[{"date_created":"2019-07-07T21:59:25Z","date_published":"2019-06-25T00:00:00Z","doi":"10.1073/pnas.1905555116","page":"12607-12608","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"25","year":"2019","isi":1,"oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","title":"On the power to detect rare recombination events","external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"article_processing_charge":"No","author":[{"first_name":"Alison E.","last_name":"Wright","full_name":"Wright, Alison E."},{"first_name":"Iulia","full_name":"Darolti, Iulia","last_name":"Darolti"},{"full_name":"Bloch, Natasha I.","last_name":"Bloch","first_name":"Natasha I."},{"last_name":"Oostra","full_name":"Oostra, Vicencio","first_name":"Vicencio"},{"full_name":"Sandkam, Benjamin A.","last_name":"Sandkam","first_name":"Benjamin A."},{"first_name":"Séverine D.","last_name":"Buechel","full_name":"Buechel, Séverine D."},{"last_name":"Kolm","full_name":"Kolm, Niclas","first_name":"Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"first_name":"Judith E.","last_name":"Mank","full_name":"Mank, Judith E."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"volume":116,"issue":"26","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 116","month":"06","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"department":[{"_id":"BeVi"}],"date_updated":"2023-10-17T12:44:15Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"6621"},{"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:42Z","ddc":["570"],"date_updated":"2023-10-18T08:47:08Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"6856","ec_funded":1,"issue":"3","volume":224,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-13T08:15:05Z","file_name":"2019_NewPhytologist_Pickup.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:42Z","file_size":1511958,"checksum":"21e4c95599bbcaf7c483b89954658672","file_id":"7011","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"intvolume":" 224","month":"11","scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","external_id":{"pmid":["31505037"]},"article_processing_charge":"No","author":[{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brandvain","full_name":"Brandvain, Yaniv","first_name":"Yaniv"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Yakimowski","full_name":"Yakimowski, Sarah","first_name":"Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"},{"first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva","last_name":"Cereghetti"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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.","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."},"project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"date_created":"2019-09-07T14:35:40Z","doi":"10.1111/nph.16180","date_published":"2019-11-01T00:00:00Z","page":"1035-1047","publication":"New Phytologist","day":"01","year":"2019","has_accepted_license":"1","oa":1,"publisher":"Wiley","quality_controlled":"1"},{"_id":"6647","conference":{"name":"SoCG 2019: Symposium on Computational Geometry","start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","date_updated":"2023-12-13T12:03:35Z","ddc":["000","510"],"file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 129","month":"06","publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771047"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:35Z","file_size":559837,"date_created":"2019-07-24T06:54:52Z","file_name":"2019_LIPICS_Fulek.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d6d017f8b41291b94d102294fa96ae9c","file_id":"6667"}],"related_material":{"record":[{"status":"public","id":"13974","relation":"later_version"}]},"volume":129,"project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1812.04911"]},"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Gärtner, Bernd","last_name":"Gärtner","first_name":"Bernd"},{"last_name":"Kupavskii","full_name":"Kupavskii, Andrey","first_name":"Andrey"},{"first_name":"Pavel","last_name":"Valtr","full_name":"Valtr, Pavel"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"title":"The crossing Tverberg theorem","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2019","has_accepted_license":"1","publication":"35th International Symposium on Computational Geometry","day":"01","page":"38:1-38:13","date_created":"2019-07-17T10:35:04Z","date_published":"2019-06-01T00:00:00Z","doi":"10.4230/LIPICS.SOCG.2019.38"},{"oa":1,"quality_controlled":"1","publisher":"ACM Press","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","day":"01","year":"2019","isi":1,"date_created":"2019-07-24T09:13:05Z","doi":"10.1145/3313276.3316407","date_published":"2019-06-01T00:00:00Z","page":"986-996","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","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","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"},"title":"Why extension-based proofs fail","external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"article_processing_charge":"No","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"full_name":"Zhu, Leqi","last_name":"Zhu","first_name":"Leqi"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450367059"]},"related_material":{"record":[{"status":"public","id":"14364","relation":"later_version"}]},"_id":"6676","status":"public","conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2019-06-23","end_date":"2019-06-26","location":"Phoenix, AZ, United States"},"type":"conference","date_updated":"2023-12-13T12:28:28Z","department":[{"_id":"DaAl"}]},{"language":[{"iso":"eng"}],"publication":"arXiv","day":"16","year":"2019","publication_status":"submitted","date_created":"2020-06-08T12:25:25Z","date_published":"2019-03-16T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"7944","status":"public"},{"status":"public","id":"12833","relation":"later_version"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"oa":1,"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.","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.","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. .","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."},"department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"title":"Token swapping on trees","article_processing_charge":"No","external_id":{"arxiv":["1903.06981"]},"author":[{"first_name":"Ahmad","last_name":"Biniaz","full_name":"Biniaz, Ahmad"},{"first_name":"Kshitij","last_name":"Jain","full_name":"Jain, Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"full_name":"Miltzow, Tillmann","last_name":"Miltzow","first_name":"Tillmann"},{"first_name":"Debajyoti","full_name":"Mondal, Debajyoti","last_name":"Mondal"},{"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"},{"last_name":"Turcotte","full_name":"Turcotte, Alexi","first_name":"Alexi"}],"article_number":"1903.06981","_id":"7950","status":"public","type":"preprint"},{"ec_funded":1,"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"volume":11,"issue":"4","publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1256303,"date_created":"2019-05-14T08:29:38Z","file_name":"2019_GBE_Huylmans.pdf"}],"scopus_import":"1","intvolume":" 11","month":"04","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"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T12:45:41Z","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)"},"type":"journal_article","status":"public","_id":"6418","page":"1033-1044","date_created":"2019-05-13T07:58:38Z","doi":"10.1093/gbe/evz053","date_published":"2019-04-01T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"Genome biology and evolution","day":"01","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000476569800003"]},"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","citation":{"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.","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","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","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.","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. 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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"}],"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"}],"article_processing_charge":"No","author":[{"first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","last_name":"Tomanek"}],"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","short":"I. Tomanek, (2019).","mla":"Tomanek, Isabella. 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.","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016."},"date_updated":"2024-02-21T12:45:25Z","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"status":"public","type":"research_data","_id":"7016"},{"_id":"7154","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 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.","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","short":"R. Guseinov, (2019).","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","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."},"date_updated":"2024-02-21T12:45:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"author":[{"last_name":"Guseinov","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan"}],"article_processing_charge":"No","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"BeBi"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","has_accepted_license":"1","year":"2019","day":"06","file":[{"date_updated":"2020-07-14T12:47:50Z","file_size":65307107,"creator":"dernst","date_created":"2019-12-09T07:52:17Z","file_name":"temporal_morphing_supp_data.zip","content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","checksum":"155133e6e188e85b3c0676a5e70b9341","file_id":"7155"}],"doi":"10.15479/AT:ISTA:7154","date_published":"2019-12-06T00:00:00Z","related_material":{"record":[{"id":"8433","status":"deleted","relation":"used_in_publication"},{"relation":"used_in_publication","id":"7262","status":"public"}]},"date_created":"2019-12-09T07:52:46Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","ec_funded":1,"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"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}]},{"status":"public","type":"research_data","_id":"6060","file_date_updated":"2020-07-14T12:47:17Z","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:45:42Z","citation":{"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.","ista":"Vicoso B. 2019. 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.","mla":"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, doi:10.15479/AT:ISTA:6060.","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","apa":"Vicoso, B. (2019). 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. https://doi.org/10.15479/AT:ISTA:6060","ieee":"B. Vicoso, “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.","short":"B. Vicoso, (2019)."},"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_created":"2019-02-28T10:55:15Z","doi":"10.15479/AT:ISTA:6060","date_published":"2019-02-28T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"6418"}]},"day":"28","file":[{"checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2019-02-28T10:54:27Z","file_name":"SupData.zip","creator":"bvicoso","date_updated":"2020-07-14T12:47:17Z","file_size":36646050}],"year":"2019","has_accepted_license":"1"},{"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","date_created":"2019-03-07T13:32:35Z","day":"09","file":[{"content_type":"application/zip","relation":"supplementary_material","access_level":"open_access","file_id":"6084","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_size":33202743,"date_updated":"2020-07-14T12:47:18Z","creator":"dernst","file_name":"Setd5_paper.zip","date_created":"2019-03-07T13:37:19Z"}],"has_accepted_license":"1","year":"2019","month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","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"}],"file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","department":[{"_id":"GaNo"}],"author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","short":"C. Dotter, G. Novarino, (2019).","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","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","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","status":"public","type":"research_data","_id":"6074"},{"_id":"6062","status":"public","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:46:04Z","citation":{"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.","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.","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","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","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)."},"department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","article_processing_charge":"No","author":[{"last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7)."}],"month":"03","oa":1,"publisher":"Institute of Science and Technology Austria","day":"29","file":[{"checksum":"48e7b9a02939b763417733239522a236","file_id":"6068","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2019-03-05T09:29:37Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_name":"Online_data.zip","creator":"mnardin","date_updated":"2020-07-14T12:47:18Z","file_size":37002186}],"year":"2019","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_created":"2019-03-04T14:20:58Z","related_material":{"record":[{"relation":"research_paper","id":"6194","status":"public"}]},"doi":"10.15479/AT:ISTA:6062","date_published":"2019-03-29T00:00:00Z"},{"page":"500-515","date_created":"2019-03-10T22:59:19Z","doi":"10.1093/molbev/msy246","date_published":"2019-03-01T00:00:00Z","year":"2019","isi":1,"publication":"Molecular biology and evolution","day":"01","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"article_processing_charge":"No","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","citation":{"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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"issue":"3","volume":36,"related_material":{"record":[{"id":"5757","status":"public","relation":"popular_science"}]},"publication_status":"published","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"scopus_import":"1","intvolume":" 36","month":"03","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2024-02-21T13:59:17Z","type":"journal_article","status":"public","_id":"6089"},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1144"},{"id":"6186","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6185","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6182","status":"public"},{"status":"public","id":"1012","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6184","status":"public"}]},"ec_funded":1,"file":[{"checksum":"6926f66f28079a81c4937e3764be00fc","file_id":"6180","relation":"source_file","access_level":"closed","content_type":"application/x-gzip","file_name":"2019_Schroeder_Thesis.tar.gz","date_created":"2019-03-28T08:53:52Z","creator":"dernst","file_size":7104482,"date_updated":"2020-07-14T12:47:21Z"},{"creator":"dernst","date_updated":"2020-07-14T12:47:21Z","file_size":4228794,"date_created":"2019-03-28T08:53:52Z","file_name":"2019_Schroeder_Thesis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6181","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","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"}],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:47:21Z","ddc":["515","519"],"supervisor":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"}],"date_updated":"2024-02-22T14:34:33Z","status":"public","type":"dissertation","_id":"6179","date_published":"2019-03-18T00:00:00Z","doi":"10.15479/AT:ISTA:th6179","date_created":"2019-03-28T08:58:59Z","page":"375","day":"18","has_accepted_license":"1","year":"2019","publisher":"Institute of Science and Technology Austria","oa":1,"title":"From Dyson to Pearcey: Universal statistics in random matrix theory","author":[{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","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.","ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","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","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.","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."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-05-24T09:48:36Z","date_published":"2019-02-14T00:00:00Z","doi":"10.1007/978-3-030-12939-2_18","page":"244-259","day":"14","year":"2019","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","external_id":{"arxiv":["1804.04171"]},"article_processing_charge":"No","author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"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."},"intvolume":" 11269","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04171"}],"alternative_title":["LNCS"],"scopus_import":"1","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. "}],"ec_funded":1,"related_material":{"record":[{"id":"6944","status":"public","relation":"later_version"}]},"volume":11269,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030129385","9783030129392"],"issn":["0302-9743"]},"status":"public","conference":{"name":"GCPR: Conference on Pattern Recognition","start_date":"2018-10-09","location":"Stuttgart, Germany","end_date":"2018-10-12"},"type":"conference","_id":"6482","department":[{"_id":"ChLa"}],"date_updated":"2024-02-22T14:57:29Z"},{"volume":2107,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"scopus_import":"1","intvolume":" 2107","month":"05","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."}],"oa_version":"Preprint","department":[{"_id":"ChWo"}],"date_updated":"2024-02-28T13:01:28Z","conference":{"name":"8th International Conference on Novel Trends in Rheology","start_date":"2019-07-30","end_date":"2019-07-31","location":"Zlin, Czech Republic"},"type":"conference","status":"public","_id":"6642","date_created":"2019-07-15T10:07:09Z","date_published":"2019-05-21T00:00:00Z","doi":"10.1063/1.5109493","year":"2019","isi":1,"publication":"AIP Conference Proceedings","day":"21","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","external_id":{"arxiv":["1902.07983"],"isi":["000479303100002"]},"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"}],"title":"On diffusive variants of some classical viscoelastic rate-type models","citation":{"short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"020002"},{"issue":"12","volume":60,"publication_status":"published","publication_identifier":{"issn":["00222488"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-01-07T14:59:13Z","file_name":"2019_JournalMathPhysics_Jaksic.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:54Z","file_size":1025015,"file_id":"7244","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 60","month":"12","oa_version":"Published Version","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:47:54Z","date_updated":"2024-02-28T13:01:45Z","ddc":["500"],"type":"journal_article","article_type":"letter_note","status":"public","_id":"7226","date_created":"2020-01-05T23:00:46Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1063/1.5138135","year":"2019","has_accepted_license":"1","isi":1,"publication":"Journal of Mathematical Physics","day":"01","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","external_id":{"isi":["000505529800002"]},"article_processing_charge":"No","author":[{"full_name":"Jaksic, Vojkan","last_name":"Jaksic","first_name":"Vojkan"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","citation":{"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.","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.","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.","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","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","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"123504"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-12-17T13:03:41Z","doi":"10.1103/physrevresearch.1.033177","date_published":"2019-12-16T00:00:00Z","year":"2019","has_accepted_license":"1","publication":"Physical Review Research","day":"16","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"033177","article_processing_charge":"No","external_id":{"arxiv":["1908.02483"]},"author":[{"first_name":"D.","full_name":"Huber, D.","last_name":"Huber"},{"last_name":"Hammer","full_name":"Hammer, H.-W.","first_name":"H.-W."},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 1","month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":1,"issue":"3","publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-12-18T07:13:14Z","file_name":"2019_PhysRevResearch_Huber.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","file_size":1370022,"checksum":"382eb67e62a77052a23887332d363f96","file_id":"7193","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"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","_id":"7190","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:40Z","ddc":["530"]},{"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 122","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1812.05561","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"volume":122,"issue":"22","_id":"6575","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-02-28T13:12:22Z","department":[{"_id":"MaSe"}],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Letters","day":"07","year":"2019","isi":1,"date_created":"2019-06-23T21:59:13Z","doi":"10.1103/PhysRevLett.122.220603","date_published":"2019-06-07T00:00:00Z","article_number":"220603","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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).","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","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."},"title":"Emergent SU(2) dynamics and perfect quantum many-body scars","external_id":{"isi":["000470885800005"],"arxiv":["1812.05561"]},"article_processing_charge":"No","author":[{"first_name":"Soonwon","last_name":"Choi","full_name":"Choi, Soonwon"},{"first_name":"Christopher J.","last_name":"Turner","full_name":"Turner, Christopher J."},{"first_name":"Hannes","last_name":"Pichler","full_name":"Pichler, Hannes"},{"first_name":"Wen Wei","last_name":"Ho","full_name":"Ho, Wen Wei"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Lukin","full_name":"Lukin, Mikhail D.","first_name":"Mikhail D."},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"}]},{"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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Johann H","last_name":"Mentink","full_name":"Mentink, Johann H"},{"first_name":"Mikhail","last_name":"Katsnelson","full_name":"Katsnelson, Mikhail"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.01638"],"isi":["000459223400004"]},"title":"Quantum many-body dynamics of the Einstein-de Haas effect","article_number":"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"}],"isi":1,"year":"2019","day":"01","publication":"Physical Review B","doi":"10.1103/PhysRevB.99.064428","date_published":"2019-02-01T00:00:00Z","date_created":"2019-03-10T22:59:20Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_updated":"2024-02-28T13:11:54Z","department":[{"_id":"MiLe"}],"_id":"6092","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":99,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"month":"02","intvolume":" 99"},{"author":[{"first_name":"Martín","full_name":"Carballo-Pacheco, Martín","last_name":"Carballo-Pacheco"},{"first_name":"Jonathan","last_name":"Desponds","full_name":"Desponds, Jonathan"},{"full_name":"Gavrilchenko, Tatyana","last_name":"Gavrilchenko","first_name":"Tatyana"},{"first_name":"Andreas","full_name":"Mayer, Andreas","last_name":"Mayer"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"full_name":"Reddy, Gautam","last_name":"Reddy","first_name":"Gautam"},{"last_name":"Nemenman","full_name":"Nemenman, Ilya","first_name":"Ilya"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"article_processing_charge":"No","external_id":{"isi":["000459916500007"]},"title":"Receptor crosstalk improves concentration sensing of multiple ligands","citation":{"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","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","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).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"022423","date_published":"2019-02-26T00:00:00Z","doi":"10.1103/PhysRevE.99.022423","date_created":"2019-03-10T22:59:20Z","isi":1,"year":"2019","day":"26","publication":"Physical Review E","quality_controlled":"1","publisher":"American Physical Society","oa":1,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2024-02-28T13:12:06Z","type":"journal_article","status":"public","_id":"6090","issue":"2","volume":99,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"month":"02","intvolume":" 99","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"}],"oa_version":"Preprint"}]