.org/10.1016/j.jde.2013.07.028\">10.1016/j.jde.2013.07.028</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations."}],"doi":"10.1016/j.jde.2013.07.028","_id":"1310","publication":"Journal of Differential Equations","title":"Optimal lower bounds on asymptotic support propagation rates for the thin-film equation","publisher":"Academic Press","page":"3127 - 3149","volume":255,"issue":"10","date_published":"2013-11-15T00:00:00Z","status":"public","date_created":"2018-12-11T11:51:18Z","month":"11","publist_id":"5961","intvolume":"       255"},{"publication_identifier":{"issn":["1479-5876"]},"external_id":{"pmid":["24330813"]},"file":[{"content_type":"application/pdf","creator":"dernst","file_size":777311,"relation":"main_file","date_created":"2020-08-10T13:45:19Z","file_name":"2013_JoTM_Petricevic.pdf","access_level":"open_access","success":1,"date_updated":"2020-08-10T13:45:19Z","file_id":"8247"}],"date_published":"2013-12-12T00:00:00Z","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/3.0/","language":[{"iso":"eng"}],"doi":"10.1186/1479-5876-11-307","day":"12","oa_version":"None","type":"journal_article","date_updated":"2022-08-25T14:52:39Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_number":"307","status":"public","month":"12","date_created":"2020-08-10T11:54:34Z","intvolume":"        11","publisher":"Springer Nature","file_date_updated":"2020-08-10T13:45:19Z","volume":11,"abstract":[{"text":"Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease.","lang":"eng"}],"publication_status":"published","_id":"8245","ddc":["570"],"oa":1,"pmid":1,"publication":"Journal of Translational Medicine","title":"Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients","year":"2013","tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"extern":"1","quality_controlled":"1","author":[{"last_name":"Petricevic","first_name":"Branka","full_name":"Petricevic, Branka"},{"last_name":"Laengle","first_name":"Johannes","full_name":"Laengle, Johannes"},{"last_name":"Singer","first_name":"Josef","full_name":"Singer, Josef"},{"full_name":"Sachet, Monika","first_name":"Monika","last_name":"Sachet"},{"orcid":"0000-0002-8777-3502","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","first_name":"Judit"},{"full_name":"Steger, Guenther","last_name":"Steger","first_name":"Guenther"},{"full_name":"Bartsch, Rupert","last_name":"Bartsch","first_name":"Rupert"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"},{"full_name":"Bergmann, Michael","last_name":"Bergmann","first_name":"Michael"}],"citation":{"short":"B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013).","chicago":"Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>.","ista":"Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.","ama":"Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. 2013;11. doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>","ieee":"B. Petricevic <i>et al.</i>, “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” <i>Journal of Translational Medicine</i>, vol. 11. Springer Nature, 2013.","apa":"Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>","mla":"Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>, vol. 11, 307, Springer Nature, 2013, doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>."}},{"scopus_import":1,"date_published":"2013-11-19T00:00:00Z","file":[{"file_size":953299,"content_type":"application/pdf","creator":"dernst","date_created":"2019-01-31T10:40:38Z","relation":"main_file","access_level":"open_access","file_name":"2013_FrontiersPlant_OBrien.pdf","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","date_updated":"2020-07-14T12:48:11Z","file_id":"5903"}],"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.3389/fpls.2013.00451","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"EvBe"}],"ec_funded":1,"day":"19","date_updated":"2021-01-12T08:17:50Z","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"451","date_created":"2018-12-11T11:48:43Z","month":"11","publist_id":"6821","intvolume":"         4","publisher":"Frontiers Research Foundation","file_date_updated":"2020-07-14T12:48:11Z","volume":4,"publication_status":"published","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}],"project":[{"name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"ddc":["580"],"_id":"827","title":"Cytokinin cross talking during biotic and abiotic stress responses","publication":"Frontiers in Plant Science","year":"2013","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","author":[{"full_name":"O'Brien, José","first_name":"José","last_name":"O'Brien"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"citation":{"mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451."}},{"month":"12","date_created":"2018-12-11T11:48:43Z","status":"public","article_number":"537","intvolume":"         4","publist_id":"6820","file_date_updated":"2020-07-14T12:48:11Z","publisher":"Frontiers Research Foundation","volume":4,"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"publication_status":"published","title":"Systems approaches to study root architecture dynamics","publication":"Frontiers in Plant Science","_id":"828","ddc":["580"],"oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","citation":{"apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>."},"quality_controlled":"1","author":[{"last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}],"scopus_import":1,"file":[{"checksum":"0185b3c4d7df9a94bd3ce5a66d213506","file_name":"2013_FrontiersPlant_Cuesta.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","file_id":"5902","content_type":"application/pdf","creator":"dernst","file_size":710835,"relation":"main_file","date_created":"2019-01-31T10:36:43Z"}],"date_published":"2013-12-26T00:00:00Z","ec_funded":1,"department":[{"_id":"EvBe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.3389/fpls.2013.00537","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T08:17:52Z","day":"26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"first_name":"Francesca","last_name":"Galbiati","full_name":"Galbiati, Francesca"},{"last_name":"Sinha Roy","first_name":"Dola","full_name":"Sinha Roy, Dola"},{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"full_name":"Ceccato, Luca","first_name":"Luca","last_name":"Ceccato"},{"last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela"},{"full_name":"Šimášková, Mária","last_name":"Šimášková","first_name":"Mária"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"first_name":"Yuri","last_name":"Kamiuchi","full_name":"Kamiuchi, Yuri"},{"full_name":"Aida, Mitsuhiro","last_name":"Aida","first_name":"Mitsuhiro"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Simon, Rüdiger","first_name":"Rüdiger","last_name":"Simon"},{"full_name":"Masiero, Simona","last_name":"Masiero","first_name":"Simona"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}],"extern":"1","quality_controlled":"1","citation":{"ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. <i>The Plant journal for cell and molecular biology</i>. 2013;76(3):446-455. doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>","ieee":"F. Galbiati <i>et al.</i>, “An integrative model of the control of ovule primordia formation,” <i>The Plant journal for cell and molecular biology</i>, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013.","short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>.","ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455.","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>."},"year":"2013","_id":"830","publication":"The Plant journal for cell and molecular biology","title":"An integrative model of the control of ovule primordia formation","pmid":1,"publication_status":"published","abstract":[{"text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.","lang":"eng"}],"issue":"3","volume":76,"publisher":"Wiley-Blackwell","article_type":"original","publist_id":"6818","intvolume":"        76","status":"public","date_created":"2018-12-11T11:48:44Z","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"19","type":"journal_article","date_updated":"2022-03-21T07:17:26Z","oa_version":"None","doi":"10.1111/tpj.12309","language":[{"iso":"eng"}],"acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","page":"446 - 455","date_published":"2013-09-19T00:00:00Z","external_id":{"pmid":["23941199"]},"scopus_import":"1"},{"volume":9,"date_published":"2013-10-22T00:00:00Z","publisher":"Nature Publishing Group","publist_id":"6817","intvolume":"         9","status":"public","date_created":"2018-12-11T11:48:44Z","month":"10","author":[{"first_name":"Benjamin","last_name":"Péret","full_name":"Péret, Benjamin"},{"first_name":"Alistair","last_name":"Middleton","full_name":"Middleton, Alistair M"},{"first_name":"Andrew","last_name":"French","full_name":"French, Andrew P"},{"full_name":"Larrieu, Antoine","first_name":"Antoine","last_name":"Larrieu"},{"full_name":"Bishopp, Anthony","last_name":"Bishopp","first_name":"Anthony"},{"last_name":"Njo","first_name":"Maria","full_name":"Njo, Maria"},{"full_name":"Wells, Darren M","last_name":"Wells","first_name":"Darren"},{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Mellor, Nathan","first_name":"Nathan","last_name":"Mellor"},{"full_name":"Band, Leah R","first_name":"Leah","last_name":"Band"},{"full_name":"Casimiro, Ilda","last_name":"Casimiro","first_name":"Ilda"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Sairanen, Ilkka","last_name":"Sairanen","first_name":"Ilkka"},{"full_name":"Mallet, Romain","first_name":"Romain","last_name":"Mallet"},{"first_name":"Göran","last_name":"Sandberg","full_name":"Sandberg, Göran"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"first_name":"Eva","last_name":"Benková","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"},{"full_name":"Kramer, Eric","last_name":"Kramer","first_name":"Eric"},{"first_name":"John","last_name":"King","full_name":"King, John R"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"last_name":"Pridmore","first_name":"Tony","full_name":"Pridmore, Tony"},{"full_name":"Owen, Markus","last_name":"Owen","first_name":"Markus"},{"full_name":"Bennett, Malcolm J","first_name":"Malcolm","last_name":"Bennett"}],"extern":1,"quality_controlled":0,"citation":{"apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>","mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>, vol. 9, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>.","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013).","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>.","ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.","ieee":"B. Péret <i>et al.</i>, “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” <i>Molecular Systems Biology</i>, vol. 9. Nature Publishing Group, 2013.","ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. 2013;9. doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>"},"day":"22","year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"type":"journal_article","date_updated":"2021-01-12T08:18:03Z","doi":"10.1038/msb.2013.43","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"831","title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","publication":"Molecular Systems Biology","publication_status":"published","abstract":[{"text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.","lang":"eng"}],"acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning."},{"language":[{"iso":"eng"}],"doi":"10.1007/s10858-013-9787-x","_id":"8461","title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","publication":"Journal of Biomolecular NMR","publication_status":"published","abstract":[{"lang":"eng","text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","author":[{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"citation":{"apa":"Haller, J. D., &#38; Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>","mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>.","short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>.","ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.","ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. 2013;57(3):263-280. doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>"},"day":"09","year":"2013","date_updated":"2021-01-12T08:19:26Z","type":"journal_article","oa_version":"None","publication_identifier":{"issn":["0925-2738","1573-5001"]},"intvolume":"        57","status":"public","date_created":"2020-09-18T10:09:05Z","month":"10","page":"263-280","volume":57,"issue":"3","date_published":"2013-10-09T00:00:00Z","keyword":["Spectroscopy","Biochemistry"],"publisher":"Springer Nature","article_type":"original"},{"intvolume":"       425","publication_identifier":{"issn":["0022-2836"]},"date_created":"2020-09-18T10:09:12Z","month":"08","status":"public","date_published":"2013-08-09T00:00:00Z","keyword":["Molecular Biology"],"issue":"15","volume":425,"page":"2722-2736","publisher":"Elsevier","article_type":"original","publication":"Journal of Molecular Biology","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2013.04.028","_id":"8462","publication_status":"published","abstract":[{"lang":"eng","text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration."}],"citation":{"ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>","ieee":"E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>.","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>."},"article_processing_charge":"No","author":[{"full_name":"Rennella, E.","last_name":"Rennella","first_name":"E."},{"last_name":"Cutuil","first_name":"T.","full_name":"Cutuil, T."},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"I.","last_name":"Ayala","full_name":"Ayala, I."},{"first_name":"F.","last_name":"Gabel","full_name":"Gabel, F."},{"full_name":"Forge, V.","last_name":"Forge","first_name":"V."},{"last_name":"Corazza","first_name":"A.","full_name":"Corazza, A."},{"full_name":"Esposito, G.","last_name":"Esposito","first_name":"G."},{"full_name":"Brutscher, B.","first_name":"B.","last_name":"Brutscher"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2022-08-25T14:56:24Z","type":"journal_article","oa_version":"None","day":"09","year":"2013"},{"publisher":"BioMed Central","date_published":"2013-01-01T00:00:00Z","volume":6,"issue":"1","date_created":"2018-12-11T11:49:04Z","month":"01","status":"public","intvolume":"         6","publist_id":"6752","date_updated":"2021-01-12T08:21:25Z","type":"journal_article","oa_version":"None","day":"01","year":"2013","citation":{"ama":"Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. 2013;6(1). doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>","ieee":"R. Derelle <i>et al.</i>, “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” <i>BMC Research Notes</i>, vol. 6, no. 1. BioMed Central, 2013.","short":"R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).","chicago":"Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>.","ista":"Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).","apa":"Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>","mla":"Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>, vol. 6, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>."},"author":[{"full_name":"Derelle, Romain","first_name":"Romain","last_name":"Derelle"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Vladimir","last_name":"Arkhipov","full_name":"Arkhipov, Vladimir"},{"full_name":"Corbel, Hélène","last_name":"Corbel","first_name":"Hélène"},{"first_name":"Adrien","last_name":"Frantz","full_name":"Frantz, Adrien"},{"full_name":"Gasparini, Julien","last_name":"Gasparini","first_name":"Julien"},{"full_name":"Jacquin, Lisa","last_name":"Jacquin","first_name":"Lisa"},{"full_name":"Jacob, Gwenaël","first_name":"Gwenaël","last_name":"Jacob"},{"first_name":"Sophie","last_name":"Thibault","full_name":"Thibault, Sophie"},{"full_name":"Baudry, Emmanuelle","last_name":"Baudry","first_name":"Emmanuelle"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320.","publication_status":"published","abstract":[{"text":"Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.","lang":"eng"}],"publication":"BMC Research Notes","title":"Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R","doi":"10.1186/1756-0500-6-310","language":[{"iso":"eng"}],"_id":"894"},{"publisher":"Nature Publishing Group","volume":497,"issue":"7451","page":"E2 - E3","date_published":"2013-05-30T00:00:00Z","status":"public","month":"05","date_created":"2018-12-11T11:49:05Z","publist_id":"6747","intvolume":"       497","year":"2013","day":"30","type":"journal_article","date_updated":"2021-01-12T08:21:40Z","extern":1,"quality_controlled":0,"author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"last_name":"Kemena","first_name":"Carsten","full_name":"Kemena, Carsten"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter K"},{"full_name":"Notredame, Cédric","last_name":"Notredame","first_name":"Cédric"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"}],"citation":{"apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., &#38; Kondrashov, F. (2013). Breen et al. reply. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>","mla":"Breen, Michael, et al. “Breen et Al. Reply.” <i>Nature</i>, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>.","ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. <i>Nature</i>. 2013;497(7451):E2-E3. doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” <i>Nature</i>, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013.","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>."},"abstract":[{"lang":"eng","text":"Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites."}],"publication_status":"published","_id":"899","doi":"10.1038/nature12220","publication":"Nature","title":"Breen et al. reply"},{"abstract":[{"text":"A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia.","lang":"eng"}],"publication_status":"published","acknowledgement":"We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper  conservation  programme  in  2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia.","_id":"905","oa":1,"publication":"Forktail","title":"Birds of Mys Shmidta, north Chukotka, Russia","year":"2013","day":"01","type":"journal_article","date_updated":"2021-01-12T08:21:48Z","extern":1,"author":[{"first_name":"Vladimir","last_name":"Arkhipov","full_name":"Arkhipov, Vladimir Y"},{"full_name":"Noah T","last_name":"Noah","first_name":"T"},{"full_name":"Koschkar, Steffen","first_name":"Steffen","last_name":"Koschkar"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"quality_controlled":0,"citation":{"apa":"Arkhipov, V., Noah, T., Koschkar, S., &#38; Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. <i>Forktail</i>. Oriental Bird Club.","mla":"Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” <i>Forktail</i>, no. 29, Oriental Bird Club, 2013, pp. 25–30.","ama":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. <i>Forktail</i>. 2013;(29):25-30.","ieee":"V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” <i>Forktail</i>, no. 29. Oriental Bird Club, pp. 25–30, 2013.","short":"V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.","chicago":"Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” <i>Forktail</i>. Oriental Bird Club, 2013.","ista":"Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30."},"main_file_link":[{"url":"http://orientalbirdclub.org/forktail29/","open_access":"1"}],"status":"public","month":"09","date_created":"2018-12-11T11:49:07Z","publist_id":"6741","publisher":"Oriental Bird Club","issue":"29","page":"25 - 30","date_published":"2013-09-01T00:00:00Z"},{"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"scopus_import":"1","date_published":"2013-02-22T00:00:00Z","external_id":{"pmid":["23371555"]},"keyword":["Multidisciplinary"],"page":"936-940","doi":"10.1126/science.1230020","language":[{"iso":"eng"}],"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2022-08-25T14:57:43Z","oa_version":"None","day":"22","intvolume":"       339","date_created":"2021-02-01T14:37:29Z","month":"02","status":"public","issue":"6122","volume":339,"article_type":"original","publisher":"American Association for the Advancement of Science ","title":"Living crystals of light-activated colloidal surfers","publication":"Science","pmid":1,"_id":"9055","publication_status":"published","abstract":[{"text":"Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional \"living crystals,\" which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles.","lang":"eng"}],"citation":{"ama":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. <i>Science</i>. 2013;339(6122):936-940. doi:<a href=\"https://doi.org/10.1126/science.1230020\">10.1126/science.1230020</a>","ieee":"J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” <i>Science</i>, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.","short":"J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940.","chicago":"Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” <i>Science</i>. American Association for the Advancement of Science , 2013. <a href=\"https://doi.org/10.1126/science.1230020\">https://doi.org/10.1126/science.1230020</a>.","ista":"Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940.","apa":"Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., &#38; Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. <i>Science</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/science.1230020\">https://doi.org/10.1126/science.1230020</a>","mla":"Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” <i>Science</i>, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:<a href=\"https://doi.org/10.1126/science.1230020\">10.1126/science.1230020</a>."},"quality_controlled":"1","author":[{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Sacanna, S.","first_name":"S.","last_name":"Sacanna"},{"full_name":"Steinberg, A. P.","first_name":"A. P.","last_name":"Steinberg"},{"full_name":"Pine, D. J.","first_name":"D. J.","last_name":"Pine"},{"last_name":"Chaikin","first_name":"P. M.","full_name":"Chaikin, P. M."}],"extern":"1","year":"2013"}]