[{"volume":75,"file":[{"file_name":"2021_Evolution_Stankowski.pdf","file_size":719991,"creator":"kschuh","content_type":"application/pdf","success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_id":"10921","date_updated":"2022-03-25T12:02:04Z","date_created":"2022-03-25T12:02:04Z","access_level":"open_access","relation":"main_file"}],"doi":"10.1111/evo.14215","issue":"6","_id":"9383","article_type":"original","month":"03","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","citation":{"apa":"Stankowski, S., &#38; Ravinet, M. (2021). Defining the speciation continuum. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. <i>Evolution</i>. 2021;75(6):1256-1273. doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>."},"date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","department":[{"_id":"NiBa"}],"intvolume":"        75","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","type":"journal_article","publication_status":"published","publisher":"Oxford University Press","title":"Defining the speciation continuum","date_published":"2021-03-22T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"22","isi":1,"publication":"Evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"year":"2021","page":"1256-1273","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"}],"oa_version":"Published Version","status":"public","file_date_updated":"2022-03-25T12:02:04Z","external_id":{"isi":["000647226400001"]},"article_processing_charge":"No","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"language":[{"iso":"eng"}]},{"day":"24","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"title":"Two linked loci under mutation-selection balance and Muller’s ratchet","date_published":"2021-04-24T00:00:00Z","publication":"Journal of Theoretical Biology","isi":1,"publication_status":"published","type":"journal_article","quality_controlled":"1","publisher":"Elsevier ","department":[{"_id":"GradSch"}],"date_created":"2021-05-12T05:58:42Z","date_updated":"2023-08-08T13:32:40Z","intvolume":"       524","article_type":"original","month":"04","citation":{"short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier , 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>.","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier , 2021.","chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier , 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>"},"acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","_id":"9387","volume":524,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"doi":"10.1016/j.jtbi.2021.110729","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000659161500002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"article_number":"110729","oa_version":"Preprint","status":"public","author":[{"last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"first_name":"Tatiana Yu.","full_name":"Neretina, Tatiana Yu.","last_name":"Neretina"},{"first_name":"Alexey S.","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S."}],"year":"2021","publication_identifier":{"issn":["0022-5193"]}},{"ddc":["530"],"oa":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2021-01-01T00:00:00Z","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","has_accepted_license":"1","file_date_updated":"2021-05-14T11:56:48Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"NanoFab"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for  \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al.  \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"."}],"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini"}],"citation":{"ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","mla":"Valentini, Marco. <i>Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9389\">10.15479/AT:ISTA:9389</a>.","short":"M. Valentini, (2021).","chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9389\">https://doi.org/10.15479/AT:ISTA:9389</a>."},"related_material":{"record":[{"id":"8910","relation":"used_in_publication","status":"public"}]},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_created":"2021-05-14T12:07:53Z","date_updated":"2024-02-21T12:40:09Z","status":"public","file":[{"file_name":"Notebook_Valentini.pdf","file_size":10572981,"creator":"mvalenti","content_type":"application/pdf","file_id":"9390","checksum":"80a905c4eef24dab6fb247e81a3d67f5","relation":"main_file","date_created":"2021-05-14T11:42:23Z","date_updated":"2021-05-14T11:42:23Z","access_level":"open_access"},{"creator":"mvalenti","file_name":"Experimental_data.zip","file_size":99076111,"file_id":"9391","checksum":"1e61a7e63949448a8db0091cdac23570","date_updated":"2021-05-14T11:56:48Z","date_created":"2021-05-14T11:56:48Z","access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed"}],"contributor":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","contributor_type":"contact_person"}],"tmp":{"image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"doi":"10.15479/AT:ISTA:9389","year":"2021","_id":"9389"},{"oa":1,"language":[{"iso":"eng"}],"pmid":1,"abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"page":"R428-R429","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"}],"status":"public","oa_version":"Published Version","publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"year":"2021","isi":1,"publication":"Current Biology","date_published":"2021-05-10T00:00:00Z","title":"Quantifying the use of species concepts","day":"10","publisher":"Cell Press","quality_controlled":"1","type":"journal_article","scopus_import":"1","publication_status":"published","acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","citation":{"chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429."},"month":"05","article_type":"original","intvolume":"        31","date_updated":"2023-08-08T13:34:38Z","date_created":"2021-05-16T22:01:46Z","department":[{"_id":"NiBa"}],"doi":"10.1016/j.cub.2021.03.060","volume":31,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"_id":"9392","issue":"9"},{"arxiv":1,"publisher":"Springer","quality_controlled":"1","publication_status":"published","scopus_import":"1","type":"journal_article","isi":1,"publication":"Formal Methods in System Design","date_published":"2021-09-01T00:00:00Z","title":"Faster algorithms for quantitative verification in bounded treewidth graphs","day":"01","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s10703-021-00373-5","volume":57,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07384"}],"_id":"9393","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start Grant (279307: Graph Games), and Microsoft faculty fellows award.","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2021. Faster algorithms for quantitative verification in bounded treewidth graphs. Formal Methods in System Design. 57, 401–428.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2021). Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in bounded treewidth graphs. <i>Formal Methods in System Design</i>. 2021;57:401-428. doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in bounded treewidth graphs,” <i>Formal Methods in System Design</i>, vol. 57. Springer, pp. 401–428, 2021.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Formal Methods in System Design 57 (2021) 401–428.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>, vol. 57, Springer, 2021, pp. 401–28, doi:<a href=\"https://doi.org/10.1007/s10703-021-00373-5\">10.1007/s10703-021-00373-5</a>.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Bounded Treewidth Graphs.” <i>Formal Methods in System Design</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s10703-021-00373-5\">https://doi.org/10.1007/s10703-021-00373-5</a>."},"month":"09","article_type":"original","intvolume":"        57","date_updated":"2023-10-10T11:13:20Z","date_created":"2021-05-16T22:01:47Z","department":[{"_id":"KrCh"}],"article_processing_charge":"No","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1504.07384"],"isi":["000645490300001"]},"oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1572-8102"],"issn":["0925-9856"]},"ec_funded":1,"year":"2021","page":"401-428","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"status":"public","oa_version":"Preprint"},{"oa_version":"Published Version","status":"public","author":[{"last_name":"Koch","full_name":"Koch, Eva L.","first_name":"Eva L."},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty","last_name":"Lemmon"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"page":"196-213","related_material":{"record":[{"status":"public","relation":"research_data","id":"12987"}]},"year":"2021","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication_identifier":{"eissn":["2056-3744"]},"language":[{"iso":"eng"}],"ddc":["570"],"oa":1,"external_id":{"isi":["000647846200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.","lang":"eng"}],"file_date_updated":"2021-10-15T08:26:02Z","department":[{"_id":"NiBa"}],"date_created":"2021-05-16T22:01:47Z","date_updated":"2023-08-08T13:34:08Z","intvolume":"         5","article_type":"original","month":"05","citation":{"short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>.","ieee":"E. L. Koch <i>et al.</i>, “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” <i>Evolution Letters</i>, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>.","ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. 2021;5(3):196-213. doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>"},"acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","issue":"3","_id":"9394","file":[{"creator":"cchlebak","file_name":"2021_EvolutionLetters_Koch.pdf","file_size":3021108,"access_level":"open_access","relation":"main_file","date_created":"2021-10-15T08:26:02Z","date_updated":"2021-10-15T08:26:02Z","checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_id":"10142","success":1,"content_type":"application/pdf"}],"volume":5,"doi":"10.1002/evl3.227","project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"day":"07","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","date_published":"2021-05-07T00:00:00Z","publication":"Evolution Letters","isi":1,"quality_controlled":"1","type":"journal_article","scopus_import":"1","publication_status":"published","publisher":"Wiley","has_accepted_license":"1"},{"year":"2021","publication_identifier":{"issn":["2663-337X"]},"status":"public","oa_version":"Published Version","author":[{"last_name":"Huljev","full_name":"Huljev, Karla","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"page":"101","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"article_processing_charge":"No","file_date_updated":"2022-05-21T22:30:04Z","degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"ddc":["571"],"_id":"9397","doi":"10.15479/at:ista:9397","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file":[{"embargo_to":"open_access","creator":"khuljev","file_size":47799741,"file_name":"KHuljev_Thesis_corrections.docx","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398","access_level":"closed","relation":"source_file","date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-17T12:29:12Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","embargo":"2022-05-20","checksum":"bf512f8a1e572a543778fc4b227c01ba","file_id":"9401","date_updated":"2022-05-21T22:30:04Z","access_level":"open_access","date_created":"2021-05-18T14:50:28Z","relation":"main_file","file_size":16542131,"file_name":"new_KHuljev_Thesis_corrections.pdf","creator":"khuljev"}],"department":[{"_id":"CaHe"},{"_id":"GradSch"}],"date_updated":"2023-09-07T13:32:32Z","date_created":"2021-05-17T12:31:30Z","citation":{"chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria."},"month":"05","publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","day":"18","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","date_published":"2021-05-18T00:00:00Z"},{"oa":1,"ddc":["000"],"language":[{"iso":"eng"}],"pmid":1,"file_date_updated":"2023-11-07T08:27:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability."}],"external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"page":"1292–1302","status":"public","oa_version":"Submitted Version","publication_identifier":{"eissn":["2397-3374"]},"ec_funded":1,"year":"2021","publication":"Nature Human Behaviour","isi":1,"day":"13","title":"A unified framework of direct and indirect reciprocity","date_published":"2021-05-13T00:00:00Z","has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","scopus_import":"1","quality_controlled":"1","publication_status":"published","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <i>Nature Human Behaviour</i>, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302."},"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","month":"05","article_type":"original","intvolume":"         5","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_updated":"2025-07-14T09:10:09Z","date_created":"2021-05-18T16:56:57Z","doi":"10.1038/s41562-021-01114-8","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"dernst","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","file_size":5232761,"success":1,"checksum":"34f55e173f90dc1dab731063458ac780","file_id":"14496","relation":"main_file","access_level":"open_access","date_created":"2023-11-07T08:27:23Z","date_updated":"2023-11-07T08:27:23Z","content_type":"application/pdf"}],"volume":5,"_id":"9402","issue":"10"},{"author":[{"full_name":"Schmid, Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Hilbe, Christian","last_name":"Hilbe"}],"page":"139-152","month":"03","citation":{"ama":"Schmid L, Hilbe C. The evolution of strategic ignorance in strategic interaction. In: Hertwig R, Engel C, eds. <i>Deliberate Ignorance: Choosing Not To Know</i>. Vol 29. Strüngmann Forum Reports. MIT Press; 2021:139-152.","apa":"Schmid, L., &#38; Hilbe, C. (2021). The evolution of strategic ignorance in strategic interaction. In R. Hertwig &#38; C. Engel (Eds.), <i>Deliberate Ignorance: Choosing Not To Know</i> (Vol. 29, pp. 139–152). MIT Press.","ista":"Schmid L, Hilbe C. 2021.The evolution of strategic ignorance in strategic interaction. In: Deliberate Ignorance: Choosing Not To Know. vol. 29, 139–152.","chicago":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” In <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, 29:139–52. Strüngmann Forum Reports. MIT Press, 2021.","short":"L. Schmid, C. Hilbe, in:, R. Hertwig, C. Engel (Eds.), Deliberate Ignorance: Choosing Not To Know, MIT Press, 2021, pp. 139–152.","mla":"Schmid, Laura, and Christian Hilbe. “The Evolution of Strategic Ignorance in Strategic Interaction.” <i>Deliberate Ignorance: Choosing Not To Know</i>, edited by Ralph Hertwig and Christoph Engel, vol. 29, MIT Press, 2021, pp. 139–52.","ieee":"L. Schmid and C. Hilbe, “The evolution of strategic ignorance in strategic interaction,” in <i>Deliberate Ignorance: Choosing Not To Know</i>, vol. 29, R. Hertwig and C. Engel, Eds. MIT Press, 2021, pp. 139–152."},"editor":[{"last_name":"Hertwig","full_name":"Hertwig, Ralph","first_name":"Ralph"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"}],"series_title":"Strüngmann Forum Reports","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_created":"2021-05-19T12:25:42Z","date_updated":"2023-02-23T13:57:04Z","intvolume":"        29","status":"public","volume":29,"main_file_link":[{"url":"https://esforum.de/publications/PDFs/sfr29/SFR29_09_Hilbe%20and%20Schmid.pdf","open_access":"1"}],"publication_identifier":{"isbn":["978-0-262-04559-9"]},"_id":"9403","year":"2021","oa":1,"day":"01","date_published":"2021-03-01T00:00:00Z","title":"The evolution of strategic ignorance in strategic interaction","publication":"Deliberate Ignorance: Choosing Not To Know","language":[{"iso":"eng"}],"type":"book_chapter","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"MIT Press","abstract":[{"text":"Optimal decision making requires individuals to know their available options and to anticipate correctly what consequences these options have. In many social interactions, however, we refrain from gathering all relevant information, even if this information would help us make better decisions and is costless to obtain. This chapter examines several examples of “deliberate ignorance.” Two simple models are proposed to illustrate how ignorance can evolve among self-interested and payoff - maximizing individuals, and open problems are highlighted that lie ahead for future research to explore.","lang":"eng"}],"article_processing_charge":"No"},{"status":"public","oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/smashing-the-covid-curve/"}]},"author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"first_name":"Marc","full_name":"Timme, Marc","last_name":"Timme"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"year":"2021","publication_identifier":{"eissn":["20411723"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"ddc":["570"],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000687305500044"]},"file_date_updated":"2021-05-25T14:18:40Z","article_number":"2586","intvolume":"        12","date_created":"2021-05-23T22:01:42Z","date_updated":"2023-08-08T13:45:13Z","department":[{"_id":"BjHo"}],"acknowledgement":"The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden.","citation":{"apa":"Scarselli, D., Budanur, N. B., Timme, M., &#38; Hof, B. (2021). Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-22725-9\">https://doi.org/10.1038/s41467-021-22725-9</a>.","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” <i>Nature Communications</i>, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-22725-9\">10.1038/s41467-021-22725-9</a>.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021)."},"month":"05","article_type":"original","_id":"9407","issue":"1","doi":"10.1038/s41467-021-22725-9","volume":12,"file":[{"content_type":"application/pdf","date_updated":"2021-05-25T14:18:40Z","relation":"main_file","access_level":"open_access","date_created":"2021-05-25T14:18:40Z","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1","file_id":"9426","success":1,"file_name":"2021_NatureCommunications_Scarselli.pdf","file_size":1176573,"creator":"kschuh"}],"isi":1,"publication":"Nature Communications","date_published":"2021-05-10T00:00:00Z","title":"Discontinuous epidemic transition due to limited testing","day":"10","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":"1","has_accepted_license":"1"},{"volume":53,"main_file_link":[{"url":"https://arxiv.org/abs/1910.10435","open_access":"1"}],"doi":"10.1112/blms.12442","issue":"2","_id":"6965","article_type":"original","month":"04","citation":{"chicago":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2021. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>.","mla":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, Wiley, 2021, pp. 560–74, doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>.","short":"K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.","ieee":"K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for toric varieties,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. Wiley, pp. 560–574, 2021.","ama":"Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):560-574. doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>","apa":"Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>","ista":"Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574."},"department":[{"_id":"TaHa"}],"date_created":"2019-10-24T08:04:09Z","date_updated":"2023-08-04T10:43:39Z","intvolume":"        53","arxiv":1,"publication_status":"published","quality_controlled":"1","scopus_import":"1","type":"journal_article","publisher":"Wiley","day":"01","title":"The positivity of local equivariant Hirzebruch class for toric varieties","date_published":"2021-04-01T00:00:00Z","publication":"Bulletin of the London Mathematical Society","isi":1,"publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]},"year":"2021","author":[{"full_name":"Rychlewicz, Kamil P","last_name":"Rychlewicz","first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"page":"560-574","oa_version":"Preprint","status":"public","external_id":{"isi":["000594805800001"],"arxiv":["1910.10435"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber."}],"oa":1,"language":[{"iso":"eng"}]},{"day":"23","title":"Identification of neural oscillations and epileptiform changes in human brain organoids","date_published":"2021-08-23T00:00:00Z","isi":1,"publication_status":"published","type":"technical_report","publisher":"Springer Nature","alternative_title":["Nature Neuroscience"],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"date_created":"2019-11-10T11:23:58Z","date_updated":"2023-08-04T10:49:44Z","intvolume":"        24","month":"08","citation":{"ieee":"R. A. Samarasinghe <i>et al.</i>, <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i>, vol. 24. Springer Nature, 2021.","mla":"Samarasinghe, Ranmal A., et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>.","short":"R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe, A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch, Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids, Springer Nature, 2021.","chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>.","ista":"Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification of neural oscillations and epileptiform changes in human brain organoids, Springer Nature, 32p.","apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i> (Vol. 24). Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol 24. Springer Nature; 2021. doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>"},"acknowledgement":"We thank S. Butler, T. Carmichael and members of the laboratory of B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities Research Center microscopy cores for access to imaging facilities. This work was supported by grants from the California Institute for Regenerative Medicine (CIRM) (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897 and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922, R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.; R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S. and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience Training Grant (R25NS065723), a Research and Training Fellowship from the American Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M. and A.K. were supported in part by the UCLA-California State University Northridge CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and the Quantitative and Computational Biosciences Collaboratory community, directed by M. Pellegrini.","_id":"6995","volume":24,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-021-00906-5"}],"doi":"10.1038/s41593-021-00906-5","pmid":1,"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000687516300001"],"pmid":["34426698 "]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery."}],"article_processing_charge":"Yes","oa_version":"Published Version","status":"public","author":[{"full_name":"Samarasinghe, Ranmal A.","last_name":"Samarasinghe","first_name":"Ranmal A."},{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","last_name":"Miranda"},{"first_name":"Jessie E.","last_name":"Buth","full_name":"Buth, Jessie E."},{"first_name":"Simon","last_name":"Mitchell","full_name":"Mitchell, Simon"},{"last_name":"Ferando","full_name":"Ferando, Isabella","first_name":"Isabella"},{"first_name":"Momoko","full_name":"Watanabe, Momoko","last_name":"Watanabe"},{"last_name":"Kurdian","full_name":"Kurdian, Arinnae","first_name":"Arinnae"},{"first_name":"Peyman","last_name":"Golshani","full_name":"Golshani, Peyman"},{"first_name":"Kathrin","last_name":"Plath","full_name":"Plath, Kathrin"},{"first_name":"William E.","full_name":"Lowry, William E.","last_name":"Lowry"},{"first_name":"Jack M.","last_name":"Parent","full_name":"Parent, Jack M."},{"first_name":"Istvan","last_name":"Mody","full_name":"Mody, Istvan"},{"first_name":"Bennett G.","last_name":"Novitch","full_name":"Novitch, Bennett G."}],"page":"32","year":"2021","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]}},{"date_created":"2020-02-06T16:09:14Z","date_updated":"2023-08-04T10:46:29Z","department":[{"_id":"GaTk"}],"intvolume":"       461","month":"05","article_type":"original","acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","citation":{"short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>"},"_id":"7463","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"volume":461,"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.neucom.2020.05.126","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","date_published":"2021-05-13T00:00:00Z","day":"13","isi":1,"publication":"Neurocomputing","publication_status":"published","quality_controlled":"1","scopus_import":"1","type":"journal_article","publisher":"Elsevier","oa_version":"Preprint","status":"public","page":"657-666","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"},{"first_name":"Hans J","full_name":"Herrmann, Hans J","last_name":"Herrmann"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"}],"year":"2021","ec_funded":1,"publication_identifier":{"eissn":["1872-8286"],"issn":["0925-2312"]},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000704086300015"]},"abstract":[{"text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.","lang":"eng"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"day":"11","date_published":"2021-01-11T00:00:00Z","title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","publication":"Current Biology","isi":1,"has_accepted_license":"1","quality_controlled":"1","publication_status":"published","type":"journal_article","publisher":"Elsevier","article_type":"original","month":"01","citation":{"ieee":"F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, p. P25–38.E5, 2021.","mla":"Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, p. P25–38.E5, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>.","short":"F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.","chicago":"Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner, Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>.","ista":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. Current Biology. 31(1), P25–38.E5.","apa":"Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi, K., Jösch, M. A., &#38; Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>","ama":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. 2021;31(1):P25-38.E5. doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>"},"acknowledgement":"We thank Peter Jonas and Peter Somogyi for critically reading the manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L. Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst, and Laura Burnett for technical assistance, as well as Robert Beattie for imaging assistance. This work was supported by a European Research Council Advanced Grant 694539 to R.S.","department":[{"_id":"MaJö"},{"_id":"RySh"}],"date_updated":"2023-08-04T10:47:11Z","date_created":"2020-02-28T10:56:18Z","intvolume":"        31","file":[{"file_size":4915964,"file_name":"2021_CurrentBiology_Fredes.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2020-10-19T13:31:28Z","relation":"main_file","date_updated":"2020-10-19T13:31:28Z","access_level":"open_access","file_id":"8678","checksum":"b7b9c8bc84a08befce365c675229a7d1","success":1}],"volume":31,"doi":"10.1016/j.cub.2020.09.074","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"issue":"1","_id":"7551","ddc":["570"],"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-10-19T13:31:28Z","external_id":{"isi":["000614361000020"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.","lang":"eng"}],"article_processing_charge":"No","author":[{"full_name":"Fredes Tolorza, Felipe A","last_name":"Fredes Tolorza","id":"384825DA-F248-11E8-B48F-1D18A9856A87","first_name":"Felipe A"},{"full_name":"Silva Sifuentes, Maria A","last_name":"Silva Sifuentes","id":"371B3D6E-F248-11E8-B48F-1D18A9856A87","first_name":"Maria A"},{"last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Kobayashi, Kenta","last_name":"Kobayashi","first_name":"Kenta"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"page":"P25-38.E5","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/remembering-novelty/"}]},"oa_version":"Published Version","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ec_funded":1,"year":"2021"},{"oa":1,"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems."}],"article_processing_charge":"No","external_id":{"isi":["000637809600006"]},"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}],"record":[{"id":"15020","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski"},{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"page":"1227-1241.e5","status":"public","oa_version":"Preprint","ec_funded":1,"year":"2021","publication":"Neuron","isi":1,"day":"07","date_published":"2021-04-07T00:00:00Z","title":"Statistical analysis and optimality of neural systems","publisher":"Cell Press","quality_controlled":"1","scopus_import":"1","type":"journal_article","publication_status":"published","citation":{"mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>"},"acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","month":"04","intvolume":"       109","department":[{"_id":"GaTk"}],"date_created":"2020-02-28T11:00:12Z","date_updated":"2025-06-30T13:21:05Z","doi":"10.1016/j.neuron.2021.01.020","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"volume":109,"_id":"7553","issue":"7"},{"main_file_link":[{"url":"https://arxiv.org/abs/2001.00497","open_access":"1"}],"volume":33,"doi":"10.1142/S0129055X20600065","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"issue":"1","_id":"7685","month":"01","article_type":"original","citation":{"chicago":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>. World Scientific, 2021. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>.","mla":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060006, World Scientific, 2021, doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>.","short":"C. Boccato, Reviews in Mathematical Physics 33 (2021).","ieee":"C. Boccato, “The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific, 2021.","ama":"Boccato C. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>","apa":"Boccato, C. (2021). The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. World Scientific. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>","ista":"Boccato C. 2021. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. Reviews in Mathematical Physics. 33(1), 2060006."},"department":[{"_id":"RoSe"}],"date_created":"2020-04-26T22:00:45Z","date_updated":"2023-08-04T10:50:13Z","intvolume":"        33","arxiv":1,"type":"journal_article","scopus_import":"1","publication_status":"published","quality_controlled":"1","publisher":"World Scientific","day":"01","date_published":"2021-01-01T00:00:00Z","title":"The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime","publication":"Reviews in Mathematical Physics","isi":1,"ec_funded":1,"publication_identifier":{"issn":["0129-055X"]},"year":"2021","author":[{"full_name":"Boccato, Chiara","last_name":"Boccato","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","status":"public","article_number":"2060006","external_id":{"arxiv":["2001.00497"],"isi":["000613313200007"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein."}],"article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}]},{"file":[{"content_type":"application/pdf","success":1,"checksum":"f0a7745d48afa09ea7025e876a0145a8","file_id":"8800","access_level":"open_access","date_updated":"2020-11-24T13:11:39Z","relation":"main_file","date_created":"2020-11-24T13:11:39Z","file_size":2527276,"file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","creator":"dernst"}],"doi":"10.1002/wdev.383","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord"}],"_id":"7883","article_type":"original","month":"04","citation":{"ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>"},"acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","department":[{"_id":"AnKi"}],"date_updated":"2024-03-07T15:03:00Z","date_created":"2020-05-24T22:01:00Z","has_accepted_license":"1","publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1","publisher":"Wiley","day":"15","title":"Regulation of size and scale in vertebrate spinal cord development","date_published":"2021-04-15T00:00:00Z","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","isi":1,"ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["17597692"],"issn":["17597684"]},"year":"2021","author":[{"id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna","last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14323"}]},"oa_version":"Published Version","status":"public","article_number":"e383","file_date_updated":"2020-11-24T13:11:39Z","external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern."}],"ddc":["570"],"oa":1,"pmid":1,"language":[{"iso":"eng"}]},{"quality_controlled":"1","publication_status":"published","scopus_import":"1","type":"journal_article","publisher":"World Scientific","arxiv":1,"date_published":"2021-01-01T00:00:00Z","title":"Bosonic collective excitations in Fermi gases","day":"01","isi":1,"publication":"Reviews in Mathematical Physics","issue":"1","_id":"7900","volume":33,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.08190"}],"project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"doi":"10.1142/s0129055x20600090","date_created":"2020-05-28T16:47:55Z","date_updated":"2023-09-05T16:07:40Z","department":[{"_id":"RoSe"}],"intvolume":"        33","month":"01","article_type":"original","citation":{"mla":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060009, World Scientific, 2021, doi:<a href=\"https://doi.org/10.1142/s0129055x20600090\">10.1142/s0129055x20600090</a>.","short":"N.P. Benedikter, Reviews in Mathematical Physics 33 (2021).","ieee":"N. P. Benedikter, “Bosonic collective excitations in Fermi gases,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific, 2021.","chicago":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” <i>Reviews in Mathematical Physics</i>. World Scientific, 2021. <a href=\"https://doi.org/10.1142/s0129055x20600090\">https://doi.org/10.1142/s0129055x20600090</a>.","ista":"Benedikter NP. 2021. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 33(1), 2060009.","ama":"Benedikter NP. Bosonic collective excitations in Fermi gases. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/s0129055x20600090\">10.1142/s0129055x20600090</a>","apa":"Benedikter, N. P. (2021). Bosonic collective excitations in Fermi gases. <i>Reviews in Mathematical Physics</i>. World Scientific. <a href=\"https://doi.org/10.1142/s0129055x20600090\">https://doi.org/10.1142/s0129055x20600090</a>"},"external_id":{"arxiv":["1910.08190"],"isi":["000613313200010"]},"abstract":[{"lang":"eng","text":"Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation."}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"2060009","language":[{"iso":"eng"}],"oa":1,"year":"2021","ec_funded":1,"publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"oa_version":"Preprint","status":"public","author":[{"orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P"}]},{"day":"03","title":"Correlation energy of a weakly interacting Fermi gas","date_published":"2021-05-03T00:00:00Z","publication":"Inventiones Mathematicae","isi":1,"publication_status":"published","scopus_import":"1","type":"journal_article","quality_controlled":"1","publisher":"Springer","arxiv":1,"has_accepted_license":"1","department":[{"_id":"RoSe"}],"date_updated":"2023-08-21T06:30:30Z","date_created":"2020-05-28T16:48:20Z","intvolume":"       225","month":"05","article_type":"original","citation":{"chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas.” <i>Inventiones Mathematicae</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s00222-021-01041-5\">https://doi.org/10.1007/s00222-021-01041-5</a>.","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas.” <i>Inventiones Mathematicae</i>, vol. 225, Springer, 2021, pp. 885–979, doi:<a href=\"https://doi.org/10.1007/s00222-021-01041-5\">10.1007/s00222-021-01041-5</a>.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Inventiones Mathematicae 225 (2021) 885–979.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas,” <i>Inventiones Mathematicae</i>, vol. 225. Springer, pp. 885–979, 2021.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas. <i>Inventiones Mathematicae</i>. 2021;225:885-979. doi:<a href=\"https://doi.org/10.1007/s00222-021-01041-5\">10.1007/s00222-021-01041-5</a>","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2021). Correlation energy of a weakly interacting Fermi gas. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-021-01041-5\">https://doi.org/10.1007/s00222-021-01041-5</a>","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 225, 885–979."},"acknowledgement":"We thank Christian Hainzl for helpful discussions and a referee for very careful reading of the paper and many helpful suggestions. NB and RS were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 694227). Part of the research of NB was conducted on the RZD18 Nice–Milan–Vienna–Moscow. NB thanks Elliott H. Lieb and Peter Otte for explanations about the Luttinger model. PTN has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP acknowledges financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, grant agreement No. 802901). BS gratefully acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS (grant agreement No. 834782). All authors acknowledge support for workshop participation from Mathematisches Forschungsinstitut Oberwolfach (Leibniz Association). NB, PTN, BS, and RS acknowledge support for workshop participation from Fondation des Treilles.","_id":"7901","file":[{"success":1,"file_id":"11386","checksum":"f38c79dfd828cdc7f49a34b37b83d376","date_created":"2022-05-16T12:23:40Z","relation":"main_file","access_level":"open_access","date_updated":"2022-05-16T12:23:40Z","content_type":"application/pdf","creator":"dernst","file_size":1089319,"file_name":"2021_InventMath_Benedikter.pdf"}],"volume":225,"doi":"10.1007/s00222-021-01041-5","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"ddc":["510"],"oa":1,"external_id":{"arxiv":["2005.08933"],"isi":["000646573600001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy."}],"file_date_updated":"2022-05-16T12:23:40Z","oa_version":"Published Version","status":"public","author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","last_name":"Benedikter","full_name":"Benedikter, Niels P"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"page":"885-979","year":"2021","ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]}},{"intvolume":"        65","department":[{"_id":"HeEd"}],"date_created":"2020-05-30T10:26:04Z","date_updated":"2024-03-07T15:01:58Z","citation":{"ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","apa":"Brown, A., &#38; Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. 2021;65:1166-1198. doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” <i>Discrete and Computational Geometry</i>, vol. 65. Springer Nature, pp. 1166–1198, 2021.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>.","chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>."},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","month":"06","article_type":"original","_id":"7905","doi":"10.1007/s00454-020-00206-y","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file":[{"file_size":1013730,"file_name":"2020_DiscreteCompGeometry_Brown.pdf","creator":"dernst","content_type":"application/pdf","success":1,"checksum":"487a84ea5841b75f04f66d7ebd71b67e","file_id":"8803","relation":"main_file","date_updated":"2020-11-25T09:06:41Z","access_level":"open_access","date_created":"2020-11-25T09:06:41Z"}],"volume":65,"publication":"Discrete and Computational Geometry","isi":1,"day":"01","date_published":"2021-06-01T00:00:00Z","title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","publisher":"Springer Nature","type":"journal_article","quality_controlled":"1","scopus_import":"1","publication_status":"published","arxiv":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","author":[{"last_name":"Brown","full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"last_name":"Wang","full_name":"Wang, Bei","first_name":"Bei"}],"page":"1166-1198","year":"2021","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"ddc":["510"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms.","lang":"eng"}],"external_id":{"isi":["000536324700001"],"arxiv":["1712.07734"]},"file_date_updated":"2020-11-25T09:06:41Z"}]