[{"status":"public","type":"journal_article","_id":"1898","department":[{"_id":"RySh"}],"title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","publist_id":"5197","author":[{"first_name":"Andreas","full_name":"Ritzau Jost, Andreas","last_name":"Ritzau Jost"},{"full_name":"Delvendahl, Igor","last_name":"Delvendahl","first_name":"Igor"},{"last_name":"Rings","full_name":"Rings, Annika","first_name":"Annika"},{"last_name":"Byczkowicz","full_name":"Byczkowicz, Niklas","first_name":"Niklas"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes","first_name":"Johannes"},{"full_name":"Eilers, Jens","last_name":"Eilers","first_name":"Jens"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.","ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036.","ieee":"A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014.","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036","apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036"},"date_updated":"2021-01-12T06:53:55Z","month":"10","intvolume":" 84","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling."}],"date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.neuron.2014.08.036","volume":84,"issue":"1","date_created":"2018-12-11T11:54:36Z","page":"152 - 163","day":"01","publication":"Neuron","language":[{"iso":"eng"}],"publication_status":"published","year":"2014"},{"abstract":[{"lang":"eng","text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets."}],"oa_version":"Submitted Version","scopus_import":1,"month":"09","intvolume":" 20","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5297","checksum":"5bf58942d2eb20adf03c7f9ea2e68124","file_size":13594598,"date_updated":"2020-07-14T12:45:20Z","creator":"system","file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf","date_created":"2018-12-12T10:17:41Z"}],"language":[{"iso":"eng"}],"issue":"9","volume":20,"_id":"1906","type":"journal_article","status":"public","pubrep_id":"573","date_updated":"2021-01-12T06:53:59Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"ChWo"}],"acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).","publisher":"IEEE","oa":1,"has_accepted_license":"1","year":"2014","day":"09","publication":"IEEE Transactions on Visualization and Computer Graphics","page":"1280 - 1292","date_published":"2014-09-09T00:00:00Z","doi":"10.1109/TVCG.2014.2312011","date_created":"2018-12-11T11:54:39Z","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"citation":{"mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011","ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292.","ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.","ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Murat","full_name":"Arikan, Murat","last_name":"Arikan"},{"first_name":"Reinhold","full_name":"Preiner, Reinhold","last_name":"Preiner"},{"full_name":"Scheiblauer, Claus","last_name":"Scheiblauer","first_name":"Claus"},{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"last_name":"Wimmer","full_name":"Wimmer, Michael","first_name":"Michael"}],"publist_id":"5189","title":"Large-scale point-cloud visualization through localized textured surface reconstruction"},{"publisher":"Wiley","quality_controlled":"1","acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","page":"960 - 974","date_created":"2018-12-11T11:54:38Z","date_published":"2014-04-12T00:00:00Z","doi":"10.1111/jeb.12370","year":"2014","publication":"Journal of Evolutionary Biology","day":"12","article_processing_charge":"No","external_id":{"pmid":["24725091"]},"author":[{"last_name":"Tobler","full_name":"Tobler, Michael","first_name":"Michael"},{"last_name":"Plath","full_name":"Plath, Martin","first_name":"Martin"},{"first_name":"Rüdiger","last_name":"Riesch","full_name":"Riesch, Rüdiger"},{"last_name":"Schlupp","full_name":"Schlupp, Ingo","first_name":"Ingo"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Munimanda","full_name":"Munimanda, Gopi","first_name":"Gopi"},{"full_name":"Setzer, C","last_name":"Setzer","first_name":"C"},{"first_name":"Dustin","full_name":"Penn, Dustin","last_name":"Penn"},{"first_name":"Yoshan","last_name":"Moodley","full_name":"Moodley, Yoshan"}],"publist_id":"5190","title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations","citation":{"ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974.","chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370","ieee":"M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014.","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 27","month":"04","abstract":[{"text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).","lang":"eng"}],"pmid":1,"oa_version":"None","volume":27,"issue":"5","publication_status":"published","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"1905","department":[{"_id":"SyCr"}],"date_updated":"2022-06-07T09:22:20Z"},{"citation":{"apa":"Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["24170494"]},"publist_id":"5193","author":[{"first_name":"Barry","full_name":"Hall, Barry","last_name":"Hall"},{"first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande","last_name":"Acar"},{"first_name":"Anna","full_name":"Nandipati, Anna","last_name":"Nandipati"},{"first_name":"Miriam","full_name":"Barlow, Miriam","last_name":"Barlow"}],"title":"Growth rates made easy","year":"2014","publication":"Molecular Biology and Evolution","day":"01","page":"232 - 238","date_created":"2018-12-11T11:54:37Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1093/molbev/mst187","publisher":"Oxford University Press","quality_controlled":"1","date_updated":"2022-06-07T11:08:13Z","department":[{"_id":"JoBo"}],"_id":"1902","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"language":[{"iso":"eng"}],"issue":"1","volume":31,"abstract":[{"lang":"eng","text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates."}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 31","month":"01"},{"status":"public","type":"journal_article","_id":"1901","title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","department":[{"_id":"JiFr"}],"publist_id":"5194","author":[{"first_name":"Huiyu","full_name":"Tian, Huiyu","last_name":"Tian"},{"first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"first_name":"Tiantian","last_name":"Niu","full_name":"Niu, Tiantian"},{"first_name":"Hongjiang","last_name":"Li","full_name":"Li, Hongjiang"},{"last_name":"Yu","full_name":"Yu, Qianqian","first_name":"Qianqian"},{"last_name":"Pollmann","full_name":"Pollmann, Stephan","first_name":"Stephan"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Govaerts, Willy","last_name":"Govaerts","first_name":"Willy"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.","ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.","ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118","ieee":"H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289."},"date_updated":"2021-01-12T06:53:57Z","intvolume":" 7","month":"02","publisher":"Oxford University Press","scopus_import":1,"acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","oa_version":"None","abstract":[{"text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation.","lang":"eng"}],"date_created":"2018-12-11T11:54:37Z","doi":"10.1093/mp/sst118","volume":7,"date_published":"2014-02-01T00:00:00Z","issue":"2","page":"277 - 289","language":[{"iso":"eng"}],"publication":"Molecular Plant","day":"01","year":"2014","publication_status":"published"},{"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"title":"Strichartz inequality for orthonormal functions","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"first_name":"Mathieu","full_name":"Lewin, Mathieu","last_name":"Lewin"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5191","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467.","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467","ama":"Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467.","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526."},"quality_controlled":"1","publisher":"European Mathematical Society","oa":1,"doi":"10.4171/JEMS/467","date_published":"2014-08-23T00:00:00Z","date_created":"2018-12-11T11:54:38Z","page":"1507 - 1526","day":"23","publication":"Journal of the European Mathematical Society","year":"2014","status":"public","type":"journal_article","_id":"1904","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:53:58Z","month":"08","intvolume":" 16","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.1309","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces.","lang":"eng"}],"issue":"7","volume":16,"language":[{"iso":"eng"}],"publication_status":"published"},{"author":[{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"5195","department":[{"_id":"CaHe"}],"title":"Lateral junction dynamics lead the way out","citation":{"mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913.","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014.","short":"M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913","ama":"Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913.","ista":"Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129."},"date_updated":"2021-01-12T06:53:56Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1900","page":"127 - 129","date_created":"2018-12-11T11:54:37Z","issue":"2","date_published":"2014-01-31T00:00:00Z","doi":"10.1038/ncb2913","volume":16,"publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","day":"31","publisher":"Nature Publishing Group","quality_controlled":"1","scopus_import":1,"intvolume":" 16","month":"01","abstract":[{"lang":"eng","text":"Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions."}],"oa_version":"None"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701."},"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","author":[{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rebecca","last_name":"Hoyle","full_name":"Hoyle, Rebecca"}],"publist_id":"5186","publication":"Functional Ecology","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:40Z","doi":"10.1111/1365-2435.12207","date_published":"2014-06-01T00:00:00Z","page":"693 - 701","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","oa":1,"publisher":"Wiley-Blackwell","ddc":["570"],"date_updated":"2021-01-12T06:54:00Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","_id":"1909","pubrep_id":"419","status":"public","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","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z","creator":"system","file_size":536154,"date_updated":"2020-07-14T12:45:20Z","file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","issue":"3","volume":28,"oa_version":"Published Version","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"intvolume":" 28","month":"06","scopus_import":1},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:01Z","citation":{"chicago":"Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681.","ista":"Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560.","mla":"Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681.","apa":"Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681","ama":"Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681","ieee":"S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014.","short":"S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560."},"department":[{"_id":"MiSi"}],"title":"Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2","author":[{"first_name":"Sabine","full_name":"Konradi, Sabine","last_name":"Konradi"},{"last_name":"Yasmin","full_name":"Yasmin, Nighat","first_name":"Nighat"},{"last_name":"Haslwanter","full_name":"Haslwanter, Denise","first_name":"Denise"},{"full_name":"Weber, Michele","last_name":"Weber","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","last_name":"Gesslbauer","full_name":"Gesslbauer, Bernd"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Strobl","full_name":"Strobl, Herbert","first_name":"Herbert"}],"publist_id":"5185","_id":"1910","status":"public","type":"journal_article","publication":"European Journal of Immunology","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:40Z","volume":44,"date_published":"2014-02-01T00:00:00Z","doi":"10.1002/eji.201343681","issue":"2","page":"553 - 560","acknowledgement":"FWF. Grant Number: P22058-B20","oa_version":"None","abstract":[{"lang":"eng","text":"angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration."}],"intvolume":" 44","month":"02","publisher":"Wiley-Blackwell","scopus_import":1},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:59Z","citation":{"chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.","mla":"Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125"},"department":[{"_id":"KrPi"}],"title":"Optimality of non-adaptive strategies: The case of parallel games","publist_id":"5188","author":[{"first_name":"Grégory","last_name":"Demay","full_name":"Demay, Grégory"},{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Ueli","last_name":"Maurer","full_name":"Maurer, Ueli"},{"full_name":"Tackmann, Björn","last_name":"Tackmann","first_name":"Björn"}],"article_number":"6875125","_id":"1907","status":"public","conference":{"location":"Honolulu, USA","end_date":"2014-07-04","start_date":"2014-06-29","name":"IEEE International Symposium on Information Theory Proceedings"},"type":"conference","language":[{"iso":"eng"}],"publication":"IEEE International Symposium on Information Theory","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:39Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1109/ISIT.2014.6875125","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition."}],"month":"01","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2014/299"}],"oa":1,"publisher":"IEEE","scopus_import":1,"quality_controlled":"1"},{"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:59Z","type":"journal_article","status":"public","_id":"1908","volume":196,"issue":"4","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0737"}],"month":"04","intvolume":" 196","abstract":[{"lang":"eng","text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations."}],"oa_version":"Submitted Version","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Hallatschek","full_name":"Hallatschek, Oskar","first_name":"Oskar"}],"publist_id":"5187","title":"The rate of adaptation in large sexual populations with linear chromosomes","citation":{"chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183.","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"page":"1167 - 1183","date_published":"2014-04-01T00:00:00Z","doi":"10.1534/genetics.113.160705","date_created":"2018-12-11T11:54:39Z","year":"2014","day":"01","publication":"Genetics","quality_controlled":"1","publisher":"Genetics Society of America","oa":1},{"doi":"10.1007/s00454-013-9556-3","date_published":"2014-01-01T00:00:00Z","volume":51,"issue":"1","date_created":"2018-12-11T11:54:40Z","page":"207 - 220","day":"01","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","year":"2014","publication_status":"published","month":"01","intvolume":" 51","scopus_import":1,"publisher":"Springer","oa_version":"None","acknowledgement":"Patrik Norén gratefully acknowledges support from the Wallenberg foundation","abstract":[{"lang":"eng","text":"The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma."}],"title":"Tverberg's Theorem and Graph Coloring","department":[{"_id":"CaUh"}],"publist_id":"5183","author":[{"last_name":"Engström","full_name":"Engström, Alexander","first_name":"Alexander"},{"full_name":"Noren, Patrik","last_name":"Noren","first_name":"Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3.","ista":"Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220.","mla":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3.","short":"A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.","ieee":"A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.","ama":"Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3","apa":"Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3"},"date_updated":"2021-01-12T06:54:01Z","status":"public","type":"journal_article","_id":"1911"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":343,"issue":"6170","abstract":[{"text":"Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/","open_access":"1"}],"scopus_import":1,"intvolume":" 343","month":"01","date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"GaNo"}],"_id":"1916","type":"journal_article","article_type":"original","status":"public","year":"2014","publication":"Science","day":"31","page":"506 - 511","date_created":"2018-12-11T11:54:42Z","date_published":"2014-01-31T00:00:00Z","doi":"10.1126/science.1247363","acknowledgement":"Supported by the Deutsche Forschungsgemeinschaft (G.N.)","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","citation":{"chicago":"Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363.","ista":"Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511.","mla":"Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.","ieee":"G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014.","short":"G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.","ama":"Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363","apa":"Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["24482476"]},"publist_id":"5178","author":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fenstermaker, Ali","last_name":"Fenstermaker","first_name":"Ali"},{"first_name":"Maha","full_name":"Zaki, Maha","last_name":"Zaki"},{"first_name":"Matan","last_name":"Hofree","full_name":"Hofree, Matan"},{"first_name":"Jennifer","last_name":"Silhavy","full_name":"Silhavy, Jennifer"},{"full_name":"Heiberg, Andrew","last_name":"Heiberg","first_name":"Andrew"},{"last_name":"Abdellateef","full_name":"Abdellateef, Mostafa","first_name":"Mostafa"},{"first_name":"Başak","last_name":"Rosti","full_name":"Rosti, Başak"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"last_name":"Mansour","full_name":"Mansour, Lobna","first_name":"Lobna"},{"first_name":"Amira","last_name":"Masri","full_name":"Masri, Amira"},{"first_name":"Hülya","full_name":"Kayserili, Hülya","last_name":"Kayserili"},{"last_name":"Al Aama","full_name":"Al Aama, Jumana","first_name":"Jumana"},{"last_name":"Abdel Salam","full_name":"Abdel Salam, Ghada","first_name":"Ghada"},{"first_name":"Ariana","last_name":"Karminejad","full_name":"Karminejad, Ariana"},{"last_name":"Kara","full_name":"Kara, Majdi","first_name":"Majdi"},{"last_name":"Kara","full_name":"Kara, Bülent","first_name":"Bülent"},{"first_name":"Bita","last_name":"Bozorgmehri","full_name":"Bozorgmehri, Bita"},{"first_name":"Tawfeg","last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg"},{"first_name":"Faezeh","full_name":"Mojahedi, Faezeh","last_name":"Mojahedi"},{"full_name":"Mahmoud, Iman","last_name":"Mahmoud","first_name":"Iman"},{"full_name":"Bouslam, Naïma","last_name":"Bouslam","first_name":"Naïma"},{"full_name":"Bouhouche, Ahmed","last_name":"Bouhouche","first_name":"Ahmed"},{"last_name":"Benomar","full_name":"Benomar, Ali","first_name":"Ali"},{"first_name":"Sylvain","last_name":"Hanein","full_name":"Hanein, Sylvain"},{"full_name":"Raymond, Laure","last_name":"Raymond","first_name":"Laure"},{"first_name":"Sylvie","full_name":"Forlani, Sylvie","last_name":"Forlani"},{"full_name":"Mascaro, Massimo","last_name":"Mascaro","first_name":"Massimo"},{"last_name":"Selim","full_name":"Selim, Laila","first_name":"Laila"},{"full_name":"Shehata, Nabil","last_name":"Shehata","first_name":"Nabil"},{"first_name":"Nasir","last_name":"Al Allawi","full_name":"Al Allawi, Nasir"},{"first_name":"Parayil","last_name":"Bindu","full_name":"Bindu, Parayil"},{"last_name":"Azam","full_name":"Azam, Matloob","first_name":"Matloob"},{"first_name":"Murat","full_name":"Günel, Murat","last_name":"Günel"},{"full_name":"Caglayan, Ahmet","last_name":"Caglayan","first_name":"Ahmet"},{"first_name":"Kaya","full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar"},{"first_name":"Aslihan","last_name":"Tolun","full_name":"Tolun, Aslihan"},{"full_name":"Issa, Mahmoud","last_name":"Issa","first_name":"Mahmoud"},{"first_name":"Jana","full_name":"Schroth, Jana","last_name":"Schroth"},{"last_name":"Spencer","full_name":"Spencer, Emily","first_name":"Emily"},{"full_name":"Rosti, Rasim","last_name":"Rosti","first_name":"Rasim"},{"full_name":"Akizu, Naiara","last_name":"Akizu","first_name":"Naiara"},{"full_name":"Vaux, Keith","last_name":"Vaux","first_name":"Keith"},{"last_name":"Johansen","full_name":"Johansen, Anide","first_name":"Anide"},{"first_name":"Alice","full_name":"Koh, Alice","last_name":"Koh"},{"first_name":"Hisham","last_name":"Megahed","full_name":"Megahed, Hisham"},{"full_name":"Dürr, Alexandra","last_name":"Dürr","first_name":"Alexandra"},{"last_name":"Brice","full_name":"Brice, Alexis","first_name":"Alexis"},{"first_name":"Giovanni","last_name":"Stévanin","full_name":"Stévanin, Giovanni"},{"first_name":"Stacy","last_name":"Gabriel","full_name":"Gabriel, Stacy"},{"full_name":"Ideker, Trey","last_name":"Ideker","first_name":"Trey"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"}],"title":"Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders"},{"year":"2014","publication":"Science","day":"28","page":"1025 - 1028","date_created":"2018-12-11T11:54:42Z","doi":"10.1126/science.1245125","date_published":"2014-02-28T00:00:00Z","acknowledgement":"Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","citation":{"ista":"Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028.","chicago":"Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125.","ieee":"T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014.","short":"T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028.","apa":"Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125","ama":"Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125","mla":"Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24578577"]},"article_processing_charge":"No","author":[{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"full_name":"Dai, Ning","last_name":"Dai","first_name":"Ning"},{"full_name":"Chen, Jisheng","last_name":"Chen","first_name":"Jisheng"},{"full_name":"Nagawa, Shingo","last_name":"Nagawa","first_name":"Shingo"},{"full_name":"Cao, Min","last_name":"Cao","first_name":"Min"},{"first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660"},{"full_name":"Zhou, Zimin","last_name":"Zhou","first_name":"Zimin"},{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","full_name":"Chen, Xu","last_name":"Chen"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"last_name":"Wang","full_name":"Wang, Wen","first_name":"Wen"},{"first_name":"Alan","full_name":"Jones, Alan","last_name":"Jones"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"full_name":"Patterson, Sara","last_name":"Patterson","first_name":"Sara"},{"first_name":"Anthony","full_name":"Bleecker, Anthony","last_name":"Bleecker"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"}],"publist_id":"5177","title":"Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling","publication_status":"published","language":[{"iso":"eng"}],"issue":"6174","volume":343,"abstract":[{"lang":"eng","text":"Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/"}],"scopus_import":1,"intvolume":" 343","month":"02","date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"JiFr"}],"_id":"1917","type":"journal_article","article_type":"original","status":"public"},{"page":"E188 - E193","volume":111,"doi":"10.1073/pnas.1315541111","date_published":"2014-01-07T00:00:00Z","issue":"1","date_created":"2018-12-11T11:54:43Z","publication_status":"published","year":"2014","day":"07","publication":"PNAS","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/"}],"month":"01","intvolume":" 111","abstract":[{"lang":"eng","text":"Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation."}],"oa_version":"Submitted Version","acknowledgement":"This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.).","publist_id":"5174","author":[{"first_name":"Wen","full_name":"Wang, Wen","last_name":"Wang"},{"first_name":"Kazuhiko","full_name":"Nakadate, Kazuhiko","last_name":"Nakadate"},{"first_name":"Miwako","full_name":"Masugi Tokita, Miwako","last_name":"Masugi Tokita"},{"last_name":"Shutoh","full_name":"Shutoh, Fumihiro","first_name":"Fumihiro"},{"first_name":"Wajeeha","last_name":"Aziz","full_name":"Aziz, Wajeeha"},{"last_name":"Tarusawa","full_name":"Tarusawa, Etsuko","first_name":"Etsuko"},{"full_name":"Lörincz, Andrea","last_name":"Lörincz","first_name":"Andrea"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"id":"401AB46C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebnem","full_name":"Kesaf, Sebnem","last_name":"Kesaf"},{"first_name":"Yunqing","last_name":"Li","full_name":"Li, Yunqing"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"first_name":"Soichi","last_name":"Nagao","full_name":"Nagao, Soichi"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"department":[{"_id":"RySh"}],"title":"Distinct cerebellar engrams in short-term and long-term motor learning","citation":{"ieee":"W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014.","short":"W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193.","apa":"Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111","ama":"Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111","mla":"Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111.","ista":"Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193.","chicago":"Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111."},"date_updated":"2021-01-12T06:54:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1920"},{"intvolume":" 42","month":"02","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity.","lang":"eng"}],"ec_funded":1,"volume":42,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"status":"public","type":"journal_article","article_type":"original","_id":"1915","department":[{"_id":"JiFr"}],"date_updated":"2022-06-07T11:20:56Z","quality_controlled":"1","publisher":"Portland Press","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec","date_created":"2018-12-11T11:54:41Z","doi":"10.1042/BST20130269","date_published":"2014-02-01T00:00:00Z","page":"212 - 218","publication":"Biochemical Society Transactions","day":"01","year":"2014","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"title":"Rho-GTPase-regulated vesicle trafficking in plant cell polarity","article_processing_charge":"No","external_id":{"pmid":["24450654"]},"publist_id":"5179","author":[{"last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269.","ama":"Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269","apa":"Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269","ieee":"X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014.","short":"X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.","chicago":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269.","ista":"Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218."}},{"publisher":"National Academy of Sciences","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/"}],"oa":1,"month":"01","intvolume":" 111","abstract":[{"lang":"eng","text":"Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals."}],"oa_version":"Submitted Version","acknowledgement":"his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.).","page":"E194 - E202","issue":"1","date_published":"2014-01-07T00:00:00Z","doi":"10.1073/pnas.1303317110","volume":111,"date_created":"2018-12-11T11:54:43Z","publication_status":"published","year":"2014","day":"07","publication":"PNAS","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1919","author":[{"last_name":"Aziz","full_name":"Aziz, Wajeeha","first_name":"Wajeeha"},{"first_name":"Wen","last_name":"Wang","full_name":"Wang, Wen"},{"full_name":"Kesaf, Sebnem","last_name":"Kesaf","first_name":"Sebnem","id":"401AB46C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alsayed","full_name":"Mohamed, Alsayed","last_name":"Mohamed"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5175","title":"Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning","department":[{"_id":"RySh"}],"citation":{"ama":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110","apa":"Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110","ieee":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014.","short":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202.","mla":"Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110.","ista":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202.","chicago":"Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110."},"date_updated":"2021-01-12T06:54:04Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","status":"public","_id":"1918","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:54:04Z","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1301.5370","open_access":"1"}],"month":"02","intvolume":" 26","abstract":[{"lang":"eng","text":"As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy."}],"oa_version":"Submitted Version","volume":26,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"article_number":"1350021","publist_id":"5176","author":[{"first_name":"Jacopo","last_name":"Bellazzini","full_name":"Bellazzini, Jacopo"},{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Existence of ground states for negative ions at the binding threshold","citation":{"apa":"Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219","ama":"Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219","ieee":"J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014.","short":"J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","mla":"Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219.","ista":"Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021.","chicago":"Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"doi":"10.1142/S0129055X13500219","date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:54:42Z","year":"2014","day":"01","publication":"Reviews in Mathematical Physics"},{"date_updated":"2021-01-12T06:54:02Z","citation":{"ieee":"M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.","short":"M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.","ama":"Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019","apa":"Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019","mla":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.","ista":"Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.","chicago":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5180","author":[{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"title":"Plant biology: Gatekeepers of the road to protein perdition","department":[{"_id":"JiFr"}],"_id":"1914","type":"journal_article","status":"public","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Current Biology","day":"06","page":"R27 - R29","date_created":"2018-12-11T11:54:41Z","volume":24,"issue":"1","date_published":"2014-01-06T00:00:00Z","doi":"10.1016/j.cub.2013.11.019","abstract":[{"lang":"eng","text":"Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants."}],"oa_version":"None","publisher":"Cell Press","scopus_import":1,"quality_controlled":"1","intvolume":" 24","month":"01"},{"title":"A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes","article_processing_charge":"No","publist_id":"5169","author":[{"first_name":"Constanze","full_name":"Lamprecht, Constanze","last_name":"Lamprecht"},{"first_name":"Birgit","full_name":"Plochberger, Birgit","last_name":"Plochberger"},{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","last_name":"Wieser"},{"full_name":"Rankl, Christian","last_name":"Rankl","first_name":"Christian"},{"first_name":"Elena","last_name":"Heister","full_name":"Heister, Elena"},{"full_name":"Unterauer, Barbara","last_name":"Unterauer","first_name":"Barbara"},{"first_name":"Mario","full_name":"Brameshuber, Mario","last_name":"Brameshuber"},{"full_name":"Danzberger, Jürgen","last_name":"Danzberger","first_name":"Jürgen"},{"first_name":"Petar","full_name":"Lukanov, Petar","last_name":"Lukanov"},{"full_name":"Flahaut, Emmanuel","last_name":"Flahaut","first_name":"Emmanuel"},{"full_name":"Schütz, Gerhard","last_name":"Schütz","first_name":"Gerhard"},{"first_name":"Peter","last_name":"Hinterdorfer","full_name":"Hinterdorfer, Peter"},{"full_name":"Ebner, Andreas","last_name":"Ebner","first_name":"Andreas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704.","ista":"Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704.","mla":"Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704.","apa":"Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704","ama":"Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704","short":"C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014).","ieee":"C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014."},"article_number":"125704","date_created":"2018-12-11T11:54:45Z","doi":"10.1088/0957-4484/25/12/125704","date_published":"2014-03-28T00:00:00Z","publication":"Nanotechnology","day":"28","year":"2014","has_accepted_license":"1","oa":1,"publisher":"IOP Publishing","acknowledgement":"This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:21Z","ddc":["570"],"date_updated":"2021-01-12T06:54:07Z","status":"public","article_type":"original","type":"journal_article","_id":"1925","issue":"12","volume":25,"language":[{"iso":"eng"}],"file":[{"file_name":"2014_Nanotechnology_Lamprecht.pdf","date_created":"2020-05-15T09:21:19Z","file_size":3804152,"date_updated":"2020-07-14T12:45:21Z","creator":"dernst","checksum":"df4e03d225a19179e7790f6d87a12332","file_id":"7856","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 25","month":"03","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.","lang":"eng"}]},{"status":"public","pubrep_id":"429","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":"1923","file_date_updated":"2020-07-14T12:45:21Z","department":[{"_id":"CaHe"}],"ddc":["570"],"date_updated":"2021-01-12T06:54:06Z","month":"06","intvolume":" 16","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We derive the equations for a thin, axisymmetric elastic shell subjected to an internal active stress giving rise to active tension and moments within the shell. We discuss the stability of a cylindrical elastic shell and its response to a localized change in internal active stress. This description is relevant to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving elastically at a short timescale and subjected to active internal forces arising from myosin molecular motor activity. We show that the recent observations of cell deformation following detachment of adherent cells (Maître J-L et al 2012 Science 338 253-6) are well accounted for by this mechanical description. The actin cortex elastic and bending moduli can be obtained from a quantitative analysis of cell shapes observed in these experiments. Our approach thus provides a non-invasive, imaging-based method for the extraction of cellular physical parameters."}],"volume":16,"file":[{"date_updated":"2020-07-14T12:45:21Z","file_size":941387,"creator":"system","date_created":"2018-12-12T10:16:16Z","file_name":"IST-2016-429-v1+1_document.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8dbe81ec656bf1264d8889bda9b2b985","file_id":"5202"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"065005","title":"Active elastic thin shell theory for cellular deformations","publist_id":"5171","author":[{"first_name":"Hélène","last_name":"Berthoumieux","full_name":"Berthoumieux, Hélène"},{"full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","last_name":"Maître","first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"},{"last_name":"Julicher","full_name":"Julicher, Frank","first_name":"Frank"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H. Berthoumieux, J.-L. Maître, C.-P.J. Heisenberg, E. Paluch, F. Julicher, G. Salbreux, New Journal of Physics 16 (2014).","ieee":"H. Berthoumieux, J.-L. Maître, C.-P. J. Heisenberg, E. Paluch, F. Julicher, and G. Salbreux, “Active elastic thin shell theory for cellular deformations,” New Journal of Physics, vol. 16. IOP Publishing Ltd., 2014.","apa":"Berthoumieux, H., Maître, J.-L., Heisenberg, C.-P. J., Paluch, E., Julicher, F., & Salbreux, G. (2014). Active elastic thin shell theory for cellular deformations. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/16/6/065005","ama":"Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 2014;16. doi:10.1088/1367-2630/16/6/065005","mla":"Berthoumieux, Hélène, et al. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics, vol. 16, 065005, IOP Publishing Ltd., 2014, doi:10.1088/1367-2630/16/6/065005.","ista":"Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. 2014. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 16, 065005.","chicago":"Berthoumieux, Hélène, Jean-Léon Maître, Carl-Philipp J Heisenberg, Ewa Paluch, Frank Julicher, and Guillaume Salbreux. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics. IOP Publishing Ltd., 2014. https://doi.org/10.1088/1367-2630/16/6/065005."},"quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"doi":"10.1088/1367-2630/16/6/065005","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:54:44Z","day":"01","publication":"New Journal of Physics","has_accepted_license":"1","year":"2014"},{"status":"public","type":"journal_article","_id":"1921","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:54:05Z","month":"05","intvolume":" 26","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079372/","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain-delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning."}],"volume":26,"issue":"5","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis","author":[{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"MiriamPalacios ","last_name":"Palacios-Gomez","full_name":"Palacios-Gomez, MiriamPalacios "},{"orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mareike","last_name":"Heilmann","full_name":"Heilmann, Mareike"},{"first_name":"Ringo","full_name":"Van Wijk, Ringo","last_name":"Van Wijk"},{"first_name":"Joop","last_name":"Vermeer","full_name":"Vermeer, Joop"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"first_name":"Teun","last_name":"Munnik","full_name":"Munnik, Teun"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"5173","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tejos, Ricardo, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell, vol. 26, no. 5, American Society of Plant Biologists, 2014, pp. 2114–28, doi:10.1105/tpc.114.126185.","short":"R. Tejos, M. Sauer, S. Vanneste, M. Palacios-Gomez, H. Li, M. Heilmann, R. Van Wijk, J. Vermeer, I. Heilmann, T. Munnik, J. Friml, Plant Cell 26 (2014) 2114–2128.","ieee":"R. Tejos et al., “Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis,” Plant Cell, vol. 26, no. 5. American Society of Plant Biologists, pp. 2114–2128, 2014.","apa":"Tejos, R., Sauer, M., Vanneste, S., Palacios-Gomez, M., Li, H., Heilmann, M., … Friml, J. (2014). Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.126185","ama":"Tejos R, Sauer M, Vanneste S, et al. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 2014;26(5):2114-2128. doi:10.1105/tpc.114.126185","chicago":"Tejos, Ricardo, Michael Sauer, Steffen Vanneste, MiriamPalacios Palacios-Gomez, Hongjiang Li, Mareike Heilmann, Ringo Van Wijk, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.126185.","ista":"Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H, Heilmann M, Van Wijk R, Vermeer J, Heilmann I, Munnik T, Friml J. 2014. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 26(5), 2114–2128."},"publisher":"American Society of Plant Biologists","oa":1,"acknowledgement":"This work was supported by grants from the Odysseus program of the Research Foundation-Flanders (to J.F.).","date_published":"2014-05-01T00:00:00Z","doi":"10.1105/tpc.114.126185","date_created":"2018-12-11T11:54:43Z","page":"2114 - 2128","day":"01","publication":"Plant Cell","year":"2014"},{"project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"}],"status":"public","type":"journal_article","_id":"1922","department":[{"_id":"EvBe"}],"title":"Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids","publist_id":"5172","author":[{"full_name":"Smet, Dajo","last_name":"Smet","first_name":"Dajo"},{"first_name":"Petra","full_name":"Žádníková, Petra","last_name":"Žádníková"},{"first_name":"Filip","full_name":"Vandenbussche, Filip","last_name":"Vandenbussche"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:05Z","citation":{"short":"D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, D. Van Der Straeten, New Phytologist 202 (2014) 1398–1411.","ieee":"D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, and D. Van Der Straeten, “Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids,” New Phytologist, vol. 202, no. 4. Wiley-Blackwell, pp. 1398–1411, 2014.","apa":"Smet, D., Žádníková, P., Vandenbussche, F., Benková, E., & Van Der Straeten, D. (2014). Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.12751","ama":"Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 2014;202(4):1398-1411. doi:10.1111/nph.12751","mla":"Smet, Dajo, et al. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist, vol. 202, no. 4, Wiley-Blackwell, 2014, pp. 1398–411, doi:10.1111/nph.12751.","ista":"Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. 2014. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 202(4), 1398–1411.","chicago":"Smet, Dajo, Petra Žádníková, Filip Vandenbussche, Eva Benková, and Dominique Van Der Straeten. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist. Wiley-Blackwell, 2014. https://doi.org/10.1111/nph.12751."},"month":"06","intvolume":" 202","scopus_import":1,"publisher":"Wiley-Blackwell","oa_version":"None","acknowledgement":"Funded by Ghent University; Research Foundation Flanders Grant Number: G065613N European Research Council Grant Number: CZ.1.07/2.3.00/20.0043","abstract":[{"lang":"eng","text":"Germination of Arabidopsis seeds in darkness induces apical hook development, based on a tightly regulated differential growth coordinated by a multiple hormone cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs) and cross-talk with ethylene in hook development. An automated infrared imaging system was developed to study the kinetics of hook development in etiolated Arabidopsis seedlings. To ascertain the photomorphogenic control of hook opening, the system was equipped with an automatic light dimmer. We demonstrate that ethylene and BRs are indispensable for hook formation and maintenance. Ethylene regulation of hook formation functions partly through BRs, with BR feedback inhibition of ethylene action. Conversely, BR-mediated extension of hook maintenance functions partly through ethylene. Furthermore, we revealed that a short light pulse is sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows high-resolution, kinetic imaging of up to 112 seedlings in a single experimental run. At this high throughput, it is ideally suited to rapidly gain insight in pathway networks. We demonstrate that BRs and ethylene cooperatively regulate apical hook development in a phase-dependent manner. Furthermore, we show that light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated postponement of hook opening."}],"volume":202,"issue":"4","doi":"10.1111/nph.12751","date_published":"2014-06-01T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:54:44Z","page":"1398 - 1411","day":"01","language":[{"iso":"eng"}],"publication":"New Phytologist","year":"2014","publication_status":"published"},{"date_updated":"2021-01-12T06:54:08Z","citation":{"short":"G. Fuchsbauer, M. Konstantinov, K.Z. Pietrzak, V. Rao, in:, Springer, 2014, pp. 173–192.","ieee":"G. Fuchsbauer, M. Konstantinov, K. Z. Pietrzak, and V. Rao, “Adaptive security of constrained PRFs,” presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014, vol. 8874, pp. 173–192.","ama":"Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. Adaptive security of constrained PRFs. In: Vol 8874. Springer; 2014:173-192. doi:10.1145/2591796.2591825","apa":"Fuchsbauer, G., Konstantinov, M., Pietrzak, K. Z., & Rao, V. (2014). Adaptive security of constrained PRFs (Vol. 8874, pp. 173–192). Presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer. https://doi.org/10.1145/2591796.2591825","mla":"Fuchsbauer, Georg, et al. Adaptive Security of Constrained PRFs. Vol. 8874, Springer, 2014, pp. 173–92, doi:10.1145/2591796.2591825.","ista":"Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. 2014. Adaptive security of constrained PRFs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 8874, 173–192.","chicago":"Fuchsbauer, Georg, Momchil Konstantinov, Krzysztof Z Pietrzak, and Vanishree Rao. “Adaptive Security of Constrained PRFs,” 8874:173–92. Springer, 2014. https://doi.org/10.1145/2591796.2591825."},"extern":1,"publist_id":"5167","author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Georg Fuchsbauer","last_name":"Fuchsbauer"},{"first_name":"Momchil","full_name":"Konstantinov, Momchil","last_name":"Konstantinov"},{"last_name":"Pietrzak","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rao, Vanishree","last_name":"Rao","first_name":"Vanishree"}],"title":"Adaptive security of constrained PRFs","_id":"1927","type":"conference","conference":{"name":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},"status":"public","publication_status":"published","year":"2014","day":"01","page":"173 - 192","date_published":"2014-01-01T00:00:00Z","doi":"10.1145/2591796.2591825","volume":8874,"date_created":"2018-12-11T11:54:45Z","abstract":[{"lang":"eng","text":"Constrained pseudorandom functions have recently been introduced independently by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al. (PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset S of the domain. The three above-mentioned papers all show that the classical GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly yields a constrained PRF where one can compute constrained keys to evaluate the PRF on all inputs with a given prefix. This constrained PRF has already found many interesting applications. Unfortunately, the existing security proofs only show selective security (by a reduction to the security of the underlying PRG). To achieve full security, one has to use complexity leveraging, which loses an exponential factor 2N in security, where N is the input length. The first contribution of this paper is a new reduction that only loses a quasipolynomial factor qlog N, where q is the number of adversarial queries. For this we develop a new proof technique which constructs a distinguisher by interleaving simple guessing steps and hybrid arguments a small number of times. This approach might be of interest also in other contexts where currently the only technique to achieve full security is complexity leveraging. Our second contribution is concerned with another constrained PRF, due to Boneh and Waters, which allows for constrained keys for the more general class of bit-fixing functions. Their security proof also suffers from a 2N loss, which we show is inherent. We construct a meta-reduction which shows that any “simple” reduction of full security from a noninteractive hardness assumption must incur an exponential security loss."}],"acknowledgement":"We are grateful to Mihir Bellare for his feedback on earlier versions of this paper. We are indebted to Vanishree Rao for her generous assistance in preparing this proceedings version.","quality_controlled":0,"publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2014/416"}],"oa":1,"month":"01","intvolume":" 8874"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sadel C. 2014. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 17(3–4), 409–440.","chicago":"Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9163-4.","apa":"Sadel, C. (2014). Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9163-4","ama":"Sadel C. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):409-440. doi:10.1007/s11040-014-9163-4","short":"C. Sadel, Mathematical Physics, Analysis and Geometry 17 (2014) 409–440.","ieee":"C. Sadel, “Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 409–440, 2014.","mla":"Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 409–40, doi:10.1007/s11040-014-9163-4."},"title":"Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips","author":[{"id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968"}],"publist_id":"5168","article_processing_charge":"No","external_id":{"arxiv":["1304.3862"]},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"day":"17","publication":"Mathematical Physics, Analysis and Geometry","year":"2014","date_published":"2014-12-17T00:00:00Z","doi":"10.1007/s11040-014-9163-4","date_created":"2018-12-11T11:54:45Z","page":"409 - 440","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2021-01-12T06:54:07Z","department":[{"_id":"LaEr"}],"_id":"1926","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","volume":17,"issue":"3-4","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider cross products of finite graphs with a class of trees that have arbitrarily but finitely long line segments, such as the Fibonacci tree. Such cross products are called tree-strips. We prove that for small disorder random Schrödinger operators on such tree-strips have purely absolutely continuous spectrum in a certain set."}],"month":"12","intvolume":" 17","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.3862"}]},{"publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Nature Communications","day":"27","date_created":"2018-12-11T11:54:44Z","doi":"10.1038/ncomms4090","date_published":"2014-01-27T00:00:00Z","volume":5,"abstract":[{"lang":"eng","text":"Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division."}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Nature Publishing Group","intvolume":" 5","month":"01","date_updated":"2021-01-12T06:54:06Z","citation":{"short":"J. Le, X. Liu, K. Yang, X. Chen, L. Zhu, H. Wang, M. Wang, S. Vanneste, M. Morita, M. Tasaka, Z. Ding, J. Friml, T. Beeckman, F. Sack, Nature Communications 5 (2014).","ieee":"J. Le et al., “Auxin transport and activity regulate stomatal patterning and development,” Nature Communications, vol. 5. Nature Publishing Group, 2014.","ama":"Le J, Liu X, Yang K, et al. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 2014;5. doi:10.1038/ncomms4090","apa":"Le, J., Liu, X., Yang, K., Chen, X., Zhu, L., Wang, H., … Sack, F. (2014). Auxin transport and activity regulate stomatal patterning and development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4090","mla":"Le, Jie, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications, vol. 5, 3090, Nature Publishing Group, 2014, doi:10.1038/ncomms4090.","ista":"Le J, Liu X, Yang K, Chen X, Zhu L, Wang H, Wang M, Vanneste S, Morita M, Tasaka M, Ding Z, Friml J, Beeckman T, Sack F. 2014. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 5, 3090.","chicago":"Le, Jie, Xuguang Liu, Kezhen Yang, Xiaolan Chen, Lingling Zhu, Hongzhe Wang, Ming Wang, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4090."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Le","full_name":"Le, Jie","first_name":"Jie"},{"last_name":"Liu","full_name":"Liu, Xuguang","first_name":"Xuguang"},{"first_name":"Kezhen","full_name":"Yang, Kezhen","last_name":"Yang"},{"full_name":"Chen, Xiaolan","last_name":"Chen","first_name":"Xiaolan"},{"full_name":"Zhu, Lingling","last_name":"Zhu","first_name":"Lingling"},{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"first_name":"Ming","last_name":"Wang","full_name":"Wang, Ming"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Morita, Miyo","last_name":"Morita","first_name":"Miyo"},{"full_name":"Tasaka, Masao","last_name":"Tasaka","first_name":"Masao"},{"first_name":"Zhaojun","last_name":"Ding","full_name":"Ding, Zhaojun"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"}],"publist_id":"5170","department":[{"_id":"JiFr"}],"title":"Auxin transport and activity regulate stomatal patterning and development","_id":"1924","article_number":"3090","type":"journal_article","status":"public"},{"year":"2014","publication_status":"published","publication":"Journal of Theoretical Biology","language":[{"iso":"eng"}],"day":"07","page":"149 - 162","date_created":"2018-12-11T11:54:46Z","volume":360,"date_published":"2014-11-07T00:00:00Z","doi":"10.1016/j.jtbi.2014.06.039","abstract":[{"text":"In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen.","lang":"eng"}],"acknowledgement":"J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague.","oa_version":"None","scopus_import":1,"publisher":"Elsevier","intvolume":" 360","month":"11","citation":{"ama":"Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039","apa":"Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039","short":"J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.","ieee":"J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014.","mla":"Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.","ista":"Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162.","chicago":"Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039."},"date_updated":"2021-01-12T06:54:08Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5166","author":[{"first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan","last_name":"Humplik"},{"full_name":"Hill, Alison","last_name":"Hill","first_name":"Alison"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"department":[{"_id":"GaTk"}],"title":"Evolutionary dynamics of infectious diseases in finite populations","_id":"1928","type":"journal_article","status":"public"},{"publication_identifier":{"issn":["1072-3374"],"eissn":["1573-8795"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":203,"issue":"6","abstract":[{"text":"We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"11","intvolume":" 203","date_updated":"2022-05-24T10:39:06Z","department":[{"_id":"HeEd"}],"_id":"1929","article_type":"original","type":"journal_article","status":"public","year":"2014","day":"16","publication":"Journal of Mathematical Sciences","page":"754 - 760","date_published":"2014-11-16T00:00:00Z","doi":"10.1007/s10958-014-2165-8","date_created":"2018-12-11T11:54:46Z","acknowledgement":"We would like to offer our special thanks to students of the Department of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev for participation in developing the program and assistance in preparation of test data. This work was supported by grant 11.G34.31.0053 from the government of the Russian Federation.","quality_controlled":"1","publisher":"Springer","citation":{"ista":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 203(6), 754–760.","chicago":"Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences. Springer, 2014. https://doi.org/10.1007/s10958-014-2165-8.","ama":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 2014;203(6):754-760. doi:10.1007/s10958-014-2165-8","apa":"Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y., Edelsbrunner, H., & Yakimova, O. (2014). An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. Springer. https://doi.org/10.1007/s10958-014-2165-8","short":"V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner, O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760.","ieee":"V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H. Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that preserves global topology,” Journal of Mathematical Sciences, vol. 203, no. 6. Springer, pp. 754–760, 2014.","mla":"Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences, vol. 203, no. 6, Springer, 2014, pp. 754–60, doi:10.1007/s10958-014-2165-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5165","author":[{"first_name":"V V","full_name":"Alexeev, V V","last_name":"Alexeev"},{"last_name":"Bogaevskaya","full_name":"Bogaevskaya, V G","first_name":"V G"},{"last_name":"Preobrazhenskaya","full_name":"Preobrazhenskaya, M M","first_name":"M M"},{"last_name":"Ukhalov","full_name":"Ukhalov, A Y","first_name":"A Y"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Olga","last_name":"Yakimova","full_name":"Yakimova, Olga"}],"article_processing_charge":"No","title":"An algorithm for cartographic generalization that preserves global topology"},{"date_published":"2014-10-01T00:00:00Z","doi":"10.1007/s00220-014-1923-2","date_created":"2018-12-11T11:54:48Z","page":"333 - 350","day":"01","publication":"Communications in Mathematical Physics","has_accepted_license":"1","year":"2014","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"2014 by the authors. This paper may be reproduced, in its entirety, for non-commercial purposes.\r\n\r\nThe research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694; A.G. and R.S.), the U.S. National Science Foundation (Grant PHY 0965859; E.H.L.), the Simons Foundation (Grant # 230207; E.H.L) and the NSERC (R.S.). The work is part of a project started in collaboration with Joel Lebowitz, whom we thank for many useful discussions and for his constant encouragement.","title":"Formation of stripes and slabs near the ferromagnetic transition","publist_id":"5159","author":[{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"external_id":{"arxiv":["1304.6344"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Giuliani A, Lieb É, Seiringer R. 2014. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 331, 333–350.","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-1923-2.","short":"A. Giuliani, É. Lieb, R. Seiringer, Communications in Mathematical Physics 331 (2014) 333–350.","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Formation of stripes and slabs near the ferromagnetic transition,” Communications in Mathematical Physics, vol. 331. Springer, pp. 333–350, 2014.","ama":"Giuliani A, Lieb É, Seiringer R. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 2014;331:333-350. doi:10.1007/s00220-014-1923-2","apa":"Giuliani, A., Lieb, É., & Seiringer, R. (2014). Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-1923-2","mla":"Giuliani, Alessandro, et al. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics, vol. 331, Springer, 2014, pp. 333–50, doi:10.1007/s00220-014-1923-2."},"volume":331,"file":[{"checksum":"c8423271cd1e1ba9e44c47af75efe7b6","file_id":"11409","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-24T08:30:40Z","file_name":"2014_CommMathPhysics_Giuliani.pdf","creator":"dernst","date_updated":"2022-05-24T08:30:40Z","file_size":334064}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publication_status":"published","month":"10","intvolume":" 331","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.","lang":"eng"}],"file_date_updated":"2022-05-24T08:30:40Z","department":[{"_id":"RoSe"}],"ddc":["510"],"date_updated":"2022-05-24T08:32:50Z","status":"public","type":"journal_article","article_type":"original","_id":"1935"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures."}],"month":"02","intvolume":" 25","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":25,"issue":"3","ec_funded":1,"_id":"1936","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:11Z","department":[{"_id":"NiBa"}],"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"day":"13","publication":"Behavioral Ecology","year":"2014","date_published":"2014-02-13T00:00:00Z","doi":"10.1093/beheco/aru002","date_created":"2018-12-11T11:54:48Z","page":"487 - 495","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.","apa":"Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002","ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.","short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495."},"title":"An arms race between producers and scroungers can drive the evolution of social cognition","publist_id":"5157","author":[{"full_name":"Arbilly, Michal","last_name":"Arbilly","first_name":"Michal"},{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"first_name":"Marcus","full_name":"Feldman, Marcus","last_name":"Feldman"},{"last_name":"Grodzinski","full_name":"Grodzinski, Uri","first_name":"Uri"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:10Z","citation":{"mla":"Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002.","ieee":"P. Marhavý et al., “Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis,” Current Biology, vol. 24, no. 9. Cell Press, pp. 1031–1037, 2014.","short":"P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037.","apa":"Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R., … Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002","ama":"Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037. doi:10.1016/j.cub.2014.04.002","chicago":"Marhavý, Peter, Jérôme Duclercq, Benjamin Weller, Elena Feraru, Agnieszka Bielach, Remko Offringa, Jiří Friml, Claus Schwechheimer, Angus Murphy, and Eva Benková. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.04.002.","ista":"Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037."},"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis","publist_id":"5160","author":[{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"first_name":"Jérôme","full_name":"Duclercq, Jérôme","last_name":"Duclercq"},{"first_name":"Benjamin","last_name":"Weller","full_name":"Weller, Benjamin"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"last_name":"Bielach","full_name":"Bielach, Agnieszka","first_name":"Agnieszka"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"full_name":"Schwechheimer, Claus","last_name":"Schwechheimer","first_name":"Claus"},{"first_name":"Angus","last_name":"Murphy","full_name":"Murphy, Angus"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"_id":"1934","status":"public","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","day":"05","language":[{"iso":"eng"}],"publication":"Current Biology","publication_status":"published","year":"2014","date_published":"2014-05-05T00:00:00Z","volume":24,"issue":"9","doi":"10.1016/j.cub.2014.04.002","ec_funded":1,"date_created":"2018-12-11T11:54:48Z","page":"1031 - 1037","oa_version":"None","abstract":[{"text":"The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ.","lang":"eng"}],"month":"05","intvolume":" 24","scopus_import":1,"publisher":"Cell Press","quality_controlled":"1"},{"status":"public","type":"journal_article","_id":"1932","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:54:10Z","month":"12","intvolume":" 68","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations."}],"volume":68,"issue":"12","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","author":[{"first_name":"Meredith","last_name":"Trotter","full_name":"Trotter, Meredith"},{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"full_name":"Peterson, Grant","last_name":"Peterson","first_name":"Grant"},{"last_name":"Peck","full_name":"Peck, Kayla","first_name":"Kayla"},{"first_name":"Joanna","last_name":"Masel","full_name":"Masel, Joanna"}],"publist_id":"5162","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367.","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367."},"publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","date_published":"2014-12-01T00:00:00Z","doi":"10.1111/evo.12517","date_created":"2018-12-11T11:54:47Z","page":"3357 - 3367","day":"01","publication":"Evolution","year":"2014"},{"oa_version":"None","acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","abstract":[{"text":"(Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications.","lang":"eng"}],"month":"12","intvolume":" 20","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"day":"31","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Visualization and Computer Graphics","publication_status":"published","year":"2014","issue":"12","doi":"10.1109/TVCG.2014.2346432","date_published":"2014-12-31T00:00:00Z","volume":20,"date_created":"2018-12-11T11:54:46Z","page":"2585 - 2594","_id":"1930","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432.","ista":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594.","mla":"Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432.","ieee":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, and T. Weinkauf, “Fast and memory-efficient topological denoising of 2D and 3D scalar fields,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12. IEEE, pp. 2585–2594, 2014.","short":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T. Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594.","ama":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 2014;20(12):2585-2594. doi:10.1109/TVCG.2014.2346432","apa":"Günther, D., Jacobson, A., Reininghaus, J., Seidel, H., Sorkine Hornung, O., & Weinkauf, T. (2014). Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2346432"},"date_updated":"2021-01-12T06:54:09Z","title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","department":[{"_id":"HeEd"}],"author":[{"full_name":"Günther, David","last_name":"Günther","first_name":"David"},{"first_name":"Alec","full_name":"Jacobson, Alec","last_name":"Jacobson"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Seidel","full_name":"Seidel, Hans","first_name":"Hans"},{"full_name":"Sorkine Hornung, Olga","last_name":"Sorkine Hornung","first_name":"Olga"},{"full_name":"Weinkauf, Tino","last_name":"Weinkauf","first_name":"Tino"}],"publist_id":"5164"},{"_id":"1933","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:10Z","citation":{"ista":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. 2014. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682.","chicago":"Hatakeyama, Jun, Yoshio Wakamatsu, Akira Nagafuchi, Ryoichiro Kageyama, Ryuichi Shigemoto, and Kenji Shimamura. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development. Company of Biologists, 2014. https://doi.org/10.1242/dev.102988.","apa":"Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R., & Shimamura, K. (2014). Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. Company of Biologists. https://doi.org/10.1242/dev.102988","ama":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 2014;141(8):1671-1682. doi:10.1242/dev.102988","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682.","ieee":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates,” Development, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.","mla":"Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988."},"department":[{"_id":"RySh"}],"title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","publist_id":"5161","author":[{"first_name":"Jun","last_name":"Hatakeyama","full_name":"Hatakeyama, Jun"},{"last_name":"Wakamatsu","full_name":"Wakamatsu, Yoshio","first_name":"Yoshio"},{"first_name":"Akira","last_name":"Nagafuchi","full_name":"Nagafuchi, Akira"},{"first_name":"Ryoichiro","full_name":"Kageyama, Ryoichiro","last_name":"Kageyama"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"last_name":"Shimamura","full_name":"Shimamura, Kenji","first_name":"Kenji"}],"oa_version":"None","abstract":[{"lang":"eng","text":"The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors."}],"month":"04","intvolume":" 141","publisher":"Company of Biologists","scopus_import":1,"quality_controlled":"1","day":"01","publication":"Development","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","date_published":"2014-04-01T00:00:00Z","issue":"8","volume":141,"doi":"10.1242/dev.102988","date_created":"2018-12-11T11:54:47Z","page":"1671 - 1682"},{"article_number":"57","title":"Emergence of task-dependent representations in working memory circuits","publist_id":"5163","author":[{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jochen","full_name":"Triesch, Jochen","last_name":"Triesch"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057.","apa":"Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057","ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057."},"quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"acknowledgement":"Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation.","date_published":"2014-05-28T00:00:00Z","doi":"10.3389/fncom.2014.00057","date_created":"2018-12-11T11:54:46Z","day":"28","publication":"Frontiers in Computational Neuroscience","year":"2014","status":"public","type":"journal_article","_id":"1931","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:54:09Z","month":"05","intvolume":" 8","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity."}],"issue":"MAY","volume":8,"language":[{"iso":"eng"}],"publication_status":"published"},{"year":"2014","publication":"Communications in Mathematical Physics","day":"01","page":"261 - 353","date_created":"2018-12-11T11:54:48Z","date_published":"2014-11-01T00:00:00Z","doi":"10.1007/s00220-014-2120-z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"mla":"Bourgade, Paul, et al. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics, vol. 332, no. 1, Springer, 2014, pp. 261–353, doi:10.1007/s00220-014-2120-z.","ama":"Bourgade P, Erdös L, Yau H. Edge universality of beta ensembles. Communications in Mathematical Physics. 2014;332(1):261-353. doi:10.1007/s00220-014-2120-z","apa":"Bourgade, P., Erdös, L., & Yau, H. (2014). Edge universality of beta ensembles. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2120-z","short":"P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353.","ieee":"P. Bourgade, L. Erdös, and H. Yau, “Edge universality of beta ensembles,” Communications in Mathematical Physics, vol. 332, no. 1. Springer, pp. 261–353, 2014.","chicago":"Bourgade, Paul, László Erdös, and Horngtzer Yau. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2120-z.","ista":"Bourgade P, Erdös L, Yau H. 2014. Edge universality of beta ensembles. Communications in Mathematical Physics. 332(1), 261–353."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Paul","last_name":"Bourgade","full_name":"Bourgade, Paul"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Horngtzer","last_name":"Yau","full_name":"Yau, Horngtzer"}],"publist_id":"5158","title":"Edge universality of beta ensembles","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":332,"issue":"1","abstract":[{"lang":"eng","text":"We prove the edge universality of the beta ensembles for any β ≥ 1, provided that the limiting spectrum is supported on a single interval, and the external potential is C4 and regular. We also prove that the edge universality holds for generalized Wigner matrices for all symmetry classes. Moreover, our results allow us to extend bulk universality for beta ensembles from analytic potentials to potentials in class C4."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5728"}],"scopus_import":1,"intvolume":" 332","month":"11","date_updated":"2021-01-12T06:54:12Z","department":[{"_id":"LaEr"}],"_id":"1937","type":"journal_article","status":"public"},{"publist_id":"5102","author":[{"last_name":"Garvin","full_name":"Garvin, Michael R","first_name":"Michael"},{"last_name":"Bielawski","full_name":"Bielawski, Joseph P","first_name":"Joseph"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"first_name":"Anthony","full_name":"Gharrett, Anthony J","last_name":"Gharrett"}],"title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","citation":{"ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 2014;53(1):1-17. doi:10.1111/jzs.12079","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., & Gharrett, A. (2014). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/jzs.12079","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1. Wiley-Blackwell, pp. 1–17, 2014.","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1, Wiley-Blackwell, 2014, pp. 1–17, doi:10.1111/jzs.12079.","ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2014. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2014. https://doi.org/10.1111/jzs.12079."},"date_updated":"2019-04-26T07:22:06Z","extern":1,"type":"review","status":"public","_id":"1981","page":"1 - 17","volume":53,"issue":"1","doi":"10.1111/jzs.12079","date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:55:02Z","year":"2014","publication_status":"published","day":"01","publication":"Journal of Zoological Systematics and Evolutionary Research","quality_controlled":0,"publisher":"Wiley-Blackwell","month":"02","intvolume":" 53","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}],"acknowledgement":"Funded by University of Alaska Center for Global Change Student Research Cooperative Institute for Alaska Research and the Rasmuson Foundation"},{"title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","author":[{"last_name":"Heikal","full_name":"Heikal, Adam ","first_name":"Adam"},{"first_name":"Yoshio","last_name":"Nakatani","full_name":"Nakatani, Yoshio"},{"last_name":"Dunn","full_name":"Dunn, Elyse A","first_name":"Elyse"},{"last_name":"Weimar","full_name":"Weimar, Marion R","first_name":"Marion"},{"first_name":"Catherine","full_name":"Day, Catherine","last_name":"Day"},{"last_name":"Baker","full_name":"Baker, Edward N","first_name":"Edward"},{"last_name":"Lott","full_name":"Lott, Shaun J","first_name":"Shaun"},{"orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cook","full_name":"Cook, Gregory","first_name":"Gregory"}],"publist_id":"5103","extern":1,"citation":{"short":"A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A. Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.","ieee":"A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation,” Molecular Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.","ama":"Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507","apa":"Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook, G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12507","mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.","ista":"Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA, Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 91(5), 950–964.","chicago":"Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day, Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mmi.12507."},"date_updated":"2021-01-12T06:54:29Z","status":"public","type":"journal_article","_id":"1980","volume":91,"doi":"10.1111/mmi.12507","date_published":"2014-03-01T00:00:00Z","issue":"5","date_created":"2018-12-11T11:55:01Z","page":"950 - 964","day":"01","publication":"Molecular Microbiology","publication_status":"published","year":"2014","month":"03","intvolume":" 91","publisher":"Wiley-Blackwell","quality_controlled":0,"acknowledgement":"Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group","abstract":[{"text":"Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.","lang":"eng"}]},{"title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I","author":[{"last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"publist_id":"5104","extern":1,"date_updated":"2021-01-12T06:54:28Z","citation":{"chicago":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes. Springer, 2014. https://doi.org/10.1007/s10863-014-9554-z.","ista":"Sazanov LA. 2014. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 46(4), 247–253.","mla":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4, Springer, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z.","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer, pp. 247–253, 2014.","apa":"Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. Springer. https://doi.org/10.1007/s10863-014-9554-z","ama":"Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 2014;46(4):247-253. doi:10.1007/s10863-014-9554-z"},"status":"public","type":"journal_article","_id":"1979","issue":"4","volume":46,"date_published":"2014-08-01T00:00:00Z","doi":"10.1007/s10863-014-9554-z","date_created":"2018-12-11T11:55:01Z","page":"247 - 253","day":"01","publication":"Journal of Bioenergetics and Biomembranes","publication_status":"published","year":"2014","month":"08","intvolume":" 46","publisher":"Springer","quality_controlled":0,"abstract":[{"text":"NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine.","lang":"eng"}]},{"_id":"1989","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T06:54:32Z","citation":{"ama":"Nguyen P, Groen A, Loose M, et al. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 2014;346(6206):244-247. doi:10.1126/science.1256773","apa":"Nguyen, P., Groen, A., Loose, M., Ishihara, K., Wühr, M., Field, C., & Mitchison, T. (2014). Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1256773","short":"P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247.","ieee":"P. Nguyen et al., “Spatial organization of cytokinesis signaling reconstituted in a cell-free system,” Science, vol. 346, no. 6206. American Association for the Advancement of Science, pp. 244–247, 2014.","mla":"Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science, vol. 346, no. 6206, American Association for the Advancement of Science, 2014, pp. 244–47, doi:10.1126/science.1256773.","ista":"Nguyen P, Groen A, Loose M, Ishihara K, Wühr M, Field C, Mitchison T. 2014. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 346(6206), 244–247.","chicago":"Nguyen, Phuong, Aaron Groen, Martin Loose, Keisuke Ishihara, Martin Wühr, Christine Field, and Timothy Mitchison. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1256773."},"title":"Spatial organization of cytokinesis signaling reconstituted in a cell-free system","publist_id":"5093","author":[{"first_name":"Phuong","full_name":"Nguyen, Phuong A","last_name":"Nguyen"},{"first_name":"Aaron","full_name":"Groen, Aaron C","last_name":"Groen"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Martin Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Keisuke","full_name":"Ishihara, Keisuke ","last_name":"Ishihara"},{"first_name":"Martin","last_name":"Wühr","full_name":"Wühr, Martin "},{"first_name":"Christine","full_name":"Field, Christine M","last_name":"Field"},{"full_name":"Mitchison, Timothy J","last_name":"Mitchison","first_name":"Timothy"}],"acknowledgement":"This work was supported by NIH grant GM39565 (T.J.M.); MBL fellowships from the Evans Foundation, MBL Associates, and the Colwin Fund (T.J.M. and C.M.F.); HFSP fellowship LT000466/2012-L (M.L.); and NIH grant GM103785 (M.W.). ","abstract":[{"lang":"eng","text":"During animal cell division, the cleavage furrow is positioned by microtubules that signal to the actin cortex at the cell midplane. We developed a cell-free system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus eggs. Microtubules grew out as asters from artificial centrosomes and met to organize antiparallel overlap zones. These zones blocked the interpenetration of neighboring asters and recruited cytokinesis midzone proteins, including the chromosomal passenger complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid bilayers to mimic the plasma membrane, we observed the recruitment of cleavage furrow markers, including an active RhoA reporter, at microtubule overlaps. This system opens further approaches to understanding the biophysics of cytokinesis signaling."}],"month":"10","intvolume":" 346","publisher":"American Association for the Advancement of Science","quality_controlled":0,"day":"10","publication":"Science","publication_status":"published","year":"2014","doi":"10.1126/science.1256773","date_published":"2014-10-10T00:00:00Z","volume":346,"issue":"6206","date_created":"2018-12-11T11:55:04Z","page":"244 - 247"},{"_id":"1990","type":"journal_article","status":"public","citation":{"apa":"Loose, M., & Mitchison, T. (2014). The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2885","ama":"Loose M, Mitchison T. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 2014;16(1):38-46. doi:10.1038/ncb2885","short":"M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46.","ieee":"M. Loose and T. Mitchison, “The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns,” Nature Cell Biology, vol. 16, no. 1. Nature Publishing Group, pp. 38–46, 2014.","mla":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell Biology, vol. 16, no. 1, Nature Publishing Group, 2014, pp. 38–46, doi:10.1038/ncb2885.","ista":"Loose M, Mitchison T. 2014. The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 16(1), 38–46.","chicago":"Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2885."},"date_updated":"2021-01-12T06:54:33Z","extern":1,"publist_id":"5094","author":[{"orcid":"0000-0001-7309-9724","full_name":"Martin Loose","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mitchison, Timothy J","last_name":"Mitchison","first_name":"Timothy"}],"title":"The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic cytoskeletal patterns","abstract":[{"text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin superfamily GTPase, which is recruited to the membrane by the actin-related protein FtsA. Both proteins are required for the formation of the Z-ring, but if and how they influence each other's assembly dynamics is not known. Here, we reconstituted FtsA-dependent recruitment of FtsZ polymers to supported membranes, where both proteins self-organize into complex patterns, such as fast-moving filament bundles and chirally rotating rings. Using fluorescence microscopy and biochemical perturbations, we found that these large-scale rearrangements of FtsZ emerge from its polymerization dynamics and a dual, antagonistic role of FtsA: recruitment of FtsZ filaments to the membrane and negative regulation of FtsZ organization. Our findings provide a model for the initial steps of bacterial cell division and illustrate how dynamic polymers can self-organize into large-scale structures.","lang":"eng"}],"acknowledgement":"M.L. is supported by fellowships from EMBO (ALTF 394-2011) and HFSP (LT000466/2012). Cytoskeleton dynamics research in the T.J.M. group is supported by NIH-GM39565.","quality_controlled":0,"publisher":"Nature Publishing Group","month":"01","intvolume":" 16","year":"2014","publication_status":"published","day":"01","publication":"Nature Cell Biology","page":"38 - 46","doi":"10.1038/ncb2885","issue":"1","date_published":"2014-01-01T00:00:00Z","volume":16,"date_created":"2018-12-11T11:55:05Z"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Auxin polar transport, local maxima, and gradients have become an importantmodel system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels."}],"intvolume":" 111","month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/"}],"publisher":"National Academy of Sciences","quality_controlled":"1","scopus_import":1,"language":[{"iso":"eng"}],"publication":"PNAS","day":"16","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:07Z","date_published":"2014-12-16T00:00:00Z","issue":"50","volume":111,"doi":"10.1073/pnas.1413918111","page":"E5471 - E5479","_id":"1996","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:35Z","citation":{"ista":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. 2014. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. 111(50), E5471–E5479.","chicago":"Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1413918111.","apa":"Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., & Yalovsky, S. (2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1413918111","ama":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. 2014;111(50):E5471-E5479. doi:10.1073/pnas.1413918111","ieee":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal regulation of ICR1 levels generates self-organizing auxin distribution,” PNAS, vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014.","short":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111 (2014) E5471–E5479.","mla":"Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” PNAS, vol. 111, no. 50, National Academy of Sciences, 2014, pp. E5471–79, doi:10.1073/pnas.1413918111."},"title":"Bimodal regulation of ICR1 levels generates self-organizing auxin distribution","department":[{"_id":"JiFr"}],"author":[{"full_name":"Hazak, Ora","last_name":"Hazak","first_name":"Ora"},{"first_name":"Uri","full_name":"Obolski, Uri","last_name":"Obolski"},{"full_name":"Prat, Tomas","last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Lilach","last_name":"Hadany","full_name":"Hadany, Lilach"},{"full_name":"Yalovsky, Shaul","last_name":"Yalovsky","first_name":"Shaul"}],"publist_id":"5083"},{"citation":{"apa":"Viaene, T., Landberg, K., Thelander, M., Medvecka, E., Pederson, E., Feraru, E., … Friml, J. (2014). Directional auxin transport mechanisms in early diverging land plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.09.056","ama":"Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 2014;24(23):2786-2791. doi:10.1016/j.cub.2014.09.056","ieee":"T. Viaene et al., “Directional auxin transport mechanisms in early diverging land plants,” Current Biology, vol. 24, no. 23. Cell Press, pp. 2786–2791, 2014.","short":"T. Viaene, K. Landberg, M. Thelander, E. Medvecka, E. Pederson, E. Feraru, E. Cooper, M. Karimi, C. Delwiche, K. Ljung, M. Geisler, E. Sundberg, J. Friml, Current Biology 24 (2014) 2786–2791.","mla":"Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” Current Biology, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91, doi:10.1016/j.cub.2014.09.056.","ista":"Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 24(23), 2786–2791.","chicago":"Viaene, Tom, Katarina Landberg, Mattias Thelander, Eva Medvecka, Eric Pederson, Elena Feraru, Endymion Cooper, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.09.056."},"date_updated":"2021-01-12T06:54:34Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Tom","full_name":"Viaene, Tom","last_name":"Viaene"},{"full_name":"Landberg, Katarina","last_name":"Landberg","first_name":"Katarina"},{"first_name":"Mattias","last_name":"Thelander","full_name":"Thelander, Mattias"},{"full_name":"Medvecka, Eva","last_name":"Medvecka","first_name":"Eva"},{"full_name":"Pederson, Eric","last_name":"Pederson","first_name":"Eric"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"last_name":"Cooper","full_name":"Cooper, Endymion","first_name":"Endymion"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"first_name":"Charles","full_name":"Delwiche, Charles","last_name":"Delwiche"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"first_name":"Eva","full_name":"Sundberg, Eva","last_name":"Sundberg"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5088","department":[{"_id":"JiFr"}],"title":"Directional auxin transport mechanisms in early diverging land plants","_id":"1994","type":"journal_article","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"status":"public","year":"2014","publication_status":"published","publication":"Current Biology","language":[{"iso":"eng"}],"day":"01","page":"2786 - 2791","date_created":"2018-12-11T11:55:06Z","ec_funded":1,"date_published":"2014-12-01T00:00:00Z","doi":"10.1016/j.cub.2014.09.056","volume":24,"issue":"23","abstract":[{"text":"The emergence and radiation of multicellular land plants was driven by crucial innovations to their body plans [1]. The directional transport of the phytohormone auxin represents a key, plant-specific mechanism for polarization and patterning in complex seed plants [2-5]. Here, we show that already in the early diverging land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport by PIN transporters is operational and diversified into ER-localized and plasma membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates crucial developmental transitions in tip-growing filaments and waves of polarization and differentiation in leaf-like structures. Plasma membrane PIN proteins localize in a polar manner to the tips of moss filaments, revealing an unexpected relation between polarization mechanisms in moss tip-growing cells and multicellular tissues of seed plants. Our results trace the origins of polarization and auxin-mediated patterning mechanisms and highlight the crucial role of polarized auxin transport during the evolution of multicellular land plants.","lang":"eng"}],"oa_version":"None","publisher":"Cell Press","quality_controlled":"1","scopus_import":1,"intvolume":" 24","month":"12"},{"status":"public","type":"journal_article","_id":"1995","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:54:34Z","month":"12","intvolume":" 113","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.5972","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Optical transport represents a natural route towards fast communications, and it is currently used in large scale data transfer. The progressive miniaturization of devices for information processing calls for the microscopic tailoring of light transport and confinement at length scales appropriate for upcoming technologies. With this goal in mind, we present a theoretical analysis of a one-dimensional Fabry-Perot interferometer built with two highly saturable nonlinear mirrors: a pair of two-level systems. Our approach captures nonlinear and nonreciprocal effects of light transport that were not reported previously. Remarkably, we show that such an elementary device can operate as a microscopic integrated optical rectifier."}],"issue":"24","volume":113,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"243601","title":"Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification","author":[{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"},{"last_name":"Mascarenhas","full_name":"Mascarenhas, Eduardo","first_name":"Eduardo"},{"full_name":"Safari, Laleh","last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Poizat","full_name":"Poizat, Jean","first_name":"Jean"},{"last_name":"Valente","full_name":"Valente, Daniel","first_name":"Daniel"},{"first_name":"Alexia","full_name":"Auffèves, Alexia","last_name":"Auffèves"},{"full_name":"Gerace, Dario","last_name":"Gerace","first_name":"Dario"},{"first_name":"Marcelo","full_name":"Santos, Marcelo","last_name":"Santos"}],"publist_id":"5085","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves, D. Gerace, M. Santos, Physical Review Letters 113 (2014).","ieee":"F. Fratini et al., “Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification,” Physical Review Letters, vol. 113, no. 24. American Physical Society, 2014.","apa":"Fratini, F., Mascarenhas, E., Safari, L., Poizat, J., Valente, D., Auffèves, A., … Santos, M. (2014). Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.243601","ama":"Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 2014;113(24). doi:10.1103/PhysRevLett.113.243601","mla":"Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” Physical Review Letters, vol. 113, no. 24, 243601, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.243601.","ista":"Fratini F, Mascarenhas E, Safari L, Poizat J, Valente D, Auffèves A, Gerace D, Santos M. 2014. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 113(24), 243601.","chicago":"Fratini, Filippo, Eduardo Mascarenhas, Laleh Safari, Jean Poizat, Daniel Valente, Alexia Auffèves, Dario Gerace, and Marcelo Santos. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.243601."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_published":"2014-12-08T00:00:00Z","doi":"10.1103/PhysRevLett.113.243601","date_created":"2018-12-11T11:55:06Z","day":"08","publication":"Physical Review Letters","year":"2014"},{"language":[{"iso":"eng"}],"publication":"Trends in Immunology","day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:55:07Z","date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.it.2014.08.005","issue":"10","volume":35,"page":"471 - 482","acknowledgement":"This work was funded by an ERC Starting Grant by the European Research Council (to S.C.) and the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission; to L.M.).\r\nWe thank Christopher D. Pull, Sophie A.O. Armitage, Hinrich Schulenburg, Line V. Ugelvig, Matthias Konrad, Matthias Fürst, Miriam Stock, Barbara Casillas-Perez and three anonymous referees for comments on the manuscript. ","oa_version":"None","abstract":[{"text":"Immune systems are able to protect the body against secondary infection with the same parasite. In insect colonies, this protection is not restricted to the level of the individual organism, but also occurs at the societal level. Here, we review recent evidence for and insights into the mechanisms underlying individual and social immunisation in insects. We disentangle general immune-protective effects from specific immune memory (priming), and examine immunisation in the context of the lifetime of an individual and that of a colony, and of transgenerational immunisation that benefits offspring. When appropriate, we discuss parallels with disease defence strategies in human societies. We propose that recurrent parasitic threats have shaped the evolution of both the individual immune systems and colony-level social immunity in insects.","lang":"eng"}],"intvolume":" 35","month":"10","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:35Z","citation":{"ista":"El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482.","chicago":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” Trends in Immunology. Elsevier, 2014. https://doi.org/10.1016/j.it.2014.08.005.","ama":"El Masri L, Cremer S. Individual and social immunisation in insects. Trends in Immunology. 2014;35(10):471-482. doi:10.1016/j.it.2014.08.005","apa":"El Masri, L., & Cremer, S. (2014). Individual and social immunisation in insects. Trends in Immunology. Elsevier. https://doi.org/10.1016/j.it.2014.08.005","short":"L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.","ieee":"L. El Masri and S. Cremer, “Individual and social immunisation in insects,” Trends in Immunology, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.","mla":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” Trends in Immunology, vol. 35, no. 10, Elsevier, 2014, pp. 471–82, doi:10.1016/j.it.2014.08.005."},"department":[{"_id":"SyCr"}],"title":"Individual and social immunisation in insects","author":[{"full_name":"El Masri, Leila","last_name":"El Masri","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","first_name":"Leila"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"publist_id":"5081","_id":"1998","status":"public","type":"journal_article"},{"file":[{"date_updated":"2020-07-14T12:45:24Z","file_size":5179993,"creator":"system","date_created":"2018-12-12T10:14:52Z","file_name":"IST-2016-434-v1+1_journal.pone.0113124.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5107","checksum":"85e4f4ea144f827272aaf376b2830564"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"11","volume":9,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","oa_version":"Published Version","abstract":[{"text":"Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus play a key role in feedback inhibition and in the control of network activity. However, how these cells are efficiently activated in the network remains unclear. To address this question, I performed recordings from CA1 pyramidal neuron axons, the presynaptic fibers that provide feedback innervation of these interneurons. Two forms of axonal action potential (AP) modulation were identified. First, repetitive stimulation resulted in activity-dependent AP broadening. Broadening showed fast onset, with marked changes in AP shape following a single AP. Second, tonic depolarization in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced broadening summated with activity-dependent broadening. Outsideout patch recordings from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive, inactivating K+ channels, suggesting that K+ channel inactivation mechanistically contributes to AP broadening. To examine the functional consequences of axonal AP modulation for synaptic transmission, I performed paired recordings between synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation during both repetitive stimulation and tonic depolarization of the presynaptic neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they were mediated by K+ channel inactivation. Therefore, axonal AP modulation can greatly facilitate the activation of O-LM interneurons. In conclusion, modulation of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons in recurrent inhibitory microcircuits.","lang":"eng"}],"month":"11","intvolume":" 9","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:54:39Z","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:24Z","_id":"2002","status":"public","pubrep_id":"434","type":"journal_article","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"day":"19","publication":"PLoS One","has_accepted_license":"1","year":"2014","doi":"10.1371/journal.pone.0113124","date_published":"2014-11-19T00:00:00Z","date_created":"2018-12-11T11:55:09Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0113124.","ista":"Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 9(11), 0113124.","mla":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” PLoS One, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:10.1371/journal.pone.0113124.","ieee":"S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,” PLoS One, vol. 9, no. 11. Public Library of Science, 2014.","short":"S. Kim, PLoS One 9 (2014).","apa":"Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0113124","ama":"Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 2014;9(11). doi:10.1371/journal.pone.0113124"},"title":"Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus","author":[{"last_name":"Kim","full_name":"Kim, Sooyun","first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5074","article_number":"0113124","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}]},{"language":[{"iso":"eng"}],"publication":"Neuron","day":"02","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:09Z","issue":"1","date_published":"2014-07-02T00:00:00Z","doi":"10.1016/j.neuron.2014.06.013","volume":83,"page":"8 - 10","oa_version":"None","abstract":[{"text":"Learning can be facilitated by previous knowledge when it is organized into relational representations forming schemas. In this issue of Neuron, McKenzie et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical memory representations to support schema-based learning.","lang":"eng"}],"intvolume":" 83","month":"07","quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:39Z","citation":{"ama":"O’Neill J, Csicsvari JL. Learning by example in the hippocampus. Neuron. 2014;83(1):8-10. doi:10.1016/j.neuron.2014.06.013","apa":"O’Neill, J., & Csicsvari, J. L. (2014). Learning by example in the hippocampus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.06.013","ieee":"J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,” Neuron, vol. 83, no. 1. Elsevier, pp. 8–10, 2014.","short":"J. O’Neill, J.L. Csicsvari, Neuron 83 (2014) 8–10.","mla":"O’Neill, Joseph, and Jozsef L. Csicsvari. “Learning by Example in the Hippocampus.” Neuron, vol. 83, no. 1, Elsevier, 2014, pp. 8–10, doi:10.1016/j.neuron.2014.06.013.","ista":"O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10.","chicago":"O’Neill, Joseph, and Jozsef L Csicsvari. “Learning by Example in the Hippocampus.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.06.013."},"department":[{"_id":"JoCs"}],"title":"Learning by example in the hippocampus","publist_id":"5073","author":[{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"_id":"2003","status":"public","type":"journal_article"},{"publist_id":"5065","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"},{"first_name":"Alexandra","last_name":"Slaković","full_name":"Slaković, Alexandra"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"}],"title":"Scalable privacy-preserving data sharing methodology for genome-wide association studies","department":[{"_id":"CaUh"}],"citation":{"chicago":"Yu, Fei, Stephen Fienberg, Alexandra Slaković, and Caroline Uhler. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” Journal of Biomedical Informatics. Elsevier, 2014. https://doi.org/10.1016/j.jbi.2014.01.008.","ista":"Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 50, 133–141.","mla":"Yu, Fei, et al. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” Journal of Biomedical Informatics, vol. 50, Elsevier, 2014, pp. 133–41, doi:10.1016/j.jbi.2014.01.008.","ieee":"F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving data sharing methodology for genome-wide association studies,” Journal of Biomedical Informatics, vol. 50. Elsevier, pp. 133–141, 2014.","short":"F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics 50 (2014) 133–141.","ama":"Yu F, Fienberg S, Slaković A, Uhler C. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 2014;50:133-141. doi:10.1016/j.jbi.2014.01.008","apa":"Yu, F., Fienberg, S., Slaković, A., & Uhler, C. (2014). Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. Elsevier. https://doi.org/10.1016/j.jbi.2014.01.008"},"date_updated":"2021-01-12T06:54:42Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2011","page":"133 - 141","date_created":"2018-12-11T11:55:12Z","volume":50,"doi":"10.1016/j.jbi.2014.01.008","date_published":"2014-08-01T00:00:00Z","year":"2014","publication_status":"published","publication":"Journal of Biomedical Informatics","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1401.5193","open_access":"1"}],"quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"intvolume":" 50","month":"08","abstract":[{"lang":"eng","text":"The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of “an attack” on GWAS data by Homer et al. (2008). Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual’s privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private χ2χ2-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls’ data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013)."}],"acknowledgement":"This research was partially supported by NSF Awards EMSW21-RTG and BCS-0941518 to the Department of Statistics at Carnegie Mellon University, and by NSF Grant BCS-0941553 to the Department of Statistics at Pennsylvania State University. This work was also supported in part by the National Center for Research Resources, Grant UL1 RR033184, and is now at the National Center for Advancing Translational Sciences, Grant UL1 TR000127 to Pennsylvania State University. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NSF and NIH.","oa_version":"Submitted Version"},{"title":"Turning heads to remember places","department":[{"_id":"JoCs"}],"author":[{"last_name":"Dupret","full_name":"Dupret, David","first_name":"David"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"publist_id":"5071","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:40Z","citation":{"apa":"Dupret, D., & Csicsvari, J. L. (2014). Turning heads to remember places. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3700","ama":"Dupret D, Csicsvari JL. Turning heads to remember places. Nature Neuroscience. 2014;17(5):643-644. doi:10.1038/nn.3700","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.","ieee":"D. Dupret and J. L. Csicsvari, “Turning heads to remember places,” Nature Neuroscience, vol. 17, no. 5. Nature Publishing Group, pp. 643–644, 2014.","mla":"Dupret, David, and Jozsef L. Csicsvari. “Turning Heads to Remember Places.” Nature Neuroscience, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 643–44, doi:10.1038/nn.3700.","ista":"Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience. 17(5), 643–644.","chicago":"Dupret, David, and Jozsef L Csicsvari. “Turning Heads to Remember Places.” Nature Neuroscience. Nature Publishing Group, 2014. https://doi.org/10.1038/nn.3700."},"status":"public","type":"journal_article","_id":"2005","date_created":"2018-12-11T11:55:09Z","date_published":"2014-04-25T00:00:00Z","volume":17,"issue":"5","doi":"10.1038/nn.3700","page":"643 - 644","language":[{"iso":"eng"}],"publication":"Nature Neuroscience","day":"25","year":"2014","publication_status":"published","intvolume":" 17","month":"04","quality_controlled":"1","scopus_import":1,"publisher":"Nature Publishing Group","oa_version":"None","abstract":[{"lang":"eng","text":"By eliciting a natural exploratory behavior in rats, head scanning, a study reveals that hippocampal place cells form new, stable firing fields in those locations where the behavior has just occurred."}]},{"publist_id":"5069","author":[{"full_name":"Klimova, Anna","last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"article_processing_charge":"No","department":[{"_id":"CaUh"}],"title":"gIPFrm: Generalized iterative proportional fitting for relational models","date_updated":"2022-08-26T08:12:12Z","citation":{"ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.","chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.","short":"A. Klimova, T. Rudas, (2014).","ieee":"A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.","ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014.","apa":"Klimova, A., & Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","mla":"Klimova, Anna, and Tamás Rudas. GIPFrm: Generalized Iterative Proportional Fitting for Relational Models. The Comprehensive R Archive Network, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","status":"public","_id":"2007","date_published":"2014-03-20T00:00:00Z","date_created":"2018-12-11T11:55:10Z","year":"2014","day":"20","publisher":"The Comprehensive R Archive Network","oa":1,"main_file_link":[{"open_access":"1","url":"https://CRAN.R-project.org/package=gIPFrm "}],"month":"03","abstract":[{"lang":"eng","text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual"}],"oa_version":"Published Version"},{"abstract":[{"text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 34","month":"11","publication_status":"published","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6913e9bc26e9fc1c0441a739a4199229","file_id":"11410","creator":"dernst","file_size":3963728,"date_updated":"2022-05-24T08:41:41Z","file_name":"2014_JournNeuroscience_Matsukawa.pdf","date_created":"2022-05-24T08:41:41Z"}],"volume":34,"issue":"47","_id":"2018","type":"journal_article","article_type":"original","status":"public","date_updated":"2022-05-24T08:54:54Z","ddc":["570"],"department":[{"_id":"RySh"}],"file_date_updated":"2022-05-24T08:41:41Z","acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","oa":1,"publisher":"Society for Neuroscience","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"Journal of Neuroscience","day":"19","page":"15779 - 15792","date_created":"2018-12-11T11:55:14Z","date_published":"2014-11-19T00:00:00Z","doi":"10.1523/JNEUROSCI.1141-14.2014","citation":{"ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 2014;34(47):15779-15792. doi:10.1523/JNEUROSCI.1141-14.2014","apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1141-14.2014","ieee":"H. Matsukawa et al., “Netrin-G/NGL complexes encode functional synaptic diversification,” Journal of Neuroscience, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792.","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014.","ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience. Society for Neuroscience, 2014. https://doi.org/10.1523/JNEUROSCI.1141-14.2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["25411505"]},"publist_id":"5054","author":[{"first_name":"Hiroshi","full_name":"Matsukawa, Hiroshi","last_name":"Matsukawa"},{"first_name":"Sachiko","full_name":"Akiyoshi Nishimura, Sachiko","last_name":"Akiyoshi Nishimura"},{"first_name":"Qi","last_name":"Zhang","full_name":"Zhang, Qi"},{"first_name":"Rafael","full_name":"Luján, Rafael","last_name":"Luján"},{"full_name":"Yamaguchi, Kazuhiko","last_name":"Yamaguchi","first_name":"Kazuhiko"},{"first_name":"Hiromichi","last_name":"Goto","full_name":"Goto, Hiromichi"},{"full_name":"Yaguchi, Kunio","last_name":"Yaguchi","first_name":"Kunio"},{"last_name":"Hashikawa","full_name":"Hashikawa, Tsutomu","first_name":"Tsutomu"},{"first_name":"Chie","last_name":"Sano","full_name":"Sano, Chie"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Toshiaki","full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba"},{"full_name":"Itohara, Shigeyoshi","last_name":"Itohara","first_name":"Shigeyoshi"}],"title":"Netrin-G/NGL complexes encode functional synaptic diversification"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9164-3.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464.","ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","apa":"Erdös, L., & Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9164-3","ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):441-464. doi:10.1007/s11040-014-9164-3","mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3."},"title":"Phase transition in the density of states of quantum spin glasses","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J"}],"publist_id":"5053","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"day":"17","publication":"Mathematical Physics, Analysis and Geometry","year":"2014","doi":"10.1007/s11040-014-9164-3","date_published":"2014-12-17T00:00:00Z","date_created":"2018-12-11T11:55:15Z","page":"441 - 464","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2021-01-12T06:54:45Z","department":[{"_id":"LaEr"}],"_id":"2019","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"3-4","volume":17,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory.","lang":"eng"}],"month":"12","intvolume":" 17","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1407.1552","open_access":"1"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020).","date_created":"2018-12-11T11:55:12Z","doi":"10.1007/s10208-014-9205-0","date_published":"2014-10-10T00:00:00Z","page":"1079 - 1116","publication":"Foundations of Computational Mathematics","day":"10","year":"2014","title":"Hypersurfaces and their singularities in partial correlation testing","publist_id":"5063","author":[{"full_name":"Lin, Shaowei","last_name":"Lin","first_name":"Shaowei"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Bernd","full_name":"Sturmfels, Bernd","last_name":"Sturmfels"},{"full_name":"Bühlmann, Peter","last_name":"Bühlmann","first_name":"Peter"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0.","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” Foundations of Computational Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","apa":"Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0","ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0","mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0."},"intvolume":" 14","month":"10","main_file_link":[{"url":"http://arxiv.org/abs/1209.0285","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n"}],"volume":14,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"2013","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:43Z"},{"quality_controlled":0,"publisher":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/1406.4901","open_access":"1"}],"oa":1,"month":"06","abstract":[{"lang":"eng","text":" Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicitly, and a considerable body of computational literature emerged that attempted to avoid this apparent intractability. We close this question by providing an explicit representation of the G-Wishart normalizing constant for general graphs."}],"acknowledgement":"A.L.'s research was supported by Statistics for Innovation sfi2 in Oslo.\nD.R.'s research was partially supported by the U.S. National Science Foun-dation grant DMS-1309808; and by a Romberg Guest Professorship at the Heidelberg University Graduate School for Mathematical and Computational Methods in the Sciences, funded by German Universities Excellence Initiative grant GSC 220/2.","date_published":"2014-06-18T00:00:00Z","date_created":"2018-12-11T11:55:14Z","year":"2014","publication_status":"published","day":"18","publication":"ArXiv","type":"preprint","status":"public","_id":"2017","publist_id":"5058","author":[{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Caroline Uhler","orcid":"0000-0002-7008-0216"},{"last_name":"Lenkoski","full_name":"Lenkoski, Alex","first_name":"Alex"},{"full_name":"Richards, Donald","last_name":"Richards","first_name":"Donald"}],"title":" Exact formulas for the normalizing constants of Wishart distributions for graphical models","citation":{"chicago":"Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. ArXiv, 2014.","ista":"Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, .","mla":"Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014.","ieee":"C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” ArXiv. ArXiv, 2014.","short":"C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014).","apa":"Uhler, C., Lenkoski, A., & Richards, D. (2014). Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. ArXiv.","ama":"Uhler C, Lenkoski A, Richards D. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. 2014."},"date_updated":"2021-01-12T06:54:44Z","extern":1},{"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","pubrep_id":"423","status":"public","_id":"2022","department":[{"_id":"SiHi"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:45:25Z","date_updated":"2021-01-12T06:54:47Z","ddc":["570"],"scopus_import":1,"intvolume":" 159","month":"11","abstract":[{"text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"4","volume":159,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:25Z","file_size":4435787,"date_created":"2018-12-12T10:08:47Z","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6c5de8329bb2ffa71cba9fda750f14ce","file_id":"4709"}],"project":[{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"}],"author":[{"last_name":"Gao","full_name":"Gao, Peng","first_name":"Peng"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P","last_name":"Postiglione","full_name":"Postiglione, Maria P"},{"full_name":"Krieger, Teresa","last_name":"Krieger","first_name":"Teresa"},{"first_name":"Luisirene","full_name":"Hernandez, Luisirene","last_name":"Hernandez"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"last_name":"Han","full_name":"Han, Zhi","first_name":"Zhi"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Papusheva","full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Insolera","full_name":"Insolera, Ryan","first_name":"Ryan"},{"first_name":"Kritika","full_name":"Chugh, Kritika","last_name":"Chugh"},{"first_name":"Oren","last_name":"Kodish","full_name":"Kodish, Oren"},{"first_name":"Kun","last_name":"Huang","full_name":"Huang, Kun"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shi","full_name":"Shi, Song","first_name":"Song"}],"publist_id":"5050","title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","citation":{"ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788. doi:10.1016/j.cell.2014.10.027","apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027","ieee":"P. Gao et al., “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788.","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:10.1016/j.cell.2014.10.027.","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788.","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.10.027."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Cell Press","quality_controlled":"1","page":"775 - 788","date_created":"2018-12-11T11:55:16Z","date_published":"2014-11-06T00:00:00Z","doi":"10.1016/j.cell.2014.10.027","year":"2014","has_accepted_license":"1","publication":"Cell","day":"06"},{"page":"8850 - 8855","date_published":"2014-06-17T00:00:00Z","volume":111,"issue":"24","doi":"10.1073/pnas.1408233111","date_created":"2018-12-11T11:55:15Z","year":"2014","publication_status":"published","day":"17","publication":"PNAS","language":[{"iso":"eng"}],"scopus_import":1,"quality_controlled":"1","publisher":"National Academy of Sciences","month":"06","intvolume":" 111","abstract":[{"lang":"eng","text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis."}],"oa_version":"None","author":[{"last_name":"Ali","full_name":"Ali, Shah","first_name":"Shah"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Lily","last_name":"Saadat","full_name":"Saadat, Lily"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"first_name":"Irving","last_name":"Weissman","full_name":"Weissman, Irving"},{"full_name":"Ardehali, Reza","last_name":"Ardehali","first_name":"Reza"}],"publist_id":"5052","title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:54:46Z","citation":{"short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” PNAS, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., & Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1408233111","ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 2014;111(24):8850-8855. doi:10.1073/pnas.1408233111","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111.","ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1408233111."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2020"},{"department":[{"_id":"SiHi"}],"title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","author":[{"first_name":"Joo","last_name":"William","full_name":"William, Joo"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"}],"publist_id":"5051","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:10.1126/science.1258996.","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” Science, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014.","apa":"William, J., Hippenmeyer, S., & Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1258996","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 2014;346(6209):626-629. doi:10.1126/science.1258996","chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1258996.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629."},"date_updated":"2021-01-12T06:54:47Z","status":"public","type":"journal_article","_id":"2021","date_created":"2018-12-11T11:55:15Z","doi":"10.1126/science.1258996","date_published":"2014-10-31T00:00:00Z","volume":346,"issue":"6209","page":"626 - 629","publication":"Science","language":[{"iso":"eng"}],"day":"31","publication_status":"published","year":"2014","intvolume":" 346","month":"10","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"quality_controlled":"1","scopus_import":1,"publisher":"American Association for the Advancement of Science","oa_version":"Submitted Version","abstract":[{"text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development.","lang":"eng"}]},{"date_updated":"2021-01-12T06:54:49Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"2027","type":"conference","conference":{"start_date":"2014-11-03","end_date":"2014-11-07","location":"Sydney, Australia","name":"ALENEX: Algorithm Engineering and Experiments"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":8837,"ec_funded":1,"abstract":[{"text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"month":"11","intvolume":" 8837","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1007/978-3-319-11936-6_8.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8.","ieee":"T. Brázdil et al., “Verification of markov decision processes using learning algorithms,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 98–114.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. https://doi.org/10.1007/978-3-319-11936-6_8","ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:10.1007/978-3-319-11936-6_8"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Marta","full_name":"Kwiatkowska, Marta","last_name":"Kwiatkowska"},{"first_name":"David","last_name":"Parker","full_name":"Parker, David"},{"first_name":"Mateusz","full_name":"Ujma, Mateusz","last_name":"Ujma"}],"publist_id":"5046","title":"Verification of markov decision processes using learning algorithms","editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"24696","name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING","_id":"26241A12-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"year":"2014","day":"01","publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"98 - 114","date_published":"2014-11-01T00:00:00Z","doi":"10.1007/978-3-319-11936-6_8","date_created":"2018-12-11T11:55:17Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","quality_controlled":"1","publisher":"Society of Industrial and Applied Mathematics","oa":1},{"project":[{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.04057.","ista":"Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3.","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol. 3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057.","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” eLife, vol. 3. eLife Sciences Publications, 2014.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","ama":"Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057","apa":"Arai, itaru, & Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.04057"},"title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","publist_id":"5041","author":[{"full_name":"Arai, Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","publication":"eLife","day":"09","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:19Z","doi":"10.7554/eLife.04057","date_published":"2014-12-09T00:00:00Z","_id":"2031","pubrep_id":"421","status":"public","type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:54:51Z","file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"PeJo"}],"oa_version":"Submitted Version","abstract":[{"text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release.","lang":"eng"}],"intvolume":" 3","month":"12","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":2239563,"date_updated":"2020-07-14T12:45:26Z","file_name":"IST-2016-421-v1+1_e04057.full.pdf","date_created":"2018-12-12T10:14:41Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"c240f915450d4ebe8f95043a2a8c7b1a","file_id":"5094"}],"publication_status":"published","ec_funded":1,"volume":3},{"_id":"2024","type":"journal_article","status":"public","pubrep_id":"616","date_updated":"2021-01-12T06:54:48Z","ddc":["570"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:45:25Z","abstract":[{"lang":"eng","text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway."}],"oa_version":"Submitted Version","scopus_import":1,"month":"03","intvolume":" 5","publication_status":"published","file":[{"file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","date_created":"2018-12-12T10:11:11Z","creator":"system","file_size":4803515,"date_updated":"2020-07-14T12:45:25Z","file_id":"4864","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":5,"article_number":"3498","citation":{"mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications, vol. 5, 3498, Nature Publishing Group, 2014, doi:10.1038/ncomms4498.","short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","ieee":"J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” Nature Communications, vol. 5. Nature Publishing Group, 2014.","apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4498","ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 2014;5. doi:10.1038/ncomms4498","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4498.","ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"first_name":"Show","full_name":"Nishinoaki, Show","last_name":"Nishinoaki"},{"first_name":"Yoshifumi","full_name":"Sato, Yoshifumi","last_name":"Sato"},{"last_name":"Yamamoto","full_name":"Yamamoto, Wataru","first_name":"Wataru"},{"first_name":"Daiki","full_name":"Furukawa, Daiki","last_name":"Furukawa"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"full_name":"Sawaguchi, Akira","last_name":"Sawaguchi","first_name":"Akira"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"publist_id":"5048","title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"25","publication":"Nature Communications","doi":"10.1038/ncomms4498","date_published":"2014-03-25T00:00:00Z","date_created":"2018-12-11T11:55:16Z"},{"citation":{"chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54.","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.","ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041","apa":"Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5043","author":[{"last_name":"Bodova","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Paydarfar","full_name":"Paydarfar, David"},{"full_name":"Forger, Daniel","last_name":"Forger","first_name":"Daniel"}],"article_processing_charge":"No","title":"Characterizing spiking in noisy type II neurons","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","quality_controlled":"1","publisher":"Academic Press","oa":1,"has_accepted_license":"1","year":"2014","day":"12","publication":" Journal of Theoretical Biology","page":"40 - 54","doi":"10.1016/j.jtbi.2014.09.041","date_published":"2014-10-12T00:00:00Z","date_created":"2018-12-11T11:55:18Z","_id":"2028","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"444","date_updated":"2022-08-25T14:00:47Z","ddc":["570"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:25Z","abstract":[{"lang":"eng","text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model."}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 365","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5316","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","creator":"system","file_size":2679222,"date_updated":"2020-07-14T12:45:25Z","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","date_created":"2018-12-12T10:17:58Z"}],"language":[{"iso":"eng"}],"volume":365,"related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"date_updated":"2021-01-12T06:54:49Z","department":[{"_id":"ToHe"}],"_id":"2026","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Sydney, Australia","end_date":"2014-11-07","start_date":"2014-11-03"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8837,"abstract":[{"text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata.","lang":"eng"}],"oa_version":"None","alternative_title":["LNCS"],"intvolume":" 8837","month":"01","citation":{"chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_17.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:10.1007/978-3-319-11936-6_17.","apa":"Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 235–241."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5045","author":[{"first_name":"Zuzana","full_name":"Komárková, Zuzana","last_name":"Komárková"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"}],"editor":[{"last_name":"Cassez","full_name":"Cassez, Franck","first_name":"Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"year":"2014","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","page":"235 - 241","date_created":"2018-12-11T11:55:17Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-11936-6_17","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","quality_controlled":"1","publisher":"Springer"},{"date_updated":"2021-01-12T06:54:50Z","department":[{"_id":"RoSe"}],"_id":"2029","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":108,"abstract":[{"lang":"eng","text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.4717"}],"scopus_import":1,"intvolume":" 108","month":"10","citation":{"ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” EPL, vol. 108, no. 2. IOP Publishing Ltd., 2014.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/108/20003","mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:10.1209/0295-5075/108/20003.","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL. IOP Publishing Ltd., 2014. https://doi.org/10.1209/0295-5075/108/20003."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Michele","last_name":"Correggi","full_name":"Correggi, Michele"},{"last_name":"Giuliani","full_name":"Giuliani, Alessandro","first_name":"Alessandro"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5044","title":"Validity of spin-wave theory for the quantum Heisenberg model","article_number":"20003","year":"2014","publication":"EPL","day":"13","date_created":"2018-12-11T11:55:18Z","doi":"10.1209/0295-5075/108/20003","date_published":"2014-10-13T00:00:00Z","acknowledgement":"239694; ERC; European Research Council","oa":1,"quality_controlled":"1","publisher":"IOP Publishing Ltd."},{"type":"conference","conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2014-12-13","location":"Montreal, Canada","start_date":"2014-12-08"},"status":"public","_id":"2033","publist_id":"5038","author":[{"full_name":"Hernandez Lobato, Daniel","last_name":"Hernandez Lobato","first_name":"Daniel"},{"orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska","first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kristian","full_name":"Kersting, Kristian","last_name":"Kersting"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Quadrianto","full_name":"Quadrianto, Novi","first_name":"Novi"}],"title":"Mind the nuisance: Gaussian process classification using privileged noise","department":[{"_id":"ChLa"}],"date_updated":"2023-02-23T10:25:24Z","citation":{"short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845.","ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., & Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In Advances in Neural Information Processing Systems (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: Advances in Neural Information Processing Systems. Vol 1. Neural Information Processing Systems; 2014:837-845.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” Advances in Neural Information Processing Systems, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.","ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In Advances in Neural Information Processing Systems, 1:837–45. Neural Information Processing Systems, 2014."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems","scopus_import":1,"quality_controlled":"1","main_file_link":[{"url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise","open_access":"1"}],"oa":1,"month":"12","intvolume":" 1","abstract":[{"lang":"eng","text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information."}],"oa_version":"Submitted Version","page":"837-845","volume":1,"date_published":"2014-12-08T00:00:00Z","issue":"January","date_created":"2018-12-11T11:55:20Z","year":"2014","publication_status":"published","day":"08","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems"},{"doi":"10.4161/23723548.2014.964045","date_published":"2014-12-31T00:00:00Z","date_created":"2018-12-11T11:55:19Z","day":"31","publication":"Molecular and Cellular Oncology","has_accepted_license":"1","year":"2014","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"title":"The optogenetic promise for oncology: Episode I","publist_id":"5040","author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Karin","full_name":"Schelch, Karin","last_name":"Schelch"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"first_name":"Michael","full_name":"Grusch, Michael","last_name":"Grusch"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” Molecular and Cellular Oncology, vol. 1, no. 4. Taylor & Francis, 2014.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., & Grusch, M. (2014). The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. Taylor & Francis. https://doi.org/10.4161/23723548.2014.964045","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 2014;1(4). doi:10.4161/23723548.2014.964045","mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology, vol. 1, no. 4, e964045, Taylor & Francis, 2014, doi:10.4161/23723548.2014.964045.","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology. Taylor & Francis, 2014. https://doi.org/10.4161/23723548.2014.964045."},"article_number":"e964045","issue":"4","volume":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"file_id":"6464","checksum":"44e17ad40577ab46eb602e88a8b0b8fd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2014_Taylor_Alvaro.pdf","date_created":"2019-05-16T13:39:11Z","creator":"kschuh","file_size":1765933,"date_updated":"2020-07-14T12:45:26Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 1","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression."}],"file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"HaJa"}],"ddc":["570"],"date_updated":"2021-01-12T06:54:51Z","status":"public","type":"journal_article","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)"},"_id":"2032"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8383,"abstract":[{"lang":"eng","text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 8383","month":"01","date_updated":"2021-01-12T06:54:57Z","department":[{"_id":"KrPi"}],"_id":"2045","conference":{"name":"PKC: Public Key Crypography","start_date":"2014-03-26","end_date":"2014-03-28","location":"Buenos Aires, Argentina"},"type":"conference","status":"public","year":"2014","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","page":"329 - 344","date_created":"2018-12-11T11:55:24Z","doi":"10.1007/978-3-642-54631-0_19","date_published":"2014-01-01T00:00:00Z","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","oa":1,"quality_controlled":"1","publisher":"Springer","citation":{"chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_19.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19.","short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344.","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., & O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_19","ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:329-344. doi:10.1007/978-3-642-54631-0_19"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5006","author":[{"last_name":"Dachman Soled","full_name":"Dachman Soled, Dana","first_name":"Dana"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"first_name":"Payman","full_name":"Mohassel, Payman","last_name":"Mohassel"},{"last_name":"O’Neill","full_name":"O’Neill, Adam","first_name":"Adam"}],"editor":[{"first_name":"Hugo","full_name":"Krawczyk, Hugo","last_name":"Krawczyk"}],"title":"Enhanced chosen-ciphertext security and applications","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}]},{"oa":1,"quality_controlled":"1","publisher":"BioMed Central","year":"2014","has_accepted_license":"1","publication":"BMC Genomics","day":"08","date_created":"2018-12-11T11:55:23Z","date_published":"2014-08-08T00:00:00Z","doi":"10.1186/1471-2164-15-663","article_number":"663","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","apa":"Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5009","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","abstract":[{"lang":"eng","text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 15","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3f6d2776b90a842a28359cc957d3d04b","file_id":"4878","date_updated":"2020-07-14T12:45:26Z","file_size":1489769,"creator":"system","date_created":"2018-12-12T10:11:24Z","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","issue":"1","volume":15,"_id":"2042","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"journal_article","pubrep_id":"396","status":"public","date_updated":"2021-01-12T06:54:56Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"JoBo"}]},{"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in Proceedings of the Workshop on Algorithm Engineering and Experiments, Portland, USA, 2014, pp. 31–38.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38.","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In: McGeoch C, Meyer U, eds. Proceedings of the Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2014:31-38. doi:10.1137/1.9781611973198.4","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Distributed computation of persistent homology. In C. McGeoch & U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973198.4","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973198.4.","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38."},"editor":[{"first_name":"Catherine","full_name":" McGeoch, Catherine","last_name":" McGeoch"},{"first_name":"Ulrich","full_name":"Meyer, Ulrich","last_name":"Meyer"}],"title":"Distributed computation of persistent homology","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer"},{"last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","first_name":"Michael"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}],"publist_id":"5008","oa":1,"publisher":"Society of Industrial and Applied Mathematics","quality_controlled":"1","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","day":"01","year":"2014","date_created":"2018-12-11T11:55:23Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1137/1.9781611973198.4","page":"31 - 38","_id":"2043","status":"public","conference":{"start_date":"2014-01-05","end_date":"2014-01-05","location":"Portland, USA","name":"ALENEX: Algorithm Engineering and Experiments"},"type":"conference","date_updated":"2021-01-12T06:54:56Z","department":[{"_id":"HeEd"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node."}],"month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.0710"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1},{"author":[{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"last_name":"Lisman","full_name":"Lisman, John","first_name":"John"}],"publist_id":"5010","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","citation":{"chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncir.2014.00107.","ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:10.3389/fncir.2014.00107.","apa":"Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014)."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","article_number":"2p","doi":"10.3389/fncir.2014.00107","date_published":"2014-09-10T00:00:00Z","date_created":"2018-12-11T11:55:22Z","has_accepted_license":"1","year":"2014","day":"10","publication":"Frontiers in Neural Circuits","quality_controlled":"1","publisher":"Frontiers Research Foundation","oa":1,"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:26Z","date_updated":"2021-01-12T06:54:55Z","ddc":["570"],"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":"424","_id":"2041","volume":8,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3ca57b164045523f876407e9f13a9fb8","file_id":"5294","date_updated":"2020-07-14T12:45:26Z","file_size":201110,"creator":"system","date_created":"2018-12-12T10:17:38Z","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"09","intvolume":" 8","abstract":[{"text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time.","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems"}],"citation":{"ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_7.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:10.1007/978-3-319-04099-8_7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer"},{"first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}],"publist_id":"5007","title":"Clear and Compress: Computing Persistent Homology in Chunks","editor":[{"first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo","last_name":"Bremer"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"},{"last_name":"Pascucci","full_name":"Pascucci, Valerio","first_name":"Valerio"},{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"}],"quality_controlled":"1","publisher":"Springer","oa":1,"year":"2014","day":"19","publication":"Topological Methods in Data Analysis and Visualization III","page":"103 - 117","doi":"10.1007/978-3-319-04099-8_7","date_published":"2014-03-19T00:00:00Z","date_created":"2018-12-11T11:55:23Z","series_title":"Mathematics and Visualization","_id":"2044","type":"book_chapter","status":"public","date_updated":"2021-01-12T06:54:56Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1303.0477","open_access":"1"}],"month":"03","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1},{"citation":{"ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254927.","ieee":"A. Kicheva et al., “Coordination of progenitor specification and growth in mouse and chick spinal cord,” Science, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 2014;345(6204). doi:10.1126/science.1254927","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254927","mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927."},"date_updated":"2021-01-12T06:54:55Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5011","author":[{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana","last_name":"Ribeiro","full_name":"Ribeiro, Ana"},{"full_name":"Pérez Valle, Helena","last_name":"Pérez Valle","first_name":"Helena"},{"full_name":"Lovell Badge, Robin","last_name":"Lovell Badge","first_name":"Robin"},{"full_name":"Episkopou, Vasso","last_name":"Episkopou","first_name":"Vasso"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"}],"department":[{"_id":"ToBo"}],"title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","_id":"2040","article_number":"1254927","type":"journal_article","status":"public","year":"2014","publication_status":"published","day":"26","publication":"Science","language":[{"iso":"eng"}],"volume":345,"doi":"10.1126/science.1254927","issue":"6204","date_published":"2014-09-26T00:00:00Z","date_created":"2018-12-11T11:55:22Z","abstract":[{"lang":"eng","text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. "}],"oa_version":"Submitted Version","scopus_import":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/"}],"month":"09","intvolume":" 345"},{"date_created":"2018-12-11T11:55:24Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-11257-2_14","page":"170 - 184","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","year":"2014","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","editor":[{"last_name":"Domingo Ferrer","full_name":"Domingo Ferrer, Josep","first_name":"Josep"}],"title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","external_id":{"arxiv":["1407.8067"]},"author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"full_name":"Rybar, Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Stephen","full_name":"Fienberg, Stephen","last_name":"Fienberg"}],"publist_id":"5004","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14.","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","apa":"Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14","mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14."},"project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"volume":8744,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 8744","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance.","lang":"eng"}],"department":[{"_id":"KrPi"},{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:57Z","status":"public","conference":{"name":"PSD: Privacy in Statistical Databases","end_date":"2014-09-19","location":"Ibiza, Spain","start_date":"2014-09-17"},"type":"conference","_id":"2047"},{"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T06:55:00Z","type":"conference","conference":{"location":"Rome, Italy","end_date":"2014-09-05","start_date":"2014-09-02","name":"CONCUR: Concurrency Theory"},"status":"public","_id":"2053","volume":8704,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5084"}],"month":"09","intvolume":" 8704","abstract":[{"lang":"eng","text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems."}],"oa_version":"Submitted Version","publist_id":"4993","author":[{"first_name":"Holger","full_name":"Hermanns, Holger","last_name":"Hermanns"},{"last_name":"Krčál","full_name":"Krčál, Jan","first_name":"Jan"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"title":"Probabilistic bisimulation: Naturally on distributions","editor":[{"first_name":"Paolo","full_name":"Baldan, Paolo","last_name":"Baldan"},{"first_name":"Daniele","full_name":"Gorla, Daniele","last_name":"Gorla"}],"citation":{"chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265.","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18","apa":"Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"page":"249 - 265","doi":"10.1007/978-3-662-44584-6_18","date_published":"2014-09-01T00:00:00Z","date_created":"2018-12-11T11:55:27Z","year":"2014","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams."},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:59Z","citation":{"ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124.","short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.","chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9."},"department":[{"_id":"KrCh"}],"title":"Parameterized model checking of rendezvous systems","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"first_name":"Daniele","full_name":"Gorla, Daniele","last_name":"Gorla"}],"publist_id":"4994","author":[{"last_name":"Aminof","full_name":"Aminof, Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin"},{"first_name":"Tomer","last_name":"Kotek","full_name":"Kotek, Tomer"},{"first_name":"Sacha","full_name":"Rubin, Sacha","last_name":"Rubin"},{"full_name":"Spegni, Francesco","last_name":"Spegni","first_name":"Francesco"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"_id":"2052","status":"public","conference":{"name":"CONCUR: Concurrency Theory","location":"Rome, Italy","end_date":"2014-09-05","start_date":"2014-09-02"},"type":"conference","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:26Z","date_published":"2014-09-01T00:00:00Z","doi":"10.1007/978-3-662-44584-6_9","volume":8704,"page":"109 - 124","acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","oa_version":"None","abstract":[{"lang":"eng","text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata."}],"intvolume":" 8704","month":"09","alternative_title":["LNCS"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1"},{"project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"editor":[{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"}],"title":"Policy-based signatures","author":[{"full_name":"Bellare, Mihir","last_name":"Bellare","first_name":"Mihir"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"}],"publist_id":"5005","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_30.","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30","apa":"Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:10.1007/978-3-642-54631-0_30."},"publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","doi":"10.1007/978-3-642-54631-0_30","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:55:24Z","page":"520 - 537","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","status":"public","type":"conference","conference":{"start_date":"2014-05-26","end_date":"2014-05-28","location":"Buenos Aires, Argentina","name":"PKC: Public Key Crypography"},"_id":"2046","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:54:57Z","month":"01","intvolume":" 8383","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2013/413"}],"oa_version":"Submitted Version","abstract":[{"text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications.","lang":"eng"}],"volume":8383,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"doi":"10.1017/jfm.2013.603","date_published":"2014-01-10T00:00:00Z","date_created":"2018-12-11T11:55:25Z","page":"463 - 491","day":"10","publication":"Journal of Fluid Mechanics","year":"2014","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"title":"Experimental investigation of transitional flow in a toroidal pipe","author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179"},{"first_name":"Markus","full_name":"Holzner, Markus","last_name":"Holzner"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"first_name":"Hendrik","last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik"}],"publist_id":"5001","external_id":{"arxiv":["1508.06546"]},"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491.","ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol. 738. Cambridge University Press, pp. 463–491, 2014.","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491. doi:10.1017/jfm.2013.603","apa":"Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.603","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603.","ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491."},"volume":738,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 738","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06546"}],"oa_version":"Submitted Version","abstract":[{"text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably.","lang":"eng"}],"department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T06:54:59Z","status":"public","type":"journal_article","_id":"2050"},{"date_created":"2018-12-11T11:55:26Z","date_published":"2014-01-01T00:00:00Z","day":"01","publication_status":"published","year":"2014","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01065586"}],"quality_controlled":0,"publisher":"Neural Information Processing Systems","abstract":[{"lang":"eng","text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach."}],"title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","author":[{"first_name":"Mario","last_name":"Marchand","full_name":"Marchand, Mario"},{"first_name":"Su","last_name":"Hongyu","full_name":"Hongyu, Su"},{"first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","last_name":"Morvant","orcid":"0000-0002-8301-7240","full_name":"Emilie Morvant"},{"first_name":"Juho","full_name":"Rousu, Juho","last_name":"Rousu"},{"first_name":"John","last_name":"Shawe Taylor","full_name":"Shawe-Taylor, John"}],"publist_id":"4996","extern":1,"date_updated":"2021-01-12T06:54:59Z","citation":{"mla":"Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014.","short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” Neural Information Processing Systems, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems."},"status":"public","conference":{"name":"NIPS: Neural Information Processing Systems"},"type":"conference","_id":"2051"},{"abstract":[{"lang":"eng","text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 251","month":"02","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5353","checksum":"d570a6073765118fc0bb83c31d96fa53","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","date_created":"2018-12-12T10:18:31Z","creator":"system","file_size":6377990,"date_updated":"2020-07-14T12:45:27Z"}],"volume":251,"issue":"5","_id":"2059","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","pubrep_id":"394","status":"public","date_updated":"2021-01-12T06:55:02Z","ddc":["580"],"file_date_updated":"2020-07-14T12:45:27Z","department":[{"_id":"EvBe"}],"acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"Protoplasma","day":"20","page":"1077 - 1087","date_created":"2018-12-11T11:55:29Z","doi":"10.1007/s00709-014-0616-1","date_published":"2014-02-20T00:00:00Z","citation":{"mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","ieee":"E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1.","ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ewa","full_name":"Dubas, Ewa","last_name":"Dubas"},{"full_name":"Moravčíková, Jana","last_name":"Moravčíková","first_name":"Jana"},{"first_name":"Jana","last_name":"Libantová","full_name":"Libantová, Jana"},{"first_name":"Ildikó","full_name":"Matušíková, Ildikó","last_name":"Matušíková"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Zur, Iwona","last_name":"Zur","first_name":"Iwona"},{"last_name":"Krzewska","full_name":"Krzewska, Monika","first_name":"Monika"}],"publist_id":"4987","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos"},{"article_number":"1255263","project":[{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 2014;345(6196). doi:10.1126/science.1255263","apa":"Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1255263","ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” Science, vol. 345, no. 6196. American Association for the Advancement of Science, 2014.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4984","author":[{"last_name":"Hu","full_name":"Hu, Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua"},{"id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian","last_name":"Gan","full_name":"Gan, Jian"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"has_accepted_license":"1","year":"2014","day":"01","publication":"Science","doi":"10.1126/science.1255263","date_published":"2014-08-01T00:00:00Z","date_created":"2018-12-11T11:55:29Z","_id":"2062","type":"journal_article","status":"public","pubrep_id":"821","date_updated":"2021-01-12T06:55:03Z","ddc":["570"],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:27Z","abstract":[{"lang":"eng","text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes."}],"oa_version":"Submitted Version","scopus_import":1,"month":"08","intvolume":" 345","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5185","checksum":"a0036a589037d37e86364fa25cc0a82f","date_updated":"2020-07-14T12:45:27Z","file_size":215514,"creator":"system","date_created":"2018-12-12T10:16:00Z","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf"},{"date_created":"2018-12-12T10:16:01Z","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","date_updated":"2020-07-14T12:45:27Z","file_size":1732723,"creator":"system","file_id":"5186","checksum":"e1f57d2713725449cb898fdcb8ef47b8","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"6196","volume":345,"ec_funded":1},{"project":[{"grant_number":"11-NSF-1070","name":"ROOTS Genome-wide Analysis of Root Traits","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"article_number":"137","title":"Blending liquids","article_processing_charge":"No","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"first_name":"Greg","last_name":"Türk","full_name":"Türk, Greg"}],"publist_id":"4988","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014.","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126","apa":"Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126","mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126."},"oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2018-12-11T11:55:28Z","date_published":"2014-07-01T00:00:00Z","doi":"10.1145/2601097.2601126","publication":"ACM Transactions on Graphics","day":"01","year":"2014","has_accepted_license":"1","pubrep_id":"606","status":"public","conference":{"name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","start_date":"2014-08-10","end_date":"2014-08-14","location":"Vancouver, Canada"},"type":"conference","_id":"2058","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:27Z","ddc":["000"],"date_updated":"2022-08-25T14:02:46Z","intvolume":" 33","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations.","lang":"eng"}],"issue":"4","volume":33,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1752760a2e71e254537f31c0d10d9c6c","file_id":"4688","creator":"system","file_size":8387384,"date_updated":"2020-07-14T12:45:27Z","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","date_created":"2018-12-12T10:08:27Z"}],"publication_status":"published"},{"status":"public","conference":{"location":"Joensuu, Finland","end_date":"2014-08-22","start_date":"2014-08-20","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition"},"type":"conference","_id":"2057","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:55:01Z","intvolume":" 8621","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1404.7796","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark."}],"ec_funded":1,"volume":8621,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"title":"Majority vote of diverse classifiers for late fusion","external_id":{"arxiv":["1404.7796"]},"publist_id":"4989","author":[{"first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","full_name":"Morvant, Emilie","orcid":"0000-0002-8301-7240","last_name":"Morvant"},{"first_name":"Amaury","full_name":"Habrard, Amaury","last_name":"Habrard"},{"first_name":"Stéphane","full_name":"Ayache, Stéphane","last_name":"Ayache"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16","apa":"Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16."},"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:55:28Z","doi":"10.1007/978-3-662-44415-3_16","date_published":"2014-01-01T00:00:00Z","page":"153 - 162","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","year":"2014"},{"type":"journal_article","status":"public","_id":"2056","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:55:01Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.4532"}],"month":"11","intvolume":" 69","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"oa_version":"Submitted Version","issue":"3","volume":69,"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"4990","author":[{"first_name":"Arnab","last_name":"Ganguly","full_name":"Ganguly, Arnab"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"}],"title":"Markov chain aggregation and its applications to combinatorial reaction networks","citation":{"ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7","apa":"Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","page":"767 - 797","doi":"10.1007/s00285-013-0738-7","date_published":"2014-11-20T00:00:00Z","date_created":"2018-12-11T11:55:28Z","year":"2014","day":"20","publication":"Journal of Mathematical Biology"},{"publist_id":"4985","author":[{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"first_name":"Ewa","full_name":"Kurczyñska, Ewa","last_name":"Kurczyñska"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:55:03Z","citation":{"mla":"Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:10.1007/s00709-014-0620-5.","apa":"Mazur, E., Kurczyñska, E., & Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0620-5","ama":"Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 2014;251(5):1125-1139. doi:10.1007/s00709-014-0620-5","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","ieee":"E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” Protoplasma, vol. 251, no. 5. Springer, pp. 1125–1139, 2014.","chicago":"Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0620-5.","ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2061","page":"1125 - 1139","date_published":"2014-02-14T00:00:00Z","issue":"5","doi":"10.1007/s00709-014-0620-5","volume":251,"date_created":"2018-12-11T11:55:29Z","year":"2014","publication_status":"published","day":"14","language":[{"iso":"eng"}],"publication":"Protoplasma","quality_controlled":"1","publisher":"Springer","scopus_import":1,"month":"02","intvolume":" 251","abstract":[{"text":"Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.","lang":"eng"}],"oa_version":"None"},{"date_updated":"2021-01-12T06:55:05Z","department":[{"_id":"RySh"}],"_id":"2064","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"18","volume":522,"abstract":[{"lang":"eng","text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses."}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/","open_access":"1"}],"scopus_import":1,"intvolume":" 522","month":"07","citation":{"ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654.","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” Journal of Comparative Neurology, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042. doi:10.1002/cne.23654","apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23654","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Rubio, Maía","last_name":"Rubio","first_name":"Maía"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"last_name":"Clarkson","full_name":"Clarkson, Cheryl","first_name":"Cheryl"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"publist_id":"4974","title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus","year":"2014","publication":"Journal of Comparative Neurology","day":"29","page":"4023 - 4042","date_created":"2018-12-11T11:55:30Z","date_published":"2014-07-29T00:00:00Z","doi":"10.1002/cne.23654","acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell"},{"abstract":[{"text":"We propose an interactive, optimization-in-the-loop tool for designing inflatable structures. Given a target shape, the user draws a network of seams defining desired segment boundaries in 3D. Our method computes optimally-shaped flat panels for the segments, such that the inflated structure is as close as possible to the target while satisfying the desired seam positions. Our approach is underpinned by physics-based pattern optimization, accurate coarse-scale simulation using tension field theory, and a specialized constraint-optimization method. Our system is fast enough to warrant interactive exploration of different seam layouts, including internal connections, and their effects on the inflated shape. We demonstrate the resulting design process on a varied set of simulation examples, some of which we have fabricated, demonstrating excellent agreement with the design intent.","lang":"eng"}],"oa_version":"None","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF.","publisher":"ACM","month":"07","intvolume":" 33","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"date_published":"2014-07-01T00:00:00Z","volume":33,"doi":"10.1145/2601097.2601166","issue":"4","date_created":"2018-12-11T11:55:36Z","_id":"2081","article_number":"63","type":"conference","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"status":"public","citation":{"mla":"Skouras, Mélina, et al. Designing Inflatable Structures. Vol. 33, no. 4, 63, ACM, 2014, doi:10.1145/2601097.2601166.","apa":"Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun, E., & Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601166","ama":"Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601166","ieee":"M. Skouras et al., “Designing inflatable structures,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","short":"M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun, M. Gross, in:, ACM, 2014.","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601166.","ista":"Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 33, 63."},"date_updated":"2021-01-12T06:55:11Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4957","author":[{"full_name":"Skouras, Mélina","last_name":"Skouras","first_name":"Mélina"},{"first_name":"Bernhard","last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard"},{"full_name":"Kaufmann, Peter","last_name":"Kaufmann","first_name":"Peter"},{"last_name":"Garg","full_name":"Garg, Akash","first_name":"Akash"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Grinspun","full_name":"Grinspun, Eitan","first_name":"Eitan"},{"first_name":"Markus","last_name":"Gross","full_name":"Gross, Markus"}],"title":"Designing inflatable structures"},{"title":"Spin-It: Optimizing moment of inertia for spinnable objects","author":[{"first_name":"Moritz","full_name":"Bac̈her, Moritz","last_name":"Bac̈Her"},{"first_name":"Emily","full_name":"Whiting, Emily","last_name":"Whiting"},{"last_name":"Bickel","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olga","full_name":"Sorkine-Hornung, Olga","last_name":"Sorkine Hornung"}],"publist_id":"4958","extern":1,"citation":{"ieee":"M. Bac̈Her, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing moment of inertia for spinnable objects,” presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","short":"M. Bac̈Her, E. Whiting, B. Bickel, O. Sorkine Hornung, in:, ACM, 2014.","apa":"Bac̈Her, M., Whiting, E., Bickel, B., & Sorkine Hornung, O. (2014). Spin-It: Optimizing moment of inertia for spinnable objects (Vol. 33). Presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601157","ama":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment of inertia for spinnable objects. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601157","mla":"Bac̈Her, Moritz, et al. Spin-It: Optimizing Moment of Inertia for Spinnable Objects. Vol. 33, no. 4, ACM, 2014, doi:10.1145/2601097.2601157.","ista":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing moment of inertia for spinnable objects. SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33.","chicago":"Bac̈Her, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601157."},"date_updated":"2019-04-26T07:22:07Z","status":"public","conference":{"name":"SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"type":"conference","_id":"2080","date_created":"2018-12-11T11:55:35Z","date_published":"2014-01-01T00:00:00Z","volume":33,"doi":"10.1145/2601097.2601157","issue":"4","day":"01","publication_status":"published","year":"2014","intvolume":" 33","month":"01","quality_controlled":0,"publisher":"ACM","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND Postdoctoral Fellowship.","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. We present an algorithm to generate designs for spinning objects by optimizing rotational dynamics properties. As input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. We augment the model by creating voids inside its volume, with interior fill represented by an adaptive multi-resolution vox-elization. The discrete voxel fill values are optimized using a continuous, nonlinear formulation. Further, we optimize for rotational stability by maximizing the dominant principal moment. We extend our technique to incorporate deformation and multiple materials for cases where internal voids alone are insufficient. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. "}]},{"type":"journal_article","status":"public","_id":"2115","author":[{"last_name":"Bermano","full_name":"Bermano, Amit H","first_name":"Amit"},{"full_name":"Bradley, Derek J","last_name":"Bradley","first_name":"Derek"},{"first_name":"Thabo","last_name":"Beeler","full_name":"Beeler, Thabo"},{"first_name":"Fabio","full_name":"Zund, Fabio","last_name":"Zund"},{"first_name":"Derek","last_name":"Nowrouzezahrai","full_name":"Nowrouzezahrai, Derek"},{"first_name":"Ilya","last_name":"Baran","full_name":"Baran, Ilya"},{"last_name":"Sorkine Hornung","full_name":"Sorkine-Hornung, Olga","first_name":"Olga"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"first_name":"Robert","full_name":"Sumner, Robert W","last_name":"Sumner"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385"},{"first_name":"Markus","full_name":"Groß, Markus S","last_name":"Groß"}],"publist_id":"4919","title":"Facial performance enhancement using dynamic shape space analysis","citation":{"ista":"Bermano A, Bradley D, Beeler T, Zund F, Nowrouzezahrai D, Baran I, Sorkine Hornung O, Pfister H, Sumner R, Bickel B, Groß M. 2014. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 33(2).","chicago":"Bermano, Amit, Derek Bradley, Thabo Beeler, Fabio Zund, Derek Nowrouzezahrai, Ilya Baran, Olga Sorkine Hornung, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2546276.","apa":"Bermano, A., Bradley, D., Beeler, T., Zund, F., Nowrouzezahrai, D., Baran, I., … Groß, M. (2014). Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2546276","ama":"Bermano A, Bradley D, Beeler T, et al. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2546276","short":"A. Bermano, D. Bradley, T. Beeler, F. Zund, D. Nowrouzezahrai, I. Baran, O. Sorkine Hornung, H. Pfister, R. Sumner, B. Bickel, M. Groß, ACM Transactions on Graphics 33 (2014).","ieee":"A. Bermano et al., “Facial performance enhancement using dynamic shape space analysis,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014.","mla":"Bermano, Amit, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics, vol. 33, no. 2, ACM, 2014, doi:10.1145/2546276."},"date_updated":"2021-01-12T06:55:24Z","extern":1,"publisher":"ACM","quality_controlled":0,"month":"03","intvolume":" 33","abstract":[{"text":"The facial performance of an individual is inherently rich in subtle deformation and timing details. Although these subtleties make the performance realistic and compelling, they often elude both motion capture and hand animation. We present a technique for adding fine-scale details and expressiveness to low-resolution art-directed facial performances, such as those created manually using a rig, via marker-based capture, by fitting a morphable model to a video, or through Kinect reconstruction using recent faceshift technology. We employ a high-resolution facial performance capture system to acquire a representative performance of an individual in which he or she explores the full range of facial expressiveness. From the captured data, our system extracts an expressiveness model that encodes subtle spatial and temporal deformation details specific to that particular individual. Once this model has been built, these details can be transferred to low-resolution art-directed performances. We demonstrate results on various forms of input; after our enhancement, the resulting animations exhibit the same nuances and fine spatial details as the captured performance, with optional temporal enhancement to match the dynamics of the actor. Finally, we show that our technique outperforms the current state-of-the-art in example-based facial animation.","lang":"eng"}],"doi":"10.1145/2546276","issue":"2","volume":33,"date_published":"2014-03-01T00:00:00Z","date_created":"2018-12-11T11:55:48Z","year":"2014","publication_status":"published","day":"01","publication":"ACM Transactions on Graphics"},{"abstract":[{"text":"Let ℭ denote the Clifford algebra over ℝ𝑛, which is the von Neumann algebra generated by n self-adjoint operators Q j , j = 1,…,n satisfying the canonical anticommutation relations, Q i Q j + Q j Q i = 2δ ij I, and let τ denote the normalized trace on ℭ. This algebra arises in quantum mechanics as the algebra of observables generated by n fermionic degrees of freedom. Let 𝔓 denote the set of all positive operators 𝜌∈ℭ such that τ(ρ) = 1; these are the non-commutative analogs of probability densities in the non-commutative probability space (ℭ,𝜏). The fermionic Fokker–Planck equation is a quantum-mechanical analog of the classical Fokker–Planck equation with which it has much in common, such as the same optimal hypercontractivity properties. In this paper we construct a Riemannian metric on 𝔓 that we show to be a natural analog of the classical 2-Wasserstein metric, and we show that, in analogy with the classical case, the fermionic Fokker–Planck equation is gradient flow in this metric for the relative entropy with respect to the ground state. We derive a number of consequences of this, such as a sharp Talagrand inequality for this metric, and we prove a number of results pertaining to this metric. Several open problems are raised.","lang":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1203.5377 "}],"oa":1,"month":"11","intvolume":" 331","publication_status":"published","year":"2014","day":"01","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"page":"887 - 926","volume":331,"doi":"10.1007/s00220-014-2124-8","date_published":"2014-11-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:55:54Z","_id":"2133","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:30Z","citation":{"chicago":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2124-8.","ista":"Carlen E, Maas J. 2014. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 331(3), 887–926.","mla":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics, vol. 331, no. 3, Springer, 2014, pp. 887–926, doi:10.1007/s00220-014-2124-8.","ieee":"E. Carlen and J. Maas, “An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy,” Communications in Mathematical Physics, vol. 331, no. 3. Springer, pp. 887–926, 2014.","short":"E. Carlen, J. Maas, Communications in Mathematical Physics 331 (2014) 887–926.","apa":"Carlen, E., & Maas, J. (2014). An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2124-8","ama":"Carlen E, Maas J. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 2014;331(3):887-926. doi:10.1007/s00220-014-2124-8"},"extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4901","author":[{"full_name":"Carlen, Eric","last_name":"Carlen","first_name":"Eric"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"title":"An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy"},{"type":"journal_article","status":"public","_id":"2131","publist_id":"4902","author":[{"full_name":"Hairer, Martin M","last_name":"Hairer","first_name":"Martin"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Jan Maas","last_name":"Maas"},{"last_name":"Weber","full_name":"Weber, Hendrik","first_name":"Hendrik"}],"title":"Approximating Rough Stochastic PDEs","citation":{"ama":"Hairer M, Maas J, Weber H. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 2014;67(5):776-870. doi:10.1002/cpa.21495","apa":"Hairer, M., Maas, J., & Weber, H. (2014). Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21495","ieee":"M. Hairer, J. Maas, and H. Weber, “Approximating Rough Stochastic PDEs,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley-Blackwell, pp. 776–870, 2014.","short":"M. Hairer, J. Maas, H. Weber, Communications on Pure and Applied Mathematics 67 (2014) 776–870.","mla":"Hairer, Martin, et al. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley-Blackwell, 2014, pp. 776–870, doi:10.1002/cpa.21495.","ista":"Hairer M, Maas J, Weber H. 2014. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 67(5), 776–870.","chicago":"Hairer, Martin, Jan Maas, and Hendrik Weber. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2014. https://doi.org/10.1002/cpa.21495."},"date_updated":"2021-01-12T06:55:30Z","extern":1,"publisher":"Wiley-Blackwell","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/1202.3094 ","open_access":"1"}],"oa":1,"month":"05","intvolume":" 67","abstract":[{"lang":"eng","text":"We study approximations to a class of vector-valued equations of Burgers type driven by a multiplicative space-time white noise. A solution theory for this class of equations has been developed recently in Probability Theory Related Fields by Hairer and Weber. The key idea was to use the theory of controlled rough paths to give definitions of weak/mild solutions and to set up a Picard iteration argument. In this article the limiting behavior of a rather large class of (spatial) approximations to these equations is studied. These approximations are shown to converge and convergence rates are given, but the limit may depend on the particular choice of approximation. This effect is a spatial analogue to the Itô-Stratonovich correction in the theory of stochastic ordinary differential equations, where it is well known that different approximation schemes may converge to different solutions."}],"acknowledgement":"JM is supported by Rubicon grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). MH is supported by EPSRC grant EP/D071593/1 and by the Royal Society through a Wolfson Research Merit Award. Both MH and HW are supported by the Le","page":"776 - 870","volume":67,"issue":"5","doi":"10.1002/cpa.21495","date_published":"2014-05-01T00:00:00Z","date_created":"2018-12-11T11:55:53Z","publication_status":"published","year":"2014","day":"01","publication":"Communications on Pure and Applied Mathematics"},{"_id":"2132","status":"public","type":"journal_article","extern":1,"citation":{"chicago":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University, 2014. https://doi.org/10.3934/dcds.2014.34.1355 .","ista":"Erbar M, Maas J. 2014. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 34(4), 1355–1374.","mla":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4, Southwest Missouri State University, 2014, pp. 1355–74, doi:10.3934/dcds.2014.34.1355 .","ama":"Erbar M, Maas J. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 2014;34(4):1355-1374. doi:10.3934/dcds.2014.34.1355 ","apa":"Erbar, M., & Maas, J. (2014). Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University. https://doi.org/10.3934/dcds.2014.34.1355 ","short":"M. Erbar, J. Maas, Discrete and Continuous Dynamical Systems- Series A 34 (2014) 1355–1374.","ieee":"M. Erbar and J. Maas, “Gradient flow structures for discrete porous medium equations,” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4. Southwest Missouri State University, pp. 1355–1374, 2014."},"date_updated":"2021-01-12T06:55:30Z","title":"Gradient flow structures for discrete porous medium equations","publist_id":"4903","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Jan Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"We consider discrete porous medium equations of the form ∂tρt=Δϕ(ρt), where Δ is the generator of a reversible continuous time Markov chain on a finite set χ, and ϕ is an increasing function. We show that these equations arise as gradient flows of certain entropy functionals with respect to suitable non-local transportation metrics. This may be seen as a discrete analogue of the Wasserstein gradient flow structure for porous medium equations in ℝn discovered by Otto. We present a one-dimensional counterexample to geodesic convexity and discuss Gromov-Hausdorff convergence to the Wasserstein metric."}],"intvolume":" 34","month":"04","main_file_link":[{"url":"http://arxiv.org/abs/1212.1129","open_access":"1"}],"oa":1,"quality_controlled":0,"publisher":"Southwest Missouri State University","publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:54Z","date_published":"2014-04-01T00:00:00Z","volume":34,"doi":"10.3934/dcds.2014.34.1355 ","issue":"4","page":"1355 - 1374"},{"acknowledgement":"This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory as well as the Harvard Quantum Optics Center.","oa_version":"Submitted Version","abstract":[{"text":"We propose a technique for engineering momentum-dependent dissipation in Bose-Einstein condensates with non-local interactions. The scheme relies on the use of momentum-dependent dark-states in close analogy to velocity-selective coherent population trapping. During the short-time dissipative dynamics, the system is driven into a particular finite-momentum phonon mode, which in real space corresponds to an ordered structure with non-local density-density correlations. Dissipation-induced ordering can be observed and studied in present-day experiments using cold atoms with dipole-dipole or off-resonant Rydberg interactions. Due to its dissipative nature, the ordering does not require artificial breaking of translational symmetry by an opticallattice or harmonic trap. This opens up a perspective of direct cooling of quantum gases into strongly-interacting phases.","lang":"eng"}],"intvolume":" 113","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1308.5905","open_access":"1"}],"oa":1,"publisher":"American Physical Society","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"11","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:56Z","date_published":"2014-08-11T00:00:00Z","issue":"7","doi":"10.1103/PhysRevLett.113.070401","volume":113,"article_number":"070401","_id":"2140","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters, vol. 113, no. 7, 070401, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.070401.","ieee":"J. Otterbach and M. Lemeshko, “Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates,” Physical Review Letters, vol. 113, no. 7. American Physical Society, 2014.","short":"J. Otterbach, M. Lemeshko, Physical Review Letters 113 (2014).","apa":"Otterbach, J., & Lemeshko, M. (2014). Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.070401","ama":"Otterbach J, Lemeshko M. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 2014;113(7). doi:10.1103/PhysRevLett.113.070401","chicago":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.070401.","ista":"Otterbach J, Lemeshko M. 2014. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 113(7), 070401."},"date_updated":"2021-01-12T06:55:33Z","title":"Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates","publist_id":"4884","author":[{"first_name":"Johannes","last_name":"Otterbach","full_name":"Otterbach, Johannes"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}]},{"day":"01","publication":"Proceedings of the Annual Symposium on Computational Geometry","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582168","ec_funded":1,"date_created":"2018-12-11T11:56:01Z","page":"355 - 364","oa_version":"Submitted Version","abstract":[{"text":"We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s).","lang":"eng"}],"month":"06","scopus_import":1,"publisher":"ACM","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1311.3681","open_access":"1"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:38Z","citation":{"short":"U. Bauer, M. Lesnick, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–364.","ieee":"U. Bauer and M. Lesnick, “Induced matchings of barcodes and the algebraic stability of persistence,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 355–364.","apa":"Bauer, U., & Lesnick, M. (2014). Induced matchings of barcodes and the algebraic stability of persistence. In Proceedings of the Annual Symposium on Computational Geometry (pp. 355–364). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582168","ama":"Bauer U, Lesnick M. Induced matchings of barcodes and the algebraic stability of persistence. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:355-364. doi:10.1145/2582112.2582168","mla":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–64, doi:10.1145/2582112.2582168.","ista":"Bauer U, Lesnick M. 2014. Induced matchings of barcodes and the algebraic stability of persistence. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 355–364.","chicago":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” In Proceedings of the Annual Symposium on Computational Geometry, 355–64. ACM, 2014. https://doi.org/10.1145/2582112.2582168."},"department":[{"_id":"HeEd"}],"title":"Induced matchings of barcodes and the algebraic stability of persistence","author":[{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"first_name":"Michael","last_name":"Lesnick","full_name":"Lesnick, Michael"}],"publist_id":"4853","_id":"2153","status":"public","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan"}},{"date_updated":"2021-01-12T06:55:38Z","department":[{"_id":"UlWa"}],"_id":"2154","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":52,"issue":"1","abstract":[{"lang":"eng","text":"A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1102.3515","open_access":"1"}],"month":"07","intvolume":" 52","citation":{"ista":"Matoušek J, Wagner U. 2014. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 52(1), 1–33.","chicago":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9584-7.","ieee":"J. Matoušek and U. Wagner, “On Gromov’s method of selecting heavily covered points,” Discrete & Computational Geometry, vol. 52, no. 1. Springer, pp. 1–33, 2014.","short":"J. Matoušek, U. Wagner, Discrete & Computational Geometry 52 (2014) 1–33.","apa":"Matoušek, J., & Wagner, U. (2014). On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9584-7","ama":"Matoušek J, Wagner U. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 2014;52(1):1-33. doi:10.1007/s00454-014-9584-7","mla":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry, vol. 52, no. 1, Springer, 2014, pp. 1–33, doi:10.1007/s00454-014-9584-7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"4852","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"title":"On Gromov's method of selecting heavily covered points","project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948"}],"year":"2014","day":"01","publication":"Discrete & Computational Geometry","page":"1 - 33","doi":"10.1007/s00454-014-9584-7","date_published":"2014-07-01T00:00:00Z","date_created":"2018-12-11T11:56:01Z","acknowledgement":"Swiss National Science Foundation (SNF 200021-125309, 200020-138230, 200020-12507)","publisher":"Springer","quality_controlled":"1","oa":1},{"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bauer, Ulrich, Xiaoyin Ge, and Yusu Wang. “Measuring Distance between Reeb Graphs.” In Proceedings of the Annual Symposium on Computational Geometry, 464–73. ACM, 2014. https://doi.org/10.1145/2582112.2582169.","ista":"Bauer U, Ge X, Wang Y. 2014. Measuring distance between Reeb graphs. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 464–473.","mla":"Bauer, Ulrich, et al. “Measuring Distance between Reeb Graphs.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–73, doi:10.1145/2582112.2582169.","apa":"Bauer, U., Ge, X., & Wang, Y. (2014). Measuring distance between Reeb graphs. In Proceedings of the Annual Symposium on Computational Geometry (pp. 464–473). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582169","ama":"Bauer U, Ge X, Wang Y. Measuring distance between Reeb graphs. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:464-473. doi:10.1145/2582112.2582169","short":"U. Bauer, X. Ge, Y. Wang, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–473.","ieee":"U. Bauer, X. Ge, and Y. Wang, “Measuring distance between Reeb graphs,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 464–473."},"title":"Measuring distance between Reeb graphs","author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Ge, Xiaoyin","last_name":"Ge","first_name":"Xiaoyin"},{"last_name":"Wang","full_name":"Wang, Yusu","first_name":"Yusu"}],"publist_id":"4850","acknowledgement":"National Science Foundation under grants CCF-1319406, CCF-1116258.","publisher":"ACM","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the Annual Symposium on Computational Geometry","year":"2014","doi":"10.1145/2582112.2582169","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:56:02Z","page":"464 - 473","_id":"2156","status":"public","type":"conference","conference":{"start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry"},"date_updated":"2021-01-12T06:55:39Z","department":[{"_id":"HeEd"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s)."}],"month":"06","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.2839","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1},{"acknowledgement":"This research is partially supported by ESF under the ACAT Research Network Programme, and by the Russian Government under mega project 11.G34.31.0053","oa":1,"publisher":"ACM","quality_controlled":"1","year":"2014","publication":"Proceedings of the Annual Symposium on Computational Geometry","day":"01","page":"484 - 490","date_created":"2018-12-11T11:56:01Z","doi":"10.1145/2582112.2582167","date_published":"2014-06-01T00:00:00Z","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"citation":{"chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” In Proceedings of the Annual Symposium on Computational Geometry, 484–90. ACM, 2014. https://doi.org/10.1145/2582112.2582167.","ista":"Bauer U, Edelsbrunner H. 2014. The morse theory of Čech and Delaunay filtrations. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 484–490.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–90, doi:10.1145/2582112.2582167.","apa":"Bauer, U., & Edelsbrunner, H. (2014). The morse theory of Čech and Delaunay filtrations. In Proceedings of the Annual Symposium on Computational Geometry (pp. 484–490). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582167","ama":"Bauer U, Edelsbrunner H. The morse theory of Čech and Delaunay filtrations. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:484-490. doi:10.1145/2582112.2582167","short":"U. Bauer, H. Edelsbrunner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–490.","ieee":"U. Bauer and H. Edelsbrunner, “The morse theory of Čech and Delaunay filtrations,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 484–490."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"publist_id":"4851","title":"The morse theory of Čech and Delaunay filtrations","abstract":[{"text":"Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s).","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1312.1231","open_access":"1"}],"scopus_import":1,"month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"_id":"2155","conference":{"start_date":"2014-06-08","location":"Kyoto, Japan","end_date":"2014-06-11","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","date_updated":"2021-01-12T06:55:38Z","department":[{"_id":"HeEd"}]},{"title":"New paradigms in the establishment and maintenance of gradients during directed cell migration","author":[{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Carole","last_name":"Parent","full_name":"Parent, Carole"}],"publist_id":"4848","external_id":{"pmid":["24959970"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Majumdar R, Sixt MK, Parent C. 2014. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 30(1), 33–40.","chicago":"Majumdar, Ritankar, Michael K Sixt, and Carole Parent. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology. Elsevier, 2014. https://doi.org/10.1016/j.ceb.2014.05.010.","ama":"Majumdar R, Sixt MK, Parent C. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 2014;30(1):33-40. doi:10.1016/j.ceb.2014.05.010","apa":"Majumdar, R., Sixt, M. K., & Parent, C. (2014). New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2014.05.010","ieee":"R. Majumdar, M. K. Sixt, and C. Parent, “New paradigms in the establishment and maintenance of gradients during directed cell migration,” Current Opinion in Cell Biology, vol. 30, no. 1. Elsevier, pp. 33–40, 2014.","short":"R. Majumdar, M.K. Sixt, C. Parent, Current Opinion in Cell Biology 30 (2014) 33–40.","mla":"Majumdar, Ritankar, et al. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology, vol. 30, no. 1, Elsevier, 2014, pp. 33–40, doi:10.1016/j.ceb.2014.05.010."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This effort was supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health and the European Research Council (ERC).","date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.ceb.2014.05.010","date_created":"2018-12-11T11:56:03Z","page":"33 - 40","day":"01","publication":"Current Opinion in Cell Biology","year":"2014","status":"public","type":"journal_article","_id":"2158","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T06:55:40Z","month":"10","intvolume":" 30","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177954/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Directional guidance of migrating cells is relatively well explored in the reductionist setting of cell culture experiments. Here spatial gradients of chemical cues as well as gradients of mechanical substrate characteristics prove sufficient to attract single cells as well as their collectives. How such gradients present and act in the context of an organism is far less clear. Here we review recent advances in understanding how guidance cues emerge and operate in the physiological context.","lang":"eng"}],"volume":30,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published"},{"date_created":"2018-12-11T11:56:05Z","ec_funded":1,"volume":51,"doi":"10.1016/j.patrec.2014.08.013","date_published":"2014-10-01T00:00:00Z","page":"37-43","publication":"Pattern Recognition Letters","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","intvolume":" 51","month":"10","main_file_link":[{"url":"http://arxiv.org/abs/1410.0334","open_access":"1"}],"oa":1,"publisher":"Elsevier","quality_controlled":"1","oa_version":"Submitted Version","abstract":[{"text":"In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions. A key applied issue is thus the design of algorithms able to generalize on a new distribution, for which we have no label information. We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012). Justified by a theoretical bound on the target risk of the vote, we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar. We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem.","lang":"eng"}],"title":"Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling","author":[{"id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie","full_name":"Morvant, Emilie","orcid":"0000-0002-8301-7240","last_name":"Morvant"}],"publist_id":"4819","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T06:55:43Z","citation":{"chicago":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters. Elsevier, 2014. https://doi.org/10.1016/j.patrec.2014.08.013.","ista":"Morvant E. 2014. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 51, 37–43.","mla":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters, vol. 51, Elsevier, 2014, pp. 37–43, doi:10.1016/j.patrec.2014.08.013.","ieee":"E. Morvant, “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling,” Pattern Recognition Letters, vol. 51. Elsevier, pp. 37–43, 2014.","short":"E. Morvant, Pattern Recognition Letters 51 (2014) 37–43.","apa":"Morvant, E. (2014). Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2014.08.013","ama":"Morvant E. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 2014;51:37-43. doi:10.1016/j.patrec.2014.08.013"},"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"status":"public","type":"journal_article","_id":"2165"},{"author":[{"full_name":"Chai, Xuejun","last_name":"Chai","first_name":"Xuejun"},{"first_name":"Gert","full_name":"Münzner, Gert","last_name":"Münzner"},{"last_name":"Zhao","full_name":"Zhao, Shanting","first_name":"Shanting"},{"first_name":"Stefanie","full_name":"Tinnes, Stefanie","last_name":"Tinnes"},{"first_name":"Janina","id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","full_name":"Kowalski, Janina","last_name":"Kowalski"},{"first_name":"Ute","full_name":"Häussler, Ute","last_name":"Häussler"},{"full_name":"Young, Christina","last_name":"Young","first_name":"Christina"},{"last_name":"Haas","full_name":"Haas, Carola","first_name":"Carola"},{"first_name":"Michael","full_name":"Frotscher, Michael","last_name":"Frotscher"}],"publist_id":"4820","department":[{"_id":"PeJo"}],"title":"Epilepsy-induced motility of differentiated neurons","citation":{"mla":"Chai, Xuejun, et al. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex, vol. 24, no. 8, Oxford University Press, 2014, pp. 2130–40, doi:10.1093/cercor/bht067.","ama":"Chai X, Münzner G, Zhao S, et al. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 2014;24(8):2130-2140. doi:10.1093/cercor/bht067","apa":"Chai, X., Münzner, G., Zhao, S., Tinnes, S., Kowalski, J., Häussler, U., … Frotscher, M. (2014). Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bht067","ieee":"X. Chai et al., “Epilepsy-induced motility of differentiated neurons,” Cerebral Cortex, vol. 24, no. 8. Oxford University Press, pp. 2130–2140, 2014.","short":"X. Chai, G. Münzner, S. Zhao, S. Tinnes, J. Kowalski, U. Häussler, C. Young, C. Haas, M. Frotscher, Cerebral Cortex 24 (2014) 2130–2140.","chicago":"Chai, Xuejun, Gert Münzner, Shanting Zhao, Stefanie Tinnes, Janina Kowalski, Ute Häussler, Christina Young, Carola Haas, and Michael Frotscher. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex. Oxford University Press, 2014. https://doi.org/10.1093/cercor/bht067.","ista":"Chai X, Münzner G, Zhao S, Tinnes S, Kowalski J, Häussler U, Young C, Haas C, Frotscher M. 2014. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 24(8), 2130–2140."},"date_updated":"2021-01-12T06:55:43Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2164","page":"2130 - 2140","date_created":"2018-12-11T11:56:04Z","doi":"10.1093/cercor/bht067","volume":24,"issue":"8","date_published":"2014-08-01T00:00:00Z","year":"2014","publication_status":"published","publication":"Cerebral Cortex","language":[{"iso":"eng"}],"day":"01","quality_controlled":"1","publisher":"Oxford University Press","scopus_import":1,"intvolume":" 24","month":"08","abstract":[{"text":"Neuronal ectopia, such as granule cell dispersion (GCD) in temporal lobe epilepsy (TLE), has been assumed to result from a migration defect during development. Indeed, recent studies reported that aberrant migration of neonatal-generated dentate granule cells (GCs) increased the risk to develop epilepsy later in life. On the contrary, in the present study, we show that fully differentiated GCs become motile following the induction of epileptiform activity, resulting in GCD. Hippocampal slice cultures from transgenic mice expressing green fluorescent protein in differentiated, but not in newly generated GCs, were incubated with the glutamate receptor agonist kainate (KA), which induced GC burst activity and GCD. Using real-time microscopy, we observed that KA-exposed, differentiated GCs translocated their cell bodies and changed their dendritic organization. As found in human TLE, KA application was associated with decreased expression of the extracellular matrix protein Reelin, particularly in hilar interneurons. Together these findings suggest that KA-induced motility of differentiated GCs contributes to the development of GCD and establish slice cultures as a model to study neuronal changes induced by epileptiform activity. ","lang":"eng"}],"oa_version":"None"},{"_id":"2168","status":"public","pubrep_id":"391","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":["570"],"date_updated":"2021-01-12T06:55:44Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:31Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail."}],"month":"08","intvolume":" 95","scopus_import":1,"file":[{"file_id":"4839","checksum":"979d7a8034e9df198f068f0d251f31bd","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:49Z","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","creator":"system","date_updated":"2020-07-14T12:45:31Z","file_size":569005}],"language":[{"iso":"eng"}],"publication_status":"published","volume":95,"ec_funded":1,"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001.","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.","short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001","apa":"Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001"},"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","author":[{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"4816","publisher":"Academic Press","quality_controlled":"1","oa":1,"day":"01","publication":"Theoretical Population Biology","has_accepted_license":"1","year":"2014","date_published":"2014-08-01T00:00:00Z","doi":"10.1016/j.tpb.2014.05.001","date_created":"2018-12-11T11:56:06Z","page":"13 - 23"},{"_id":"2169","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:45Z","citation":{"chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111","apa":"Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111"},"department":[{"_id":"NiBa"}],"title":"Diverse forms of selection in evolution and computer science","publist_id":"4815","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","month":"07","intvolume":" 111","quality_controlled":"1","scopus_import":1,"publisher":"National Academy of Sciences","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/","open_access":"1"}],"day":"22","publication":"PNAS","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","date_published":"2014-07-22T00:00:00Z","volume":111,"issue":"29","doi":"10.1073/pnas.1410107111","date_created":"2018-12-11T11:56:07Z","page":"10398 - 10399"}]