[{"date_published":"2019-06-13T00:00:00Z","date_created":"2019-06-20T18:23:03Z","page":"5142-5151","day":"13","publication":"Proceedings of the 36th International Conference on Machine Learning","has_accepted_license":"1","year":"2019","publisher":"ML Research Press","quality_controlled":"1","oa":1,"title":"Towards understanding knowledge distillation","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 5142–51.","apa":"Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.","ama":"Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151.","ieee":"M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.","chicago":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” In Proceedings of the 36th International Conference on Machine Learning, 97:5142–51. ML Research Press, 2019.","ista":"Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151."},"volume":97,"file":[{"date_updated":"2020-07-14T12:47:33Z","file_size":686432,"creator":"bphuong","date_created":"2019-06-20T18:22:56Z","file_name":"paper.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6570","checksum":"a66d00e2694d749250f8507f301320ca"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 97","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows."}],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:33Z","ddc":["000"],"date_updated":"2023-10-17T12:31:38Z","status":"public","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","location":"Long Beach, CA, United States","end_date":"2019-06-15","start_date":"2019-06-10"},"_id":"6569"},{"publisher":"ML Research Press","quality_controlled":"1","oa":1,"year":"2019","day":"01","publication":"Proceedings of the 36th International Conference on Machine Learning","page":"3488-3498","date_published":"2019-06-01T00:00:00Z","date_created":"2019-06-27T14:18:23Z","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"mla":"Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 3488–98.","ieee":"N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498.","short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","apa":"Konstantinov, N. H., & Lampert, C. (2019). Robust learning from untrusted sources. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019.","ista":"Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 3488–3498."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"external_id":{"arxiv":["1901.10310"]},"article_processing_charge":"No","title":"Robust learning from untrusted sources","abstract":[{"text":"Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. ","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"month":"06","intvolume":" 97","publication_status":"published","language":[{"iso":"eng"}],"volume":97,"related_material":{"record":[{"id":"10799","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"6590","type":"conference","conference":{"end_date":"2919-06-15","location":"Long Beach, CA, USA","start_date":"2019-06-10","name":"ICML: International Conference on Machine Learning"},"status":"public","date_updated":"2023-10-17T12:31:55Z","department":[{"_id":"ChLa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116","apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","ieee":"D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019."},"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","author":[{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"first_name":"Y","last_name":"Sun","full_name":"Sun, Y"},{"first_name":"Z","last_name":"Ma","full_name":"Ma, Z"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"first_name":"Y","last_name":"Cui","full_name":"Cui, Y"},{"first_name":"Z","full_name":"Chen, Z","last_name":"Chen"},{"first_name":"C","full_name":"Chen, C","last_name":"Chen"},{"first_name":"C","last_name":"Ji","full_name":"Ji, C"},{"first_name":"TM","full_name":"Tran, TM","last_name":"Tran"},{"first_name":"L","full_name":"Yang, L","last_name":"Yang"},{"full_name":"Lam, SM","last_name":"Lam","first_name":"SM"},{"first_name":"Y","full_name":"Han, Y","last_name":"Han"},{"first_name":"G","full_name":"Shu, G","last_name":"Shu"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"first_name":"L","last_name":"Jiang","full_name":"Jiang, L"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"}],"external_id":{"pmid":["31575745"],"isi":["000490183000068"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"day":"15","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-10-15T00:00:00Z","doi":"10.1073/pnas.1911892116","date_created":"2019-11-12T11:42:05Z","page":"21274-21284","_id":"6999","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"ddc":["580"],"date_updated":"2023-10-17T12:32:37Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:46Z","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading."}],"month":"10","intvolume":" 116","scopus_import":"1","file":[{"date_created":"2019-11-13T08:22:28Z","file_name":"2019_PNAS_Huang.pdf","date_updated":"2020-07-14T12:47:46Z","file_size":3287466,"creator":"dernst","checksum":"258c666bc6253eab81961f61169eefae","file_id":"7012","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"volume":116,"issue":"42"},{"year":"2019","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"25","page":"12607-12608","date_created":"2019-07-07T21:59:25Z","date_published":"2019-06-25T00:00:00Z","doi":"10.1073/pnas.1905555116","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","citation":{"ista":"Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608.","chicago":"Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116.","apa":"Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116","ama":"Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116","ieee":"A. E. Wright et al., “On the power to detect rare recombination events,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608, 2019.","short":"A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608.","mla":"Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08, doi:10.1073/pnas.1905555116."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"article_processing_charge":"No","author":[{"first_name":"Alison E.","full_name":"Wright, Alison E.","last_name":"Wright"},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"first_name":"Natasha I.","last_name":"Bloch","full_name":"Bloch, Natasha I."},{"last_name":"Oostra","full_name":"Oostra, Vicencio","first_name":"Vicencio"},{"last_name":"Sandkam","full_name":"Sandkam, Benjamin A.","first_name":"Benjamin A."},{"first_name":"Séverine D.","full_name":"Buechel, Séverine D.","last_name":"Buechel"},{"full_name":"Kolm, Niclas","last_name":"Kolm","first_name":"Niclas"},{"first_name":"Felix","full_name":"Breden, Felix","last_name":"Breden"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"last_name":"Mank","full_name":"Mank, Judith E.","first_name":"Judith E."}],"title":"On the power to detect rare recombination events","publication_status":"published","language":[{"iso":"eng"}],"issue":"26","volume":116,"abstract":[{"text":"We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"scopus_import":"1","intvolume":" 116","month":"06","date_updated":"2023-10-17T12:44:15Z","department":[{"_id":"BeVi"}],"_id":"6621","type":"journal_article","article_type":"letter_note","status":"public"},{"project":[{"grant_number":"329960","name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"name":"Sex chromosomes and species barriers","grant_number":"M02463","call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["31505037"]},"article_processing_charge":"No","author":[{"last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yaniv","last_name":"Brandvain","full_name":"Brandvain, Yaniv"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Sarah","last_name":"Yakimowski","full_name":"Yakimowski, Sarah"},{"full_name":"Dixit, Tanmay","last_name":"Dixit","first_name":"Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"full_name":"Cereghetti, Eva","last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"}],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2019","has_accepted_license":"1","publication":"New Phytologist","day":"01","page":"1035-1047","date_created":"2019-09-07T14:35:40Z","doi":"10.1111/nph.16180","date_published":"2019-11-01T00:00:00Z","_id":"6856","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-18T08:47:08Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 224","month":"11","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-13T08:15:05Z","file_name":"2019_NewPhytologist_Pickup.pdf","date_updated":"2020-07-14T12:47:42Z","file_size":1511958,"creator":"dernst"}],"ec_funded":1,"volume":224,"issue":"3"},{"_id":"14299","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-11-07T12:17:31Z","pmid":1,"oa_version":"Published Version","abstract":[{"text":"DNA origami nano-objects are usually designed around generic single-stranded “scaffolds”. Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation.","lang":"eng"}],"intvolume":" 13","month":"04","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.9b01025","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086x"]},"issue":"5","volume":13,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027.","chicago":"FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler, B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.","ieee":"E. FAS et al., “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019.","short":"E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick, K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027.","ama":"FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027. doi:10.1021/acsnano.9b01025","apa":"FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025","mla":"FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:10.1021/acsnano.9b01025."},"title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","external_id":{"pmid":["30990672"]},"article_processing_charge":"No","author":[{"full_name":"FAS, Engelhardt","last_name":"FAS","first_name":"Engelhardt"},{"full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"first_name":"CH","full_name":"Wachauf, CH","last_name":"Wachauf"},{"first_name":"G","last_name":"Brüggenthies","full_name":"Brüggenthies, G"},{"last_name":"Kohler","full_name":"Kohler, F","first_name":"F"},{"full_name":"Kick, B","last_name":"Kick","first_name":"B"},{"first_name":"KL","full_name":"Kadletz, KL","last_name":"Kadletz"},{"first_name":"PN","last_name":"Pham","full_name":"Pham, PN"},{"last_name":"Behler","full_name":"Behler, KL","first_name":"KL"},{"first_name":"T","last_name":"Gerling","full_name":"Gerling, T"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"}],"oa":1,"quality_controlled":"1","publisher":"ACS Publications","publication":"ACS Nano","day":"16","year":"2019","date_created":"2023-09-06T12:48:47Z","doi":"10.1021/acsnano.9b01025","date_published":"2019-04-16T00:00:00Z","page":"5015-5027"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"doi":"10.4230/LIPICS.SOCG.2019.38","date_published":"2019-06-01T00:00:00Z","date_created":"2019-07-17T10:35:04Z","page":"38:1-38:13","day":"01","publication":"35th International Symposium on Computational Geometry","has_accepted_license":"1","year":"2019","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"The crossing Tverberg theorem","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Bernd","full_name":"Gärtner, Bernd","last_name":"Gärtner"},{"first_name":"Andrey","full_name":"Kupavskii, Andrey","last_name":"Kupavskii"},{"first_name":"Pavel","last_name":"Valtr","full_name":"Valtr, Pavel"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1812.04911"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38"},"month":"06","intvolume":" 129","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2.","lang":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"13974","status":"public"}]},"volume":129,"file":[{"file_id":"6667","checksum":"d6d017f8b41291b94d102294fa96ae9c","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-24T06:54:52Z","file_name":"2019_LIPICS_Fulek.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:35Z","file_size":559837}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771047"]},"publication_status":"published","status":"public","type":"conference","conference":{"name":"SoCG 2019: Symposium on Computational Geometry","end_date":"2019-06-21","location":"Portland, OR, United States","start_date":"2019-06-18"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6647","file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"UlWa"}],"ddc":["000","510"],"date_updated":"2023-12-13T12:03:35Z"},{"type":"conference","conference":{"end_date":"2019-06-26","location":"Phoenix, AZ, United States","start_date":"2019-06-23","name":"STOC: Symposium on Theory of Computing"},"status":"public","_id":"6676","department":[{"_id":"DaAl"}],"date_updated":"2023-12-13T12:28:28Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"month":"06","abstract":[{"lang":"eng","text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"later_version","status":"public","id":"14364"}]},"publication_identifier":{"isbn":["9781450367059"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"first_name":"Faith","full_name":"Ellen, Faith","last_name":"Ellen"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"first_name":"Leqi","full_name":"Zhu, Leqi","last_name":"Zhu"}],"article_processing_charge":"No","external_id":{"arxiv":["1811.01421"],"isi":["000523199100089"]},"title":"Why extension-based proofs fail","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM Press","quality_controlled":"1","oa":1,"page":"986-996","date_published":"2019-06-01T00:00:00Z","doi":"10.1145/3313276.3316407","date_created":"2019-07-24T09:13:05Z","isi":1,"year":"2019","day":"01","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"7944","status":"public"},{"id":"12833","status":"public","relation":"later_version"}]},"date_published":"2019-03-16T00:00:00Z","date_created":"2020-06-08T12:25:25Z","day":"16","publication":"arXiv","language":[{"iso":"eng"}],"year":"2019","publication_status":"submitted","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1903.06981","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"title":"Token swapping on trees","author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"last_name":"Jain","full_name":"Jain, Kshitij","first_name":"Kshitij"},{"first_name":"Anna","full_name":"Lubiw, Anna","last_name":"Lubiw"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322"},{"first_name":"Tillmann","full_name":"Miltzow, Tillmann","last_name":"Miltzow"},{"last_name":"Mondal","full_name":"Mondal, Debajyoti","first_name":"Debajyoti"},{"first_name":"Anurag Murty","full_name":"Naredla, Anurag Murty","last_name":"Naredla"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Alexi","last_name":"Turcotte","full_name":"Turcotte, Alexi"}],"article_processing_charge":"No","external_id":{"arxiv":["1903.06981"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-04T12:42:08Z","citation":{"mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","ieee":"A. Biniaz et al., “Token swapping on trees,” arXiv. .","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981."},"status":"public","type":"preprint","article_number":"1903.06981","_id":"7950"},{"ddc":["570"],"date_updated":"2024-02-21T12:45:41Z","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"BeVi"}],"_id":"6418","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2020-07-14T12:47:29Z","file_size":1256303,"creator":"dernst","date_created":"2019-05-14T08:29:38Z","file_name":"2019_GBE_Huylmans.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6446","checksum":"7d0ede297b6741f3dc89cd59017c7642"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","issue":"4","volume":11,"related_material":{"record":[{"relation":"popular_science","id":"6060","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"04","intvolume":" 11","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053"},"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","author":[{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Gammerdinger","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000476569800003"]},"article_processing_charge":"No","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"day":"01","publication":"Genome biology and evolution","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1093/gbe/evz053","date_published":"2019-04-01T00:00:00Z","date_created":"2019-05-13T07:58:38Z","page":"1033-1044","publisher":"Oxford University Press","quality_controlled":"1","oa":1},{"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"11","year":"2019","has_accepted_license":"1","day":"13","file":[{"checksum":"72441055043eda4cbf1398a422e2c118","file_id":"7017","description":"Illumina whole genome sequence data for Locus 1 - amplified.","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","file_name":"D8_S35_R2_001.fastq","title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","file_size":2456192500,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek"},{"description":"Illumina whole genome sequence data for Locus 1 - ancestral.","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","file_id":"7018","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","file_size":2833452234,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_name":"IT028_S11_R2_001.fastq","date_created":"2019-11-13T08:52:59Z","title":"Locus1_ancestral"},{"description":"Illumina whole genome sequence data for Locus 1 - 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Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"article_processing_charge":"No","author":[{"last_name":"Tomanek","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","file_date_updated":"2020-07-14T12:47:47Z","department":[{"_id":"CaGu"}]},{"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","related_material":{"record":[{"relation":"used_in_publication","id":"8433","status":"deleted"},{"id":"7262","status":"public","relation":"used_in_publication"}]},"date_created":"2019-12-09T07:52:46Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","contributor":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov"},{"last_name":"McMahan","first_name":"Connor"},{"first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez"},{"last_name":"Daraio","first_name":"Chiara"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"}],"ec_funded":1,"has_accepted_license":"1","year":"2019","day":"06","file":[{"file_name":"temporal_morphing_supp_data.zip","date_created":"2019-12-09T07:52:17Z","creator":"dernst","file_size":65307107,"date_updated":"2020-07-14T12:47:50Z","file_id":"7155","checksum":"155133e6e188e85b3c0676a5e70b9341","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","oa_version":"Published Version","author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"BeBi"}],"title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","citation":{"mla":"Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154.","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","short":"R. Guseinov, (2019).","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","ista":"Guseinov R. 2019. 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Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060."},"date_updated":"2024-02-21T12:45:42Z","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"BeVi"}],"title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","author":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"article_processing_charge":"No","_id":"6060","status":"public","type":"research_data","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"6061","checksum":"a338a622d728af0e3199cb07e6dd64d3","creator":"bvicoso","date_updated":"2020-07-14T12:47:17Z","file_size":36646050,"date_created":"2019-02-28T10:54:27Z","file_name":"SupData.zip"}],"day":"28","has_accepted_license":"1","year":"2019","related_material":{"record":[{"id":"6418","status":"public","relation":"research_paper"}]},"date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","date_created":"2019-02-28T10:55:15Z","oa_version":"Published Version","month":"02","publisher":"Institute of Science and Technology Austria","oa":1},{"date_created":"2019-03-07T13:32:35Z","doi":"10.15479/AT:ISTA:6074","related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"date_published":"2019-01-09T00:00:00Z","year":"2019","has_accepted_license":"1","file":[{"checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_id":"6084","content_type":"application/zip","access_level":"open_access","relation":"supplementary_material","date_created":"2019-03-07T13:37:19Z","file_name":"Setd5_paper.zip","date_updated":"2020-07-14T12:47:18Z","file_size":33202743,"creator":"dernst"}],"day":"09","oa":1,"publisher":"Institute of Science and Technology Austria","month":"01","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:47:18Z","citation":{"ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","short":"C. Dotter, G. Novarino, (2019).","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074."},"date_updated":"2024-02-21T13:41:01Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","status":"public","_id":"6074"},{"year":"2019","has_accepted_license":"1","file":[{"title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","date_created":"2019-03-05T09:29:37Z","file_name":"Online_data.zip","date_updated":"2020-07-14T12:47:18Z","file_size":37002186,"creator":"mnardin","checksum":"48e7b9a02939b763417733239522a236","file_id":"6068","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"day":"29","date_created":"2019-03-04T14:20:58Z","related_material":{"record":[{"status":"public","id":"6194","relation":"research_paper"}]},"date_published":"2019-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:6062","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"03","date_updated":"2024-02-21T12:46:04Z","citation":{"mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","short":"M. Nardin, (2019).","ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062.","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"}],"file_date_updated":"2020-07-14T12:47:18Z","department":[{"_id":"JoCs"}],"title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","_id":"6062","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"research_data","status":"public"},{"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2024-02-21T13:59:17Z","status":"public","type":"journal_article","_id":"6089","volume":36,"related_material":{"record":[{"status":"public","id":"5757","relation":"popular_science"}]},"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publication_status":"published","month":"03","intvolume":" 36","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"No","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246."},"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"date_published":"2019-03-01T00:00:00Z","doi":"10.1093/molbev/msy246","date_created":"2019-03-10T22:59:19Z","page":"500-515","day":"01","publication":"Molecular biology and evolution","isi":1,"year":"2019","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"title":"From Dyson to Pearcey: Universal statistics in random matrix theory","article_processing_charge":"No","author":[{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","apa":"Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179","ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"date_created":"2019-03-28T08:58:59Z","date_published":"2019-03-18T00:00:00Z","doi":"10.15479/AT:ISTA:th6179","page":"375","day":"18","year":"2019","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:47:21Z","ddc":["515","519"],"date_updated":"2024-02-22T14:34:33Z","supervisor":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"status":"public","type":"dissertation","_id":"6179","ec_funded":1,"related_material":{"record":[{"id":"1144","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6186","relation":"part_of_dissertation"},{"id":"6185","status":"public","relation":"part_of_dissertation"},{"id":"6182","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1012"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_Schroeder_Thesis.tar.gz","date_created":"2019-03-28T08:53:52Z","file_size":7104482,"date_updated":"2020-07-14T12:47:21Z","creator":"dernst","file_id":"6180","checksum":"6926f66f28079a81c4937e3764be00fc","content_type":"application/x-gzip","relation":"source_file","access_level":"closed"},{"file_name":"2019_Schroeder_Thesis.pdf","date_created":"2019-03-28T08:53:52Z","file_size":4228794,"date_updated":"2020-07-14T12:47:21Z","creator":"dernst","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","file_id":"6181","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure.","lang":"eng"}]},{"_id":"6482","status":"public","type":"conference","conference":{"start_date":"2018-10-09","end_date":"2018-10-12","location":"Stuttgart, Germany","name":"GCPR: Conference on Pattern Recognition"},"date_updated":"2024-02-22T14:57:29Z","department":[{"_id":"ChLa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. "}],"month":"02","intvolume":" 11269","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030129385","9783030129392"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"6944","status":"public"}]},"volume":11269,"ec_funded":1,"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","apa":"Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-12939-2_18","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-12939-2_18.","ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259."},"title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","author":[{"full_name":"Sun, Rémy","last_name":"Sun","first_name":"Rémy"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"external_id":{"arxiv":["1804.04171"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"14","year":"2019","doi":"10.1007/978-3-030-12939-2_18","date_published":"2019-02-14T00:00:00Z","date_created":"2019-05-24T09:48:36Z","page":"244-259"},{"article_number":"020002","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493.","ieee":"M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech Republic, 2019, vol. 2107.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","ama":"Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing; 2019. doi:10.1063/1.5109493","apa":"Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493","chicago":"Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.","ista":"Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002."},"title":"On diffusive variants of some classical viscoelastic rate-type models","external_id":{"isi":["000479303100002"],"arxiv":["1902.07983"]},"article_processing_charge":"No","author":[{"last_name":"Dostalík","full_name":"Dostalík, Mark","first_name":"Mark"},{"first_name":"Vít","full_name":"Pruša, Vít","last_name":"Pruša"},{"full_name":"Skrivan, Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"}],"oa":1,"quality_controlled":"1","publisher":"AIP Publishing","publication":"AIP Conference Proceedings","day":"21","year":"2019","isi":1,"date_created":"2019-07-15T10:07:09Z","doi":"10.1063/1.5109493","date_published":"2019-05-21T00:00:00Z","_id":"6642","status":"public","conference":{"name":"8th International Conference on Novel Trends in Rheology","start_date":"2019-07-30","location":"Zlin, Czech Republic","end_date":"2019-07-31"},"type":"conference","date_updated":"2024-02-28T13:01:28Z","department":[{"_id":"ChWo"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models."}],"intvolume":" 2107","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":2107},{"year":"2019","has_accepted_license":"1","isi":1,"publication":"Journal of Mathematical Physics","day":"01","date_created":"2020-01-05T23:00:46Z","doi":"10.1063/1.5138135","date_published":"2019-12-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","citation":{"ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135","apa":"Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000505529800002"]},"article_processing_charge":"No","author":[{"full_name":"Jaksic, Vojkan","last_name":"Jaksic","first_name":"Vojkan"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","article_number":"123504","publication_status":"published","publication_identifier":{"issn":["00222488"]},"language":[{"iso":"eng"}],"file":[{"checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","file_id":"7244","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_JournalMathPhysics_Jaksic.pdf","date_created":"2020-01-07T14:59:13Z","file_size":1025015,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst"}],"volume":60,"issue":"12","oa_version":"Published Version","scopus_import":"1","intvolume":" 60","month":"12","date_updated":"2024-02-28T13:01:45Z","ddc":["500"],"file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"RoSe"}],"_id":"7226","type":"journal_article","article_type":"letter_note","status":"public"},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7190","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:40Z","ddc":["530"],"month":"12","intvolume":" 1","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"oa_version":"Published Version","issue":"3","volume":1,"ec_funded":1,"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"382eb67e62a77052a23887332d363f96","file_id":"7193","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","file_size":1370022,"date_created":"2019-12-18T07:13:14Z","file_name":"2019_PhysRevResearch_Huber.pdf"}],"language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"033177","author":[{"full_name":"Huber, D.","last_name":"Huber","first_name":"D."},{"last_name":"Hammer","full_name":"Hammer, H.-W.","first_name":"H.-W."},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"external_id":{"arxiv":["1908.02483"]},"article_processing_charge":"No","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","citation":{"ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.","chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.","apa":"Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019.","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/physrevresearch.1.033177","date_published":"2019-12-16T00:00:00Z","date_created":"2019-12-17T13:03:41Z","has_accepted_license":"1","year":"2019","day":"16","publication":"Physical Review Research"},{"date_created":"2019-06-23T21:59:13Z","doi":"10.1103/PhysRevLett.122.220603","date_published":"2019-06-07T00:00:00Z","year":"2019","isi":1,"publication":"Physical Review Letters","day":"07","oa":1,"quality_controlled":"1","publisher":"American Physical Society","external_id":{"arxiv":["1812.05561"],"isi":["000470885800005"]},"article_processing_charge":"No","author":[{"first_name":"Soonwon","last_name":"Choi","full_name":"Choi, Soonwon"},{"first_name":"Christopher J.","full_name":"Turner, Christopher J.","last_name":"Turner"},{"full_name":"Pichler, Hannes","last_name":"Pichler","first_name":"Hannes"},{"full_name":"Ho, Wen Wei","last_name":"Ho","first_name":"Wen Wei"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"full_name":"Lukin, Mikhail D.","last_name":"Lukin","first_name":"Mikhail D."},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."}],"title":"Emergent SU(2) dynamics and perfect quantum many-body scars","citation":{"mla":"Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.220603.","apa":"Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603","ama":"Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603","ieee":"S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society, 2019.","short":"S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).","chicago":"Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.","ista":"Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"220603","issue":"22","volume":122,"publication_status":"published","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1812.05561","open_access":"1"}],"scopus_import":"1","intvolume":" 122","month":"06","abstract":[{"lang":"eng","text":"Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit."}],"oa_version":"Preprint","department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:12:22Z","article_type":"original","type":"journal_article","status":"public","_id":"6575"},{"title":"Quantum many-body dynamics of the Einstein-de Haas effect","article_processing_charge":"No","external_id":{"arxiv":["1802.01638"],"isi":["000459223400004"]},"author":[{"full_name":"Mentink, Johann H","last_name":"Mentink","first_name":"Johann H"},{"full_name":"Katsnelson, Mikhail","last_name":"Katsnelson","first_name":"Mikhail"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428.","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428.","ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","apa":"Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428","ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428"},"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"article_number":"064428","date_created":"2019-03-10T22:59:20Z","date_published":"2019-02-01T00:00:00Z","doi":"10.1103/PhysRevB.99.064428","publication":"Physical Review B","day":"01","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:54Z","status":"public","type":"journal_article","_id":"6092","issue":"6","volume":99,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 99","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales."}]},{"date_updated":"2024-02-28T13:12:06Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"6090","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":99,"oa_version":"Preprint","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"month":"02","intvolume":" 99","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423."},"title":"Receptor crosstalk improves concentration sensing of multiple ligands","author":[{"last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín","first_name":"Martín"},{"first_name":"Jonathan","last_name":"Desponds","full_name":"Desponds, Jonathan"},{"last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana","first_name":"Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"last_name":"Nemenman","full_name":"Nemenman, Ilya","first_name":"Ilya"},{"last_name":"Mora","full_name":"Mora, Thierry","first_name":"Thierry"}],"external_id":{"isi":["000459916500007"]},"article_processing_charge":"No","article_number":"022423","day":"26","publication":"Physical Review E","isi":1,"year":"2019","date_published":"2019-02-26T00:00:00Z","doi":"10.1103/PhysRevE.99.022423","date_created":"2019-03-10T22:59:20Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations."}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 9","publication_identifier":{"eissn":["2160-3308"]},"publication_status":"published","file":[{"file_size":1193550,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_name":"2019_PhysReviewX_Hubert.pdf","date_created":"2019-08-12T12:14:18Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6802","checksum":"065ff82ee4a1d2c3773ce4b76ff4213c"}],"language":[{"iso":"eng"}],"issue":"2","volume":9,"_id":"6786","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-02-28T13:12:48Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:47:40Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"08","publication":"Physical Review X","doi":"10.1103/PhysRevX.9.021026","date_published":"2019-05-08T00:00:00Z","date_created":"2019-08-11T21:59:20Z","article_number":"021026","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"citation":{"ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.","short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026.","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Colin","last_name":"Hubert","full_name":"Hubert, Colin"},{"full_name":"Baruchi, Yifat","last_name":"Baruchi","first_name":"Yifat"},{"first_name":"Yotam","last_name":"Mazuz-Harpaz","full_name":"Mazuz-Harpaz, Yotam"},{"last_name":"Cohen","full_name":"Cohen, Kobi","first_name":"Kobi"},{"full_name":"Biermann, Klaus","last_name":"Biermann","first_name":"Klaus"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ken","full_name":"West, Ken","last_name":"West"},{"first_name":"Loren","last_name":"Pfeiffer","full_name":"Pfeiffer, Loren"},{"full_name":"Rapaport, Ronen","last_name":"Rapaport","first_name":"Ronen"},{"first_name":"Paulo","last_name":"Santos","full_name":"Santos, Paulo"}],"article_processing_charge":"No","external_id":{"arxiv":["1807.11238"],"isi":["000467402900001"]},"title":"Attractive dipolar coupling between stacked exciton fluids"},{"department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:13:13Z","status":"public","type":"journal_article","article_type":"original","_id":"7013","issue":"13","volume":100,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"intvolume":" 100","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.","lang":"eng"}],"title":"Probing the many-body localization phase transition with superconducting circuits","article_processing_charge":"No","external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"author":[{"full_name":"Orell, Tuure","last_name":"Orell","first_name":"Tuure"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"full_name":"Silveri, Matti","last_name":"Silveri","first_name":"Matti"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.","apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019.","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504."},"article_number":"134504","date_created":"2019-11-13T08:25:48Z","date_published":"2019-10-01T00:00:00Z","doi":"10.1103/physrevb.100.134504","publication":"Physical Review B","day":"01","year":"2019","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1"},{"date_updated":"2024-02-28T13:14:08Z","department":[{"_id":"MaSe"}],"_id":"7200","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"volume":100,"issue":"17","abstract":[{"lang":"eng","text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario)."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"scopus_import":"1","intvolume":" 100","month":"11","citation":{"ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518","apa":"Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019.","mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000498845700006"],"arxiv":["1907.13579"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"},{"full_name":"Grilli, Marco","last_name":"Grilli","first_name":"Marco"},{"first_name":"Brigitte","last_name":"Leridon","full_name":"Leridon, Brigitte"},{"last_name":"Caprara","full_name":"Caprara, Sergio","first_name":"Sergio"}],"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","article_number":"174518","year":"2019","isi":1,"publication":"Physical Review B","day":"25","date_created":"2019-12-22T23:00:41Z","doi":"10.1103/PhysRevB.100.174518","date_published":"2019-11-25T00:00:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1"},{"intvolume":" 100","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.05860"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace.","lang":"eng"}],"ec_funded":1,"issue":"1","volume":100,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"status":"public","article_type":"original","type":"journal_article","_id":"6779","department":[{"_id":"BjHo"}],"ddc":["532"],"date_updated":"2024-02-28T13:13:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-08-09T09:40:41Z","doi":"10.1103/physreve.100.013112","date_published":"2019-07-25T00:00:00Z","publication":"Physical Review E","day":"25","year":"2019","isi":1,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"013112","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"article_processing_charge":"No","author":[{"last_name":"Suri","full_name":"Suri, Balachandra","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pallantla","full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar"},{"first_name":"Michael F.","full_name":"Schatz, Michael F.","last_name":"Schatz"},{"last_name":"Grigoriev","full_name":"Grigoriev, Roman O.","first_name":"Roman O."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112."}},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"25","publication":"Physical Review B","isi":1,"year":"2019","doi":"10.1103/physrevb.100.035127","date_published":"2019-07-25T00:00:00Z","date_created":"2019-11-13T08:41:48Z","article_number":"035127","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127.","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127."},"title":"Floating Wigner crystal with no boundary charge fluctuations","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"last_name":"Lieb","full_name":"Lieb, Elliott H.","first_name":"Elliott H."},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_processing_charge":"No","external_id":{"isi":["000477888200001"],"arxiv":["1905.09138"]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential."}],"month":"07","intvolume":" 100","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","issue":"3","volume":100,"ec_funded":1,"_id":"7015","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-28T13:13:23Z","department":[{"_id":"RoSe"}]},{"article_number":"205412","external_id":{"arxiv":["1908.05549"],"isi":["000495967500006"]},"article_processing_charge":"No","author":[{"full_name":"Anselmetti, G. L. R.","last_name":"Anselmetti","first_name":"G. L. R."},{"last_name":"Martinez","full_name":"Martinez, E. A.","first_name":"E. A."},{"last_name":"Ménard","full_name":"Ménard, G. C.","first_name":"G. C."},{"first_name":"D.","last_name":"Puglia","full_name":"Puglia, D."},{"first_name":"F. K.","full_name":"Malinowski, F. K.","last_name":"Malinowski"},{"first_name":"J. S.","full_name":"Lee, J. S.","last_name":"Lee"},{"first_name":"S.","last_name":"Choi","full_name":"Choi, S."},{"first_name":"M.","last_name":"Pendharkar","full_name":"Pendharkar, M."},{"last_name":"Palmstrøm","full_name":"Palmstrøm, C. J.","first_name":"C. J."},{"first_name":"C. M.","full_name":"Marcus, C. M.","last_name":"Marcus"},{"last_name":"Casparis","full_name":"Casparis, L.","first_name":"L."},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"title":"End-to-end correlated subgap states in hybrid nanowires","citation":{"ieee":"G. L. R. Anselmetti et al., “End-to-end correlated subgap states in hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical Society, 2019.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.205412","mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:10.1103/physrevb.100.205412.","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2019-12-04T16:02:25Z","date_published":"2019-11-15T00:00:00Z","doi":"10.1103/physrevb.100.205412","year":"2019","isi":1,"publication":"Physical Review B","day":"15","article_type":"original","type":"journal_article","status":"public","_id":"7145","department":[{"_id":"AnHi"}],"date_updated":"2024-02-28T13:13:51Z","main_file_link":[{"url":"https://arxiv.org/abs/1908.05549","open_access":"1"}],"scopus_import":"1","intvolume":" 100","month":"11","abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"oa_version":"Preprint","volume":100,"issue":"20","publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2019-02-01T08:22:28Z","doi":"10.1103/physrevlett.122.040601","date_published":"2019-02-01T00:00:00Z","publication":"Physical Review Letters","day":"01","year":"2019","isi":1,"article_number":"040601","title":"Analytically solvable renormalization group for the many-body localization transition","external_id":{"arxiv":["1807.04285"],"isi":["000456783700001"]},"article_processing_charge":"No","author":[{"last_name":"Goremykina","full_name":"Goremykina, Anna","first_name":"Anna"},{"first_name":"Romain","full_name":"Vasseur, Romain","last_name":"Vasseur"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization group for the many-body localization transition,” Physical Review Letters, vol. 122, no. 4. American Physical Society, 2019.","short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).","apa":"Goremykina, A., Vasseur, R., & Serbyn, M. (2019). Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.040601","ama":"Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 2019;122(4). doi:10.1103/physrevlett.122.040601","mla":"Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters, vol. 122, no. 4, 040601, American Physical Society, 2019, doi:10.1103/physrevlett.122.040601.","ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 040601.","chicago":"Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.040601."},"intvolume":" 122","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1807.04285","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a simple, exactly solvable strong-randomness renormalization group (RG) model for the many-body localization (MBL) transition in one dimension. Our approach relies on a family of RG flows parametrized by the asymmetry between thermal and localized phases. We identify the physical MBL transition in the limit of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions. We find a critical point that is localized with power-law distributed thermal inclusions. The typical size of critical inclusions remains finite at the transition, while the average size is logarithmically diverging. We propose a two-parameter scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless universality class, with the MBL phase corresponding to a stable line of fixed points with multifractal behavior."}],"issue":"4","volume":122,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"status":"public","article_type":"original","type":"journal_article","_id":"5906","department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:13:38Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Karle, Volker, Nicolò Defenu, and Tilman Enss. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A. American Physical Society, 2019. https://doi.org/10.1103/PhysRevA.99.063627.","ista":"Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 99(6), 063627.","mla":"Karle, Volker, et al. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A, vol. 99, no. 6, 063627, American Physical Society, 2019, doi:10.1103/PhysRevA.99.063627.","short":"V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).","ieee":"V. Karle, N. Defenu, and T. Enss, “Coupled superfluidity of binary Bose mixtures in two dimensions,” Physical Review A, vol. 99, no. 6. American Physical Society, 2019.","ama":"Karle V, Defenu N, Enss T. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 2019;99(6). doi:10.1103/PhysRevA.99.063627","apa":"Karle, V., Defenu, N., & Enss, T. (2019). Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.99.063627"},"title":"Coupled superfluidity of binary Bose mixtures in two dimensions","external_id":{"isi":["000473133600007"],"arxiv":["1903.06759"]},"article_processing_charge":"No","author":[{"first_name":"Volker","last_name":"Karle","full_name":"Karle, Volker"},{"last_name":"Defenu","full_name":"Defenu, Nicolò","first_name":"Nicolò"},{"first_name":"Tilman","last_name":"Enss","full_name":"Enss, Tilman"}],"article_number":"063627","publication":"Physical Review A","day":"28","year":"2019","isi":1,"date_created":"2019-07-14T21:59:17Z","doi":"10.1103/PhysRevA.99.063627","date_published":"2019-06-28T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2024-02-28T13:12:34Z","department":[{"_id":"MiLe"}],"_id":"6632","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"issue":"6","volume":99,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider a two-component Bose gas in two dimensions at a low temperature with short-range repulsive interaction. In the coexistence phase where both components are superfluid, interspecies interactions induce a nondissipative drag between the two superfluid flows (Andreev-Bashkin effect). We show that this behavior leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition in two dimensions. We extend the renormalization of the superfluid densities at finite temperature using the renormalization-group approach and find that the vortices of one component have a large influence on the superfluid properties of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the vortex unbinding transition in one of the components can induce the breakdown of superfluidity also in the other, leading to a locking phenomenon for the critical temperatures of the two gases."}],"intvolume":" 99","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1903.06759","open_access":"1"}],"scopus_import":"1"},{"year":"2019","isi":1,"publication":"Reviews of Modern Physics","day":"18","date_created":"2020-01-29T16:04:19Z","doi":"10.1103/revmodphys.91.035005","date_published":"2019-09-18T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).","ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005","apa":"Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005","mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:10.1103/revmodphys.91.035005.","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005.","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.035005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000486661700001"],"arxiv":["1810.11338"]},"author":[{"first_name":"Christiane P.","last_name":"Koch","full_name":"Koch, Christiane P."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Dominique","full_name":"Sugny, Dominique","last_name":"Sugny"}],"title":"Quantum control of molecular rotation","article_number":"035005 ","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"publication_status":"published","publication_identifier":{"issn":["0034-6861"],"eissn":["1539-0756"]},"language":[{"iso":"eng"}],"volume":91,"issue":"3","abstract":[{"text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1810.11338","open_access":"1"}],"scopus_import":"1","intvolume":" 91","month":"09","date_updated":"2024-02-28T13:15:33Z","department":[{"_id":"MiLe"}],"_id":"7396","type":"journal_article","article_type":"original","status":"public"},{"conference":{"name":"Information Theory Workshop","location":"Visby, Sweden","end_date":"2019-08-28","start_date":"2019-08-25"},"type":"conference","status":"public","_id":"7606","department":[{"_id":"GaTk"}],"date_updated":"2024-03-06T14:22:51Z","main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"scopus_import":"1","month":"08","abstract":[{"lang":"eng","text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound."}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"id":"15020","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"isbn":["9781538669006"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"8989292","external_id":{"arxiv":["1812.01475"],"isi":["000540384500015"]},"article_processing_charge":"No","author":[{"last_name":"Hledik","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"title":"A tight upper bound on mutual information","citation":{"ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292","apa":"Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby, Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.","short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"IEEE","quality_controlled":"1","date_created":"2020-03-22T23:00:47Z","doi":"10.1109/ITW44776.2019.8989292","date_published":"2019-08-01T00:00:00Z","year":"2019","isi":1,"publication":"IEEE Information Theory Workshop, ITW 2019","day":"01"},{"related_material":{"record":[{"relation":"later_version","id":"7939","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450362177"]},"publication_status":"published","month":"08","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1903.05956","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."}],"department":[{"_id":"DaAl"}],"date_updated":"2024-03-07T14:43:38Z","status":"public","type":"conference","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2019-08-02","location":"Toronto, ON, Canada","start_date":"2019-07-29"},"_id":"6933","doi":"10.1145/3293611.3331633","date_published":"2019-08-01T00:00:00Z","date_created":"2019-10-08T12:48:42Z","page":"74-83","day":"01","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","isi":1,"year":"2019","publisher":"ACM","quality_controlled":"1","oa":1,"title":"Fast approximate shortest paths in the congested clique","author":[{"first_name":"Keren","last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren"},{"full_name":"Dory, Michal","last_name":"Dory","first_name":"Michal"},{"full_name":"Korhonen, Janne","last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"last_name":"Leitersdorf","full_name":"Leitersdorf, Dean","first_name":"Dean"}],"external_id":{"arxiv":["1903.05956"],"isi":["000570442000011"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM, 2019. https://doi.org/10.1145/3293611.3331633.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633.","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83."}},{"_id":"15147","type":"preprint","status":"public","citation":{"ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2019. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv, 10.1101/740464.","chicago":"Fribourgh, Jennifer L., Ashutosh Srivastava, Colby R. Sandate, Alicia K. Michael, Peter L. Hsu, Christin Rakers, Leslee T. Nguyen, et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019. https://doi.org/10.1101/740464.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2019). Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv. https://doi.org/10.1101/740464","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv. 2019. doi:10.1101/740464","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, BioRxiv (2019).","ieee":"J. L. Fribourgh et al., “Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms,” bioRxiv. 2019.","mla":"Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019, doi:10.1101/740464."},"date_updated":"2024-03-25T12:44:44Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jennifer L.","last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L."},{"full_name":"Srivastava, Ashutosh","last_name":"Srivastava","first_name":"Ashutosh"},{"first_name":"Colby R.","last_name":"Sandate","full_name":"Sandate, Colby R."},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","last_name":"Michael"},{"first_name":"Peter L.","last_name":"Hsu","full_name":"Hsu, Peter L."},{"first_name":"Christin","full_name":"Rakers, Christin","last_name":"Rakers"},{"full_name":"Nguyen, Leslee T.","last_name":"Nguyen","first_name":"Leslee T."},{"full_name":"Torgrimson, Megan R.","last_name":"Torgrimson","first_name":"Megan R."},{"last_name":"Parico","full_name":"Parico, Gian Carlo G.","first_name":"Gian Carlo G."},{"last_name":"Tripathi","full_name":"Tripathi, Sarvind","first_name":"Sarvind"},{"first_name":"Ning","last_name":"Zheng","full_name":"Zheng, Ning"},{"full_name":"Lander, Gabriel C.","last_name":"Lander","first_name":"Gabriel C."},{"last_name":"Hirota","full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi"},{"first_name":"Florence","last_name":"Tama","full_name":"Tama, Florence"},{"last_name":"Partch","full_name":"Partch, Carrie L.","first_name":"Carrie L."}],"article_processing_charge":"No","title":"Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms","abstract":[{"lang":"eng","text":"Circadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify a key biochemical and structural difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. While both cryptochromes bind the BMAL1 transactivation domain with similar affinity to sequester it from coactivators, CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We identify a dynamic loop in the secondary pocket that regulates differential binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2 forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1 both with and without PER2."}],"oa_version":"None","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/740464"}],"month":"08","year":"2019","publication_status":"published","day":"20","language":[{"iso":"eng"}],"publication":"bioRxiv","doi":"10.1101/740464","date_published":"2019-08-20T00:00:00Z","date_created":"2024-03-21T07:51:10Z"},{"author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","citation":{"ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392","apa":"Lukacisin, M. (2019). Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"103","date_created":"2019-05-09T19:53:00Z","doi":"10.15479/AT:ISTA:6392","date_published":"2019-05-09T00:00:00Z","year":"2019","has_accepted_license":"1","day":"09","oa":1,"publisher":"IST Austria","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"ToBo"}],"date_updated":"2023-09-22T09:19:41Z","supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"ddc":["570"],"extern":"1","type":"dissertation","status":"public","_id":"6392","related_material":{"record":[{"relation":"part_of_dissertation","id":"1029","status":"public"}]},"publication_status":"published","publication_identifier":{"isbn":["978-3-99078-001-5"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_Draft_v3.4Final.docx","date_created":"2019-05-10T13:51:49Z","creator":"mlukacisin","file_size":43740796,"date_updated":"2020-07-14T12:47:29Z","file_id":"6409","checksum":"829bda074444857c7935171237bb7c0c","relation":"hidden","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"creator":"mlukacisin","date_updated":"2021-02-11T11:17:16Z","file_size":35228388,"date_created":"2019-05-10T14:13:42Z","file_name":"Thesis_Draft_v3.4FinalA.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6410","checksum":"56cb5e97f5f8fc41692401b53832d8e0","embargo":"2020-04-17"}],"alternative_title":["IST Austria Thesis"],"month":"05","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes. \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"oa_version":"Published Version"},{"_id":"6435","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"status":"public","type":"dissertation","ddc":["570","006","578","592"],"date_updated":"2023-09-07T12:57:04Z","supervisor":[{"first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M"}],"file_date_updated":"2021-02-11T11:17:15Z","department":[{"_id":"SyCr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"month":"05","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_name":"tesisDoctoradoBC.pdf","date_created":"2019-05-13T09:16:20Z","file_size":3895187,"date_updated":"2021-02-11T11:17:15Z","creator":"casillas","embargo":"2020-05-08","file_id":"6438","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"checksum":"3d221aaff7559a7060230a1ff610594f","file_id":"6439","access_level":"closed","relation":"source_file","content_type":"application/zip","embargo_to":"open_access","date_created":"2019-05-13T09:16:20Z","file_name":"tesisDoctoradoBC.zip","creator":"casillas","date_updated":"2020-07-14T12:47:30Z","file_size":7365118}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1999"}]},"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771402","name":"Epidemics in ant societies on a chip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","mla":"Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435"},"title":"Collective defenses of garden ants against a fungal pathogen","article_processing_charge":"No","author":[{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"07","year":"2019","has_accepted_license":"1","date_created":"2019-05-13T08:58:35Z","doi":"10.15479/AT:ISTA:6435","date_published":"2019-05-07T00:00:00Z","page":"183"},{"file_date_updated":"2021-02-11T23:30:15Z","department":[{"_id":"JiFr"}],"supervisor":[{"last_name":"Friml","full_name":"Friml, 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Thesis"],"month":"02","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"}],"article_processing_charge":"No","title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ","citation":{"chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"138","date_published":"2019-02-04T00:00:00Z","doi":"10.15479/at:ista:th1075","date_created":"2019-04-09T14:37:06Z","has_accepted_license":"1","year":"2019","day":"04","publisher":"Institute of Science and Technology Austria","oa":1},{"title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","author":[{"last_name":"Kim","full_name":"Kim, Olena","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019. https://doi.org/10.25006/ia.7.s1-a3.27.","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27","apa":"Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. https://doi.org/10.25006/ia.7.s1-a3.27","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” Intrinsic Activity, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27."},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"article_number":"A3.27","doi":"10.25006/ia.7.s1-a3.27","date_published":"2019-09-11T00:00:00Z","date_created":"2022-04-20T15:06:05Z","day":"11","publication":"Intrinsic Activity","year":"2019","publisher":"Austrian Pharmacological Society","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","department":[{"_id":"PeJo"}],"date_updated":"2024-03-27T23:30:07Z","status":"public","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"type":"conference_abstract","conference":{"name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society","end_date":"2019-09-27","location":"Innsbruck, Austria","start_date":"2019-09-25"},"_id":"11222","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11196"}]},"issue":"Suppl. 1","volume":7,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2309-8503"]},"publication_status":"published","month":"09","intvolume":" 7","main_file_link":[{"open_access":"1","url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/"}],"oa_version":"Published Version"},{"date_created":"2019-10-14T16:54:52Z","doi":"10.15479/AT:ISTA:6947","date_published":"2019-10-09T00:00:00Z","page":"142","day":"9","year":"2019","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","article_processing_charge":"No","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","apa":"Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947","mla":"Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"664","status":"public"},{"relation":"part_of_dissertation","id":"402","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_size":214172667,"date_updated":"2020-11-07T23:30:03Z","creator":"fassen","file_name":"PhDthesis_FrankAssen_revised2.docx","date_created":"2019-11-06T12:30:02Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6990","checksum":"53a739752a500f84d0f8ec953cbbd0b6"},{"embargo":"2020-11-06","checksum":"8c156b65d9347bb599623a4b09f15d15","file_id":"6991","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"PhDthesis_FrankAssen_revised2.pdf","date_created":"2019-11-06T12:30:57Z","creator":"fassen","file_size":83637532,"date_updated":"2020-11-07T23:30:03Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues."}],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-11-07T23:30:03Z","ddc":["570"],"date_updated":"2023-09-13T08:50:57Z","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"status":"public","type":"dissertation","_id":"6947"},{"status":"public","type":"dissertation","_id":"6849","file_date_updated":"2021-02-10T23:30:09Z","department":[{"_id":"JoCs"}],"ddc":["570"],"supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"date_updated":"2023-09-19T10:01:12Z","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. "}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"related_material":{"record":[{"id":"5914","status":"public","relation":"part_of_dissertation"}]},"file":[{"creator":"drangel","date_updated":"2021-02-10T23:30:09Z","file_size":18253100,"date_created":"2019-09-09T13:09:45Z","file_name":"Thesis_Damaris_Rangel_source.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"244dc4f74dbfc94f414156092298831f","file_id":"6865"},{"embargo":"2020-09-10","checksum":"59c73be40eeaa1c4db24067270151555","file_id":"6866","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","date_created":"2019-09-09T13:09:52Z","file_size":2160109,"date_updated":"2020-09-11T22:30:04Z","creator":"drangel","request_a_copy":0}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["9783990780039"]},"degree_awarded":"PhD","publication_status":"published","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","author":[{"full_name":"Rangel Guerrero, Dámaris K","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Dámaris K"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849.","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849"},"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:6849","date_published":"2019-09-09T00:00:00Z","date_created":"2019-09-06T06:54:16Z","page":"97","day":"09","has_accepted_license":"1","year":"2019"},{"has_accepted_license":"1","isi":1,"year":"2019","day":"02","publication":"Cell","page":"957-969.e13","doi":"10.1016/j.cell.2019.04.015","date_published":"2019-05-02T00:00:00Z","date_created":"2019-04-28T21:59:14Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"citation":{"mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Marhavá","full_name":"Marhavá, Petra","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"article_processing_charge":"No","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6411","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","file_size":10272032,"date_updated":"2020-07-14T12:47:28Z","creator":"dernst","file_name":"2019_Cell_Marhava.pdf","date_created":"2019-05-13T06:12:45Z"}],"language":[{"iso":"eng"}],"issue":"4","volume":177,"related_material":{"record":[{"status":"public","id":"9992","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}]},"ec_funded":1,"abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 177","date_updated":"2024-03-27T23:30:10Z","ddc":["570"],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:47:28Z","_id":"6351","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"external_id":{"pmid":["31585333"],"isi":["000502890600017"]},"article_processing_charge":"No","author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Targeted cell ablation-based insights into wound healing and restorative patterning","citation":{"apa":"Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130. doi:10.1016/j.pbi.2019.08.006","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” Current Opinion in Plant Biology, vol. 52. Elsevier, pp. 124–130, 2019.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology, vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006.","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"page":"124-130","date_created":"2019-10-14T07:00:24Z","doi":"10.1016/j.pbi.2019.08.006","date_published":"2019-12-01T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"Current Opinion in Plant Biology","day":"01","oa":1,"publisher":"Elsevier","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:45Z","department":[{"_id":"JiFr"}],"date_updated":"2024-03-27T23:30:11Z","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"6943","ec_funded":1,"related_material":{"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"volume":52,"publication_status":"published","publication_identifier":{"issn":["1369-5266"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1659288,"date_updated":"2020-07-14T12:47:45Z","file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","date_created":"2019-10-14T14:48:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6946","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616"}],"scopus_import":"1","intvolume":" 52","month":"12","abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"pmid":1,"oa_version":"Published Version"},{"article_processing_charge":"No","external_id":{"isi":[":000504652000020"],"pmid":["31786521"]},"author":[{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","last_name":"Tabata","full_name":"Tabata, Shigekazu"},{"full_name":"Jevtic, Marijo","last_name":"Jevtic","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo"},{"first_name":"Nobutaka","last_name":"Kurashige","full_name":"Kurashige, Nobutaka"},{"first_name":"Hirokazu","full_name":"Fuchida, Hirokazu","last_name":"Fuchida"},{"last_name":"Kido","full_name":"Kido, Munetsugu","first_name":"Munetsugu"},{"first_name":"Kazushi","last_name":"Tani","full_name":"Tani, Kazushi"},{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"first_name":"Shohei","full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya"},{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Makoto","last_name":"Itakura","full_name":"Itakura, Makoto"},{"first_name":"Itaru","full_name":"Hamachi, Itaru","last_name":"Hamachi"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ojida, Akio","last_name":"Ojida","first_name":"Akio"}],"title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","citation":{"ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268. doi:10.1016/j.isci.2019.11.025","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","ieee":"S. Tabata et al., “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"256-268","date_created":"2020-01-29T15:56:56Z","date_published":"2019-12-20T00:00:00Z","doi":"10.1016/j.isci.2019.11.025","year":"2019","has_accepted_license":"1","publication":"iScience","day":"20","oa":1,"publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:57Z","date_updated":"2024-03-27T23:30:13Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7391","ec_funded":1,"related_material":{"record":[{"status":"public","id":"11393","relation":"dissertation_contains"}]},"volume":22,"issue":"12","publication_status":"published","publication_identifier":{"issn":["2589-0042"]},"language":[{"iso":"eng"}],"file":[{"checksum":"f3e90056a49f09b205b1c4f8c739ffd1","file_id":"7448","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_iScience_Tabata.pdf","date_created":"2020-02-04T10:48:36Z","creator":"dernst","file_size":7197776,"date_updated":"2020-07-14T12:47:57Z"}],"scopus_import":"1","intvolume":" 22","month":"12","abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"pmid":1,"oa_version":"Published Version"},{"_id":"6848","status":"public","type":"journal_article","article_type":"letter_note","ddc":["572"],"date_updated":"2024-03-27T23:30:14Z","department":[{"_id":"LeSa"}],"file_date_updated":"2020-11-26T16:33:44Z","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 573","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8821","checksum":"52728cda5210a3e9b74cc204e8aed3d5","success":1,"date_updated":"2020-11-26T16:33:44Z","file_size":3066206,"creator":"lsazanov","date_created":"2020-11-26T16:33:44Z","file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"ec_funded":1,"issue":"7773","volume":573,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/","description":"News on IST Website"}],"record":[{"relation":"dissertation_contains","id":"8340","status":"public"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1519-2.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2","apa":"Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2."},"title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","article_processing_charge":"No","external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"author":[{"full_name":"Kampjut, Domen","last_name":"Kampjut","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature","day":"12","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-09-04T06:21:41Z","date_published":"2019-09-12T00:00:00Z","doi":"10.1038/s41586-019-1519-2","page":"291–295"},{"project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"citation":{"apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., & Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aav4837","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. Science. 2019;363(6434):1443-1447. doi:10.1126/science.aav4837","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447.","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” Science, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:10.1126/science.aav4837.","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aav4837."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000462738000034"]},"author":[{"first_name":"Charlotte N.","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","full_name":"Boccara, Charlotte N.","orcid":"0000-0001-7237-5109"},{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570"},{"orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"title":"The entorhinal cognitive map is attracted to goals","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","year":"2019","has_accepted_license":"1","isi":1,"publication":"Science","day":"29","page":"1443-1447","date_created":"2019-04-04T08:39:30Z","date_published":"2019-03-29T00:00:00Z","doi":"10.1126/science.aav4837","_id":"6194","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:16Z","ddc":["570"],"department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:47:23Z","abstract":[{"lang":"eng","text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space."}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 363","month":"03","publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7826","checksum":"5e6b16742cde10a560cfaf2130764da1","creator":"dernst","file_size":9045923,"date_updated":"2020-07-14T12:47:23Z","file_name":"2019_Science_Boccara.pdf","date_created":"2020-05-14T09:11:10Z"}],"ec_funded":1,"related_material":{"record":[{"relation":"popular_science","id":"6062","status":"public"},{"relation":"dissertation_contains","status":"public","id":"11932"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","relation":"press_release"}]},"volume":363,"issue":"6434"},{"citation":{"ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132.","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine"}],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2019","has_accepted_license":"1","day":"27","page":"95","date_created":"2019-11-27T09:07:14Z","doi":"10.15479/at:ista:7132","date_published":"2019-06-27T00:00:00Z","_id":"7132","type":"dissertation","status":"public","date_updated":"2024-03-27T23:30:21Z","supervisor":[{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"ddc":["571","573"],"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:47:50Z","abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"7133","checksum":"34d0fe0f6e0af97b5937205a3e350423","date_updated":"2020-07-14T12:47:50Z","file_size":5054633,"creator":"dernst","date_created":"2019-11-27T09:06:10Z","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx"},{"checksum":"140dfb5e3df7edca34f4b6fcc55d876f","file_id":"7134","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-27T09:06:10Z","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","date_updated":"2020-07-14T12:47:50Z","file_size":3231837,"creator":"dernst"}],"related_material":{"record":[{"relation":"old_edition","status":"public","id":"6266"}]}},{"ddc":["570"],"date_updated":"2024-03-27T23:30:22Z","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"JoCs"}],"_id":"5949","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5e8de271ca04aef92a5de42d6aac4404","file_id":"5950","date_updated":"2020-07-14T12:47:13Z","file_size":2132893,"creator":"dernst","date_created":"2019-02-11T10:42:51Z","file_name":"2019_Hippocampus_Kaefer.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"9","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6825"}]},"volume":29,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.","lang":"eng"}],"month":"09","intvolume":" 29","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. Wiley. https://doi.org/10.1002/hipo.23076","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 2019;29(9):802-816. doi:10.1002/hipo.23076","ieee":"K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” Hippocampus, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816."},"title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","full_name":"Käfer, Karola","last_name":"Käfer"},{"last_name":"Malagon-Vina","full_name":"Malagon-Vina, Hugo","first_name":"Hugo"},{"last_name":"Dickerson","full_name":"Dickerson, Desiree","first_name":"Desiree","id":"444EB89E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"first_name":"Svenja V.","last_name":"Trossbach","full_name":"Trossbach, Svenja V."},{"last_name":"Korth","full_name":"Korth, Carsten","first_name":"Carsten"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000480635400003"]},"project":[{"name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"01","publication":"Hippocampus","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1002/hipo.23076","date_published":"2019-09-01T00:00:00Z","date_created":"2019-02-10T22:59:18Z","page":"802-816","quality_controlled":"1","publisher":"Wiley","oa":1},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"24","year":"2019","has_accepted_license":"1","date_created":"2019-08-21T15:00:57Z","doi":"10.15479/AT:ISTA:6825","date_published":"2019-08-24T00:00:00Z","page":"89","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","apa":"Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria."},"title":"The hippocampus and medial prefrontal cortex during flexible behavior","article_processing_charge":"No","author":[{"first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","full_name":"Käfer, Karola"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. "}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"embargo":"2020-09-05","checksum":"2664420e332a33338568f4f3bfc59287","file_id":"6846","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_Kaefer_PDFA.pdf","date_created":"2019-09-03T08:07:13Z","file_size":3205202,"date_updated":"2020-09-06T22:30:03Z","creator":"kkaefer","request_a_copy":0},{"creator":"kkaefer","date_updated":"2020-09-15T22:30:05Z","file_size":2506835,"date_created":"2019-09-03T08:07:17Z","file_name":"Thesis_Kaefer.zip","access_level":"closed","relation":"main_file","content_type":"application/zip","embargo_to":"open_access","checksum":"9a154eab6f07aa590a3d2651dc0d926a","file_id":"6847"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"5949","status":"public","relation":"part_of_dissertation"}]},"_id":"6825","status":"public","type":"dissertation","ddc":["570"],"date_updated":"2023-09-07T13:01:42Z","supervisor":[{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-09-15T22:30:05Z","department":[{"_id":"JoCs"}]}]