[{"abstract":[{"lang":"eng","text":"Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware."}],"publication_identifier":{"eissn":["19406029"],"eisbn":["9781071607558"]},"day":"11","doi":"10.1007/978-1-0716-0755-8_16","type":"book_chapter","date_published":"2020-07-11T00:00:00Z","year":"2020","citation":{"ista":"Kainrath S, Janovjak HL. 2020.Design and application of light-regulated receptor tyrosine kinases. In: Photoswitching Proteins. Methods in Molecular Biology, vol. 2173, 233–246.","short":"S. Kainrath, H.L. Janovjak, in:, D. Niopek (Ed.), Photoswitching Proteins, Springer Nature, 2020, pp. 233–246.","mla":"Kainrath, Stephanie, and Harald L. Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” <i>Photoswitching Proteins</i>, edited by Dominik Niopek, vol. 2173, Springer Nature, 2020, pp. 233–46, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>.","chicago":"Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” In <i>Photoswitching Proteins</i>, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>.","ieee":"S. Kainrath and H. L. Janovjak, “Design and application of light-regulated receptor tyrosine kinases,” in <i>Photoswitching Proteins</i>, vol. 2173, D. Niopek, Ed. Springer Nature, 2020, pp. 233–246.","apa":"Kainrath, S., &#38; Janovjak, H. L. (2020). Design and application of light-regulated receptor tyrosine kinases. In D. Niopek (Ed.), <i>Photoswitching Proteins</i> (Vol. 2173, pp. 233–246). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>","ama":"Kainrath S, Janovjak HL. Design and application of light-regulated receptor tyrosine kinases. In: Niopek D, ed. <i>Photoswitching Proteins</i>. Vol 2173. MIMB. Springer Nature; 2020:233-246. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>"},"date_updated":"2021-01-12T08:17:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":2173,"intvolume":"      2173","title":"Design and application of light-regulated receptor tyrosine kinases","alternative_title":["Methods in Molecular Biology"],"month":"07","department":[{"_id":"CaGu"}],"date_created":"2020-07-26T22:01:03Z","article_processing_charge":"No","oa_version":"None","publication_status":"published","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Kainrath","full_name":"Kainrath, Stephanie"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"scopus_import":"1","publication":"Photoswitching Proteins","_id":"8173","editor":[{"first_name":"Dominik","last_name":"Niopek","full_name":"Niopek, Dominik"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"series_title":"MIMB","page":"233-246"},{"date_published":"2020-08-24T00:00:00Z","type":"software","date_updated":"2021-01-11T15:29:08Z","tmp":{"name":"The 3-Clause BSD License","short":"3-Clause BSD","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause"},"citation":{"ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","mla":"Hauschild, Robert. <i>Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","short":"R. Hauschild, (2020).","chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>.","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>"},"year":"2020","oa":1,"doi":"10.15479/AT:ISTA:8181","day":"24","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"rhauschild","file_id":"8290","checksum":"878c60885ce30afb59a884dd5eef451c","file_size":6577,"date_created":"2020-08-24T15:43:49Z","content_type":"text/plain","file_name":"centriolesDistance.m","date_updated":"2020-08-24T15:43:49Z"},{"date_updated":"2020-08-24T15:43:52Z","file_name":"goTracking.m","content_type":"text/plain","date_created":"2020-08-24T15:43:52Z","checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","file_size":2680,"file_id":"8291","creator":"rhauschild","relation":"main_file","success":1,"access_level":"open_access"}],"author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"_id":"8181","license":"https://opensource.org/licenses/BSD-3-Clause","has_accepted_license":"1","title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","month":"08","department":[{"_id":"Bio"}],"date_created":"2020-07-28T16:24:37Z","file_date_updated":"2020-08-24T15:43:52Z","publisher":"IST Austria"},{"author":[{"last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Vagia","last_name":"Tsiminaki","full_name":"Tsiminaki, Vagia"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"_id":"8186","scopus_import":"1","title":"Leveraging 2D data to learn textured 3D mesh generation","publication_status":"published","department":[{"_id":"ChLa"}],"article_processing_charge":"No","date_created":"2020-07-31T16:53:49Z","file_date_updated":"2020-07-31T16:57:12Z","page":"7498-7507","quality_controlled":"1","publisher":"IEEE","external_id":{"arxiv":["2004.04180"]},"date_updated":"2023-10-17T07:37:11Z","citation":{"short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2020, pp. 7498–507, doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2020:7498-7507. doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>","apa":"Henderson, P. M., Tsiminaki, V., &#38; Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 7498–7507). Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 7498–7507. IEEE, 2020. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Virtual, 2020, pp. 7498–7507."},"year":"2020","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n  A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n  We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}],"doi":"10.1109/CVPR42600.2020.00752","arxiv":1,"day":"01","ddc":["004"],"publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","has_accepted_license":"1","month":"07","oa_version":"Submitted Version","language":[{"iso":"eng"}],"conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2020-06-14","end_date":"2020-06-19","location":"Virtual"},"date_published":"2020-07-01T00:00:00Z","type":"conference","oa":1,"publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":10262773,"date_created":"2020-07-31T16:57:12Z","file_name":"paper.pdf","content_type":"application/pdf","date_updated":"2020-07-31T16:57:12Z","relation":"main_file","success":1,"access_level":"open_access","creator":"phenders","file_id":"8187"}],"main_file_link":[{"open_access":"1","url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf"}]},{"quality_controlled":"1","page":"3106–3117","publisher":"Curran Associates","author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"_id":"8188","intvolume":"        33","title":"Unsupervised object-centric video generation and decomposition in 3D","date_created":"2020-07-31T16:59:19Z","department":[{"_id":"ChLa"}],"article_processing_charge":"No","publication_status":"published","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","volume":33,"external_id":{"arxiv":["2007.06705"]},"citation":{"ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Curran Associates; 2020:3106–3117.","apa":"Henderson, P. M., &#38; Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 3106–3117). Vancouver, Canada: Curran Associates.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:3106–3117. Curran Associates, 2020.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Curran Associates, 2020, pp. 3106–3117.","short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 3106–3117.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 3106–3117."},"year":"2020","date_updated":"2023-04-25T09:49:58Z","abstract":[{"text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.","lang":"eng"}],"day":"07","arxiv":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2020-12-06","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","end_date":"2020-12-12"},"publication":"34th Conference on Neural Information Processing Systems","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"type":"conference","date_published":"2020-07-07T00:00:00Z","oa":1,"publication_identifier":{"isbn":["9781713829546"]}},{"publication_identifier":{"issn":["2211-2855"]},"type":"journal_article","date_published":"2020-11-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"105116","month":"11","oa_version":"None","publication":"Nano Energy","language":[{"iso":"eng"}],"abstract":[{"text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface.","lang":"eng"}],"day":"01","doi":"10.1016/j.nanoen.2020.105116","external_id":{"isi":["000581738300030"]},"isi":1,"year":"2020","citation":{"ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>, vol. 77, no. 11, 105116, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","ieee":"X. Yu <i>et al.</i>, “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” <i>Nano Energy</i>, vol. 77, no. 11. Elsevier, 2020.","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>.","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. 2020;77(11). doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>"},"date_updated":"2023-08-22T08:24:05Z","volume":77,"acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","intvolume":"        77","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","date_created":"2020-08-02T22:00:57Z","department":[{"_id":"MaIb"}],"article_processing_charge":"No","publication_status":"published","issue":"11","author":[{"last_name":"Yu","first_name":"Xiaoting","full_name":"Yu, Xiaoting"},{"last_name":"Liu","first_name":"Junfeng","full_name":"Liu, Junfeng"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"first_name":"Zhishan","last_name":"Luo","full_name":"Luo, Zhishan"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"first_name":"Déspina","last_name":"Nasiou","full_name":"Nasiou, Déspina"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Pan, Kai","last_name":"Pan","first_name":"Kai"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias","full_name":"Kleinhanns, Tobias"},{"full_name":"Xie, Ying","last_name":"Xie","first_name":"Ying"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"scopus_import":"1","_id":"8189","article_type":"original","publisher":"Elsevier","quality_controlled":"1"},{"intvolume":"       219","title":"Zena Werb (1945-2020): Cell biology in context","date_created":"2020-08-02T22:00:57Z","department":[{"_id":"MiSi"}],"article_processing_charge":"No","publication_status":"published","issue":"8","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Huttenlocher, Anna","first_name":"Anna","last_name":"Huttenlocher"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","scopus_import":"1","_id":"8190","article_type":"letter_note","publisher":"Rockefeller University Press","file_date_updated":"2021-02-02T23:30:03Z","day":"22","doi":"10.1083/jcb.202007029","external_id":{"isi":["000573631000004"]},"isi":1,"year":"2020","citation":{"ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>.","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020)."},"date_updated":"2023-10-17T10:04:49Z","ddc":["570"],"volume":219,"article_number":"e202007029","month":"07","oa_version":"Published Version","has_accepted_license":"1","publication":"The Journal of Cell Biology","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["1540-8140"]},"type":"journal_article","date_published":"2020-07-22T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_name":"2020_JCB_Sixt.pdf","date_updated":"2021-02-02T23:30:03Z","file_size":830725,"checksum":"30016d778d266b8e17d01094917873b8","embargo":"2021-02-01","date_created":"2020-08-04T13:11:52Z","creator":"dernst","file_id":"8200","access_level":"open_access","relation":"main_file"}]},{"publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","_id":"8191","scopus_import":"1","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Singhal","first_name":"Nandini","full_name":"Singhal, Nandini"}],"issue":"7","oa_version":"None","publication_status":"published","department":[{"_id":"DaAl"}],"date_created":"2020-08-02T22:00:58Z","article_processing_charge":"No","month":"07","title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","page":"37-49","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","conference":{"location":"Virtual Event, United States","end_date":"2020-07-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2020-07-15"},"date_updated":"2024-02-28T12:56:32Z","year":"2020","citation":{"apa":"Alistarh, D.-A., Brown, T. A., &#38; Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2020:37-49. doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, Virtual Event, United States, 2020, no. 7, pp. 37–49.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 37–49. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>.","mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>.","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49."},"date_published":"2020-07-06T00:00:00Z","isi":1,"type":"conference","external_id":{"isi":["000744436200004"]},"doi":"10.1145/3350755.3400213","day":"06","publication_identifier":{"isbn":["9781450369350"]},"abstract":[{"lang":"eng","text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"status":"public","related_material":{"record":[{"relation":"dissertation_contains","id":"8390","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["23340843"],"issn":["23340835"]},"date_published":"2020-06-01T00:00:00Z","type":"conference","conference":{"end_date":"2020-10-30","location":"Nancy, France","start_date":"2020-10-26","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"language":[{"iso":"eng"}],"oa_version":"None","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"month":"06","publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","volume":30,"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y.","day":"01","abstract":[{"lang":"eng","text":"Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach."}],"date_updated":"2023-09-07T13:16:18Z","citation":{"mla":"Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","short":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","ista":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56.","ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.","apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., &#38; Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i> (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","ieee":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, Nancy, France, 2020, vol. 30, pp. 48–56.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020."},"year":"2020","publisher":"Association for the Advancement of Artificial Intelligence","page":"48-56","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","department":[{"_id":"KrCh"}],"date_created":"2020-08-02T22:00:58Z","title":"Multiple-environment Markov decision processes: Efficient analysis and applications","intvolume":"        30","_id":"8193","scopus_import":"1","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Karkhanis, Deep","first_name":"Deep","last_name":"Karkhanis"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr"},{"last_name":"Royer","first_name":"Amélie","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2020-06-24T00:00:00Z","type":"conference","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030510732"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2020-07-04","location":"Paris, France","start_date":"2020-07-01","name":"IJCAR: International Joint Conference on Automated Reasoning"},"publication":"Automated Reasoning","oa_version":"Published Version","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"month":"06","volume":12166,"date_updated":"2023-08-22T08:27:25Z","year":"2020","citation":{"ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: <i>Automated Reasoning</i>. Vol 12166. Springer Nature; 2020:13-31. doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., &#38; Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In <i>Automated Reasoning</i> (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In <i>Automated Reasoning</i>, 12166:13–31. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>.","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in <i>Automated Reasoning</i>, Paris, France, 2020, vol. 12166, pp. 13–31.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” <i>Automated Reasoning</i>, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>.","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31."},"isi":1,"external_id":{"isi":["000884318000002"]},"doi":"10.1007/978-3-030-51074-9_2","day":"24","abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"page":"13-31","quality_controlled":"1","publisher":"Springer Nature","_id":"8194","scopus_import":"1","author":[{"first_name":"Marek","last_name":"Baranowski","full_name":"Baranowski, Marek"},{"full_name":"He, Shaobo","last_name":"He","first_name":"Shaobo"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"last_name":"Nguyen","first_name":"Thanh Son","full_name":"Nguyen, Thanh Son"},{"full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić","first_name":"Zvonimir"}],"publication_status":"published","date_created":"2020-08-02T22:00:59Z","article_processing_charge":"No","department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"title":"An SMT theory of fixed-point arithmetic","intvolume":"     12166"},{"publication_status":"published","date_created":"2020-08-03T11:45:35Z","article_processing_charge":"No","department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"title":"Refinement for structured concurrent programs","intvolume":"     12224","_id":"8195","scopus_import":"1","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","first_name":"Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"publisher":"Springer Nature","page":"275-298","quality_controlled":"1","file_date_updated":"2020-08-06T08:14:54Z","doi":"10.1007/978-3-030-53288-8_14","day":"14","abstract":[{"text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.","lang":"eng"}],"date_updated":"2023-09-07T13:18:00Z","year":"2020","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” <i>Computer Aided Verification</i>, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In <i>Computer Aided Verification</i>, 12224:275–98. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in <i>Computer Aided Verification</i>, 2020, vol. 12224, pp. 275–298.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: <i>Computer Aided Verification</i>. Vol 12224. Springer Nature; 2020:275-298. doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2020). Refinement for structured concurrent programs. In <i>Computer Aided Verification</i> (Vol. 12224, pp. 275–298). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>"},"isi":1,"external_id":{"isi":["000695276000014"]},"acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","volume":12224,"ddc":["000"],"oa_version":"Published Version","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"07","publication":"Computer Aided Verification","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783030532888"],"isbn":["9783030532871"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-07-14T00:00:00Z","type":"conference","file":[{"file_name":"2020_LNCS_Kragl.pdf","content_type":"application/pdf","date_updated":"2020-08-06T08:14:54Z","file_size":804237,"date_created":"2020-08-06T08:14:54Z","creator":"dernst","file_id":"8201","relation":"main_file","success":1,"access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"8332","relation":"dissertation_contains","status":"public"}]}},{"scopus_import":"1","_id":"8199","author":[{"orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias","first_name":"Tobias","last_name":"Gulden","id":"1083E038-9F73-11E9-A4B5-532AE6697425"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"},{"last_name":"Rudner","first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer"},{"last_name":"Lindner","first_name":"Netanel","full_name":"Lindner, Netanel"}],"department":[{"_id":"MaSe"}],"article_processing_charge":"No","date_created":"2020-08-04T13:04:15Z","publication_status":"published","intvolume":"         9","title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-08-06T08:56:06Z","publisher":"SciPost Foundation","article_type":"original","year":"2020","citation":{"ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>, vol. 9, 015, SciPost Foundation, 2020, doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>. SciPost Foundation, 2020. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>.","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” <i>SciPost Physics</i>, vol. 9. SciPost Foundation, 2020.","apa":"Gulden, T., Berg, E., Rudner, M. S., &#38; Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. 2020;9. doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>"},"date_updated":"2023-08-22T08:28:24Z","external_id":{"isi":["000557362300008"]},"isi":1,"day":"29","doi":"10.21468/scipostphys.9.1.015","abstract":[{"lang":"eng","text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist."}],"volume":9,"acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","ddc":["530"],"has_accepted_license":"1","publication":"SciPost Physics","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa_version":"Published Version","article_number":"015","month":"07","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-07-29T00:00:00Z","publication_identifier":{"issn":["2542-4653"]},"oa":1,"file":[{"file_size":531137,"date_created":"2020-08-06T08:56:06Z","file_name":"2020_SciPostPhys_Gulden.pdf","content_type":"application/pdf","date_updated":"2020-08-06T08:56:06Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"8202"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"language":[{"iso":"eng"}],"publication":"Nano Letters","has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"project":[{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","grant_number":"P32235","name":"Towards scalable hut wire quantum devices"},{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"month":"06","file":[{"creator":"dernst","file_id":"8204","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2020_NanoLetters_Katsaros.pdf","date_updated":"2020-08-06T09:35:37Z","file_size":3308906,"date_created":"2020-08-06T09:35:37Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"7689","relation":"research_data","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-06-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"oa":1,"page":"5201-5206","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-08-06T09:35:37Z","publisher":"American Chemical Society","article_type":"original","_id":"8203","pmid":1,"scopus_import":"1","author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukušić","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes"},{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"full_name":"Wang, Ting","orcid":"0000-0002-4619-9575","last_name":"Wang","first_name":"Ting"},{"first_name":"Jian-Jun","last_name":"Zhang","full_name":"Zhang, Jian-Jun"},{"first_name":"Karsten","last_name":"Held","full_name":"Held, Karsten"}],"issue":"7","publication_status":"published","department":[{"_id":"GeKa"}],"date_created":"2020-08-06T09:25:04Z","article_processing_charge":"Yes (via OA deal)","title":"Zero field splitting of heavy-hole states in quantum dots","intvolume":"        20","volume":20,"acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","ddc":["530"],"date_updated":"2024-02-21T12:44:01Z","citation":{"apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. 2020;20(7):5201-5206. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>","ieee":"G. Katsaros <i>et al.</i>, “Zero field splitting of heavy-hole states in quantum dots,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206."},"year":"2020","isi":1,"external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"doi":"10.1021/acs.nanolett.0c01466","day":"01","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}]},{"pmid":1,"_id":"8220","scopus_import":"1","author":[{"first_name":"Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ellenbroek","first_name":"Saskia I.J.","full_name":"Ellenbroek, Saskia I.J."},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"full_name":"Van Rheenen, Jacco","first_name":"Jacco","last_name":"Van Rheenen"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"issue":"29","publication_status":"published","department":[{"_id":"EdHa"}],"date_created":"2020-08-09T22:00:52Z","article_processing_charge":"No","title":"Stem cell lineage survival as a noisy competition for niche access","intvolume":"       117","page":"16969-16975","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-08-10T06:50:28Z","publisher":"National Academy of Sciences","article_type":"original","date_updated":"2023-08-22T08:29:30Z","year":"2020","citation":{"apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975."},"isi":1,"external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"doi":"10.1073/pnas.1921205117","day":"21","abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"volume":117,"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","ddc":["570"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"month":"07","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-07-21T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["10916490"]},"oa":1,"file":[{"file_id":"8223","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","content_type":"application/pdf","date_created":"2020-08-10T06:50:28Z","file_size":1111604}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"status":"public"},{"extern":"1","ddc":["570"],"volume":21,"external_id":{"pmid":["32784509"]},"date_updated":"2021-01-12T08:17:34Z","citation":{"ista":"Köhler VK, Crescioli S, Singer J, Bax HJ, Hofer G, Pranger CL, Hufnagl K, Bianchini R, Flicker S, Keller W, Karagiannis SN, Jensen-Jarolim E. 2020. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. International Journal of Molecular Sciences. 21(16), 5693.","short":"V.K. Köhler, S. Crescioli, J. Singer, H.J. Bax, G. Hofer, C.L. Pranger, K. Hufnagl, R. Bianchini, S. Flicker, W. Keller, S.N. Karagiannis, E. Jensen-Jarolim, International Journal of Molecular Sciences 21 (2020).","mla":"Köhler, Verena K., et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16, 5693, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21165693\">10.3390/ijms21165693</a>.","chicago":"Köhler, Verena K., Silvia Crescioli, Judit Singer, Heather J. Bax, Gerhard Hofer, Christina L. Pranger, Karin Hufnagl, et al. “Filling the Antibody Pipeline in Allergy: PIPE Cloning of IgE, IgG1 and IgG4 against the Major Birch Pollen Allergen Bet v 1.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21165693\">https://doi.org/10.3390/ijms21165693</a>.","ieee":"V. K. Köhler <i>et al.</i>, “Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 16. MDPI, 2020.","ama":"Köhler VK, Crescioli S, Singer J, et al. Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. <i>International Journal of Molecular Sciences</i>. 2020;21(16). doi:<a href=\"https://doi.org/10.3390/ijms21165693\">10.3390/ijms21165693</a>","apa":"Köhler, V. K., Crescioli, S., Singer, J., Bax, H. J., Hofer, G., Pranger, C. L., … Jensen-Jarolim, E. (2020). Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21165693\">https://doi.org/10.3390/ijms21165693</a>"},"year":"2020","abstract":[{"text":"Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy.","lang":"eng"}],"doi":"10.3390/ijms21165693","day":"08","file_date_updated":"2020-09-10T07:06:22Z","quality_controlled":"1","article_type":"original","publisher":"MDPI","author":[{"orcid":"0000-0001-5581-398X","full_name":"Köhler, Verena K.","first_name":"Verena K.","last_name":"Köhler"},{"last_name":"Crescioli","first_name":"Silvia","full_name":"Crescioli, Silvia","orcid":"0000-0002-1909-5957"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"first_name":"Heather J.","last_name":"Bax","orcid":"0000-0003-0432-4160","full_name":"Bax, Heather J."},{"full_name":"Hofer, Gerhard","first_name":"Gerhard","last_name":"Hofer"},{"last_name":"Pranger","first_name":"Christina L.","full_name":"Pranger, Christina L."},{"full_name":"Hufnagl, Karin","last_name":"Hufnagl","first_name":"Karin"},{"full_name":"Bianchini, Rodolfo","orcid":"0000-0003-0351-6937","last_name":"Bianchini","first_name":"Rodolfo"},{"orcid":"0000-0003-4768-8693","full_name":"Flicker, Sabine","first_name":"Sabine","last_name":"Flicker"},{"last_name":"Keller","first_name":"Walter","full_name":"Keller, Walter","orcid":"0000-0002-2261-958X"},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","orcid":"0000-0002-4100-7810"},{"first_name":"Erika","last_name":"Jensen-Jarolim","orcid":"0000-0003-4019-5765","full_name":"Jensen-Jarolim, Erika"}],"issue":"16","_id":"8225","pmid":1,"title":"Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1","intvolume":"        21","publication_status":"published","article_processing_charge":"No","date_created":"2020-08-10T11:47:29Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"dac7ccef7cdcea9be292664d8c488425","file_size":2680908,"date_created":"2020-09-10T07:06:22Z","content_type":"application/pdf","file_name":"2020_IntMolecSciences_Koehler.pdf","date_updated":"2020-09-10T07:06:22Z","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"8356"}],"date_published":"2020-08-08T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1422-0067"]},"language":[{"iso":"eng"}],"publication":"International Journal of Molecular Sciences","has_accepted_license":"1","month":"08","article_number":"5693","oa_version":"Published Version"},{"doi":"10.1111/all.14299","day":"04","publication_identifier":{"issn":["0105-4538","1398-9995"]},"oa":1,"date_updated":"2021-01-12T08:17:35Z","year":"2020","citation":{"short":"J. Gotovina, R. Bianchini, J. Singer, I. Herrmann, G. Pellizzari, I.D. Haidl, K. Hufnagl, S.N. Karagiannis, J.S. Marshall, E. Jensen‐Jarolim, Allergy (2020).","mla":"Gotovina, Jelena, et al. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” <i>Allergy</i>, Wiley, 2020, doi:<a href=\"https://doi.org/10.1111/all.14299\">10.1111/all.14299</a>.","ista":"Gotovina J, Bianchini R, Singer J, Herrmann I, Pellizzari G, Haidl ID, Hufnagl K, Karagiannis SN, Marshall JS, Jensen‐Jarolim E. 2020. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. Allergy.","apa":"Gotovina, J., Bianchini, R., Singer, J., Herrmann, I., Pellizzari, G., Haidl, I. D., … Jensen‐Jarolim, E. (2020). Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.14299\">https://doi.org/10.1111/all.14299</a>","ama":"Gotovina J, Bianchini R, Singer J, et al. Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro. <i>Allergy</i>. 2020. doi:<a href=\"https://doi.org/10.1111/all.14299\">10.1111/all.14299</a>","ieee":"J. Gotovina <i>et al.</i>, “Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro,” <i>Allergy</i>. Wiley, 2020.","chicago":"Gotovina, Jelena, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Giulia Pellizzari, Ian D. Haidl, Karin Hufnagl, Sophia N. Karagiannis, Jean S. Marshall, and Erika Jensen‐Jarolim. “Epinephrine Drives Human M2a Allergic Macrophages to a Regulatory Phenotype Reducing Mast Cell Degranulation in Vitro.” <i>Allergy</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/all.14299\">https://doi.org/10.1111/all.14299</a>."},"date_published":"2020-04-04T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1111/all.14299","open_access":"1"}],"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_status":"epub_ahead","article_processing_charge":"No","date_created":"2020-08-10T11:50:30Z","month":"04","title":"Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro","_id":"8226","publication":"Allergy","author":[{"last_name":"Gotovina","first_name":"Jelena","full_name":"Gotovina, Jelena","orcid":"0000-0003-1503-5276"},{"first_name":"Rodolfo","last_name":"Bianchini","orcid":"0000-0003-0351-6937","full_name":"Bianchini, Rodolfo"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer","first_name":"Judit"},{"orcid":"0000-0003-2772-9144","full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"last_name":"Pellizzari","first_name":"Giulia","full_name":"Pellizzari, Giulia","orcid":"0000-0003-0387-1912"},{"full_name":"Haidl, Ian D.","orcid":"0000-0002-5301-0822","last_name":"Haidl","first_name":"Ian D."},{"orcid":"0000-0002-2288-2468","full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"first_name":"Sophia N.","last_name":"Karagiannis","orcid":"0000-0002-4100-7810","full_name":"Karagiannis, Sophia N."},{"orcid":"0000-0002-5642-1379","full_name":"Marshall, Jean S.","first_name":"Jean S.","last_name":"Marshall"},{"last_name":"Jensen‐Jarolim","first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","orcid":"0000-0003-4019-5765"}],"publisher":"Wiley","article_type":"letter_note","quality_controlled":"1","language":[{"iso":"eng"}]},{"volume":11,"acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","ddc":["570"],"citation":{"ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17734-z\">https://doi.org/10.1038/s41467-020-17734-z</a>","ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” <i>Nature Communications</i>, vol. 11, 4013, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17734-z\">10.1038/s41467-020-17734-z</a>."},"year":"2020","date_updated":"2024-03-25T23:30:05Z","external_id":{"isi":["000562769300008"]},"isi":1,"day":"11","doi":"10.1038/s41467-020-17734-z","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.","lang":"eng"}],"quality_controlled":"1","file_date_updated":"2020-08-17T07:36:57Z","publisher":"Springer Nature","article_type":"original","_id":"8250","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X"}],"date_created":"2020-08-12T09:13:50Z","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publication_status":"published","intvolume":"        11","title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","file":[{"date_created":"2020-08-17T07:36:57Z","file_size":1965672,"checksum":"986bebb308850a55850028d3d2b5b664","date_updated":"2020-08-17T07:36:57Z","file_name":"2020_NatureComm_Kavcic.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"8275","creator":"dernst"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"dissertation_contains","id":"8657","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2020-08-11T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"4013","month":"08"},{"file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"8280","creator":"dernst","date_created":"2020-08-18T08:03:23Z","file_size":5778420,"checksum":"4f1382ed4384751b6013398c11557bf6","date_updated":"2020-08-18T08:03:23Z","content_type":"application/x-zip-compressed","file_name":"Data_Rcode_MathematicaNB.zip"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"11321"},{"relation":"later_version","id":"9192","status":"public"}]},"status":"public","ddc":["576"],"year":"2020","citation":{"apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>.","short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. <i>Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus)</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2024-02-21T12:41:09Z","type":"research_data","date_published":"2020-08-18T00:00:00Z","day":"18","doi":"10.15479/AT:ISTA:8254","oa":1,"abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"file_date_updated":"2020-08-18T08:03:23Z","contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon","contributor_type":"data_collector"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","contributor_type":"project_member","first_name":"Parvathy"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","contributor_type":"project_member","last_name":"Barton","first_name":"Nicholas H"},{"orcid":"0000-0002-4014-8478","contributor_type":"project_member","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","contributor_type":"project_member","orcid":"0000-0001-6118-0541"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett","first_name":"Carina"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","_id":"8254","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2020-08-12T12:49:23Z","oa_version":"Published Version","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","month":"08"},{"_id":"8261","pmid":1,"issue":"6","author":[{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang"},{"last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_created":"2020-08-14T09:36:05Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publication_status":"published","intvolume":"       107","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","quality_controlled":"1","ec_funded":1,"page":"1212-1225","file_date_updated":"2020-12-04T09:29:21Z","publisher":"Elsevier","article_type":"original","citation":{"short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. 2020;107(6):1212-1225. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>","apa":"Zhang, X., Schlögl, A., &#38; Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>."},"year":"2020","date_updated":"2023-08-22T08:30:55Z","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"isi":1,"day":"23","doi":"10.1016/j.neuron.2020.07.006","abstract":[{"text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.","lang":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","volume":107,"ddc":["570"],"has_accepted_license":"1","publication":"Neuron","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"month":"09","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_published":"2020-09-23T00:00:00Z","publication_identifier":{"issn":["0896-6273"]},"oa":1,"file":[{"date_updated":"2020-12-04T09:29:21Z","content_type":"application/pdf","file_name":"2020_Neuron_Zhang.pdf","date_created":"2020-12-04T09:29:21Z","file_size":3011120,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_id":"8920","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access"}],"status":"public","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","description":"News on IST Website","relation":"press_release"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","volume":68,"abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"day":"20","arxiv":1,"doi":"10.1109/TSP.2020.3010355","external_id":{"arxiv":["1802.04907"],"isi":["000562044500001"]},"isi":1,"year":"2020","citation":{"chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>.","ieee":"N. M. Gurel <i>et al.</i>, “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” <i>IEEE Transactions on Signal Processing</i>, vol. 68. IEEE, pp. 4268–4282, 2020.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. 2020;68:4268-4282. doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>, vol. 68, IEEE, 2020, pp. 4268–82, doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>.","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282."},"date_updated":"2023-08-22T08:40:08Z","article_type":"original","publisher":"IEEE","quality_controlled":"1","page":"4268-4282","intvolume":"        68","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","date_created":"2020-08-16T22:00:56Z","article_processing_charge":"No","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"full_name":"Gurel, Nezihe Merve","last_name":"Gurel","first_name":"Nezihe Merve"},{"full_name":"Kara, Kaan","first_name":"Kaan","last_name":"Kara"},{"last_name":"Stojanov","first_name":"Alen","full_name":"Stojanov, Alen"},{"last_name":"Smith","first_name":"Tyler","full_name":"Smith, Tyler"},{"full_name":"Lemmin, Thomas","first_name":"Thomas","last_name":"Lemmin"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Markus","last_name":"Puschel","full_name":"Puschel, Markus"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"}],"scopus_import":"1","_id":"8268","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]},"type":"journal_article","date_published":"2020-07-20T00:00:00Z","language":[{"iso":"eng"}],"month":"07","oa_version":"Preprint","publication":"IEEE Transactions on Signal Processing"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","type":"journal_article","date_published":"2020-09-07T00:00:00Z","publication_identifier":{"issn":["16742052"],"eissn":["17529867"]},"language":[{"iso":"eng"}],"publication":"Molecular Plant","oa_version":"None","month":"09","acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","volume":13,"citation":{"short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>.","ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. 2020;13(9):1238-1240. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>","apa":"He, P., Zhang, Y., &#38; Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>","ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” <i>Molecular Plant</i>, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>."},"year":"2020","date_updated":"2023-08-22T08:40:35Z","external_id":{"isi":["000566895400007"],"pmid":["32688032"]},"isi":1,"day":"07","doi":"10.1016/j.molp.2020.07.006","quality_controlled":"1","page":"1238-1240","publisher":"Elsevier","article_type":"original","scopus_import":"1","pmid":1,"_id":"8271","issue":"9","author":[{"full_name":"He, Peng","first_name":"Peng","last_name":"He"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, Guanghui","first_name":"Guanghui","last_name":"Xiao"}],"department":[{"_id":"JiFr"}],"date_created":"2020-08-16T22:00:57Z","article_processing_charge":"No","publication_status":"published","intvolume":"        13","title":"Origin of a subgenome and genome evolution of allotetraploid cotton species"}]