[{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1096-0325"],"issn":["0040-5809"]},"article_processing_charge":"Yes (via OA deal)","title":"Limits to selection on standing variation in an asexual population","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"day":"01","date_published":"2024-06-01T00:00:00Z","_id":"15358","quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank Emmanuel Schertzer and two reviewers for comments on this manuscript. NB thanks the European Research Council for support via the grant “HaplotypeStructure” 101055327. We would also like to give our sincere thanks to Alison Etheridge for her insight, inspiration and support over the years.","file":[{"file_size":1098292,"checksum":"78f36488d24f868d5913624e9c8d88bf","success":1,"date_updated":"2024-05-13T08:22:21Z","file_name":"2024_TheorPopulationBiology_Barton.pdf","file_id":"15383","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2024-05-13T08:22:21Z"}],"isi":1,"doi":"10.1016/j.tpb.2024.04.001","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"page":"129-137","pmid":1,"publication_status":"published","file_date_updated":"2024-05-13T08:22:21Z","year":"2024","month":"06","volume":157,"has_accepted_license":"1","external_id":{"pmid":["38643838"],"isi":["001237016800001"]},"status":"public","abstract":[{"lang":"eng","text":"We consider how a population of N haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values z1,…,zN, which are drawn from a distribution ψ; the fitness of individual i is proportional to [Formula: see text] . For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance V0, and show that for large N, there is a scaling limit which depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1), the variance decreases exponentially at rate 1/N, and the expected ultimate gain in log fitness (scaled by V0), is just NV0, which is the same as Robertson's (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (NV0≫1), the ultimate gain can be found by approximating the establishment of alleles by a branching process in which each allele competes independently with the population mean and the fittest allele to establish is certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0) for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution. This approach also predicts the variability of the process, and its dynamics; we show that in the strong selection regime, the expected genetic variance decreases as ∼t-3 at large times. We discuss how these results may be related to selection on standing variation that is spread along a linear chromosome."}],"type":"journal_article","corr_author":"1","date_created":"2024-05-05T22:01:03Z","publication":"Theoretical Population Biology","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Barton, Nicholas H, and Himani Sachdeva. “Limits to Selection on Standing Variation in an Asexual Population.” <i>Theoretical Population Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">https://doi.org/10.1016/j.tpb.2024.04.001</a>.","mla":"Barton, Nicholas H., and Himani Sachdeva. “Limits to Selection on Standing Variation in an Asexual Population.” <i>Theoretical Population Biology</i>, vol. 157, Elsevier, 2024, pp. 129–37, doi:<a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">10.1016/j.tpb.2024.04.001</a>.","short":"N.H. Barton, H. Sachdeva, Theoretical Population Biology 157 (2024) 129–137.","apa":"Barton, N. H., &#38; Sachdeva, H. (2024). Limits to selection on standing variation in an asexual population. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">https://doi.org/10.1016/j.tpb.2024.04.001</a>","ista":"Barton NH, Sachdeva H. 2024. Limits to selection on standing variation in an asexual population. Theoretical Population Biology. 157, 129–137.","ama":"Barton NH, Sachdeva H. Limits to selection on standing variation in an asexual population. <i>Theoretical Population Biology</i>. 2024;157:129-137. doi:<a href=\"https://doi.org/10.1016/j.tpb.2024.04.001\">10.1016/j.tpb.2024.04.001</a>","ieee":"N. H. Barton and H. Sachdeva, “Limits to selection on standing variation in an asexual population,” <i>Theoretical Population Biology</i>, vol. 157. Elsevier, pp. 129–137, 2024."},"ddc":["570"],"date_updated":"2025-09-04T13:56:11Z","intvolume":"       157","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}]},{"citation":{"chicago":"Kolisnyk, Dmytro, Friedemann Queißer, Gernot Schaller, and Ralf Schützhold. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” <i>Physical Review Applied</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevApplied.21.044050\">https://doi.org/10.1103/PhysRevApplied.21.044050</a>.","ieee":"D. Kolisnyk, F. Queißer, G. Schaller, and R. Schützhold, “Floquet analysis of a superradiant many-qutrit refrigerator,” <i>Physical Review Applied</i>, vol. 21, no. 4. American Physical Society, 2024.","ista":"Kolisnyk D, Queißer F, Schaller G, Schützhold R. 2024. Floquet analysis of a superradiant many-qutrit refrigerator. Physical Review Applied. 21(4), 044050.","ama":"Kolisnyk D, Queißer F, Schaller G, Schützhold R. Floquet analysis of a superradiant many-qutrit refrigerator. <i>Physical Review Applied</i>. 2024;21(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.21.044050\">10.1103/PhysRevApplied.21.044050</a>","apa":"Kolisnyk, D., Queißer, F., Schaller, G., &#38; Schützhold, R. (2024). Floquet analysis of a superradiant many-qutrit refrigerator. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.21.044050\">https://doi.org/10.1103/PhysRevApplied.21.044050</a>","short":"D. Kolisnyk, F. Queißer, G. Schaller, R. Schützhold, Physical Review Applied 21 (2024).","mla":"Kolisnyk, Dmytro, et al. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” <i>Physical Review Applied</i>, vol. 21, no. 4, 044050, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.21.044050\">10.1103/PhysRevApplied.21.044050</a>."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We investigate superradiant enhancements in the refrigeration performance of a set of N three-level systems that are collectively coupled to a hot and a cold thermal reservoir and are additionally subject to collective periodic (circular) driving. Assuming the system-reservoir coupling to be weak, we explore the regime of stronger periodic driving strengths by comparing collective weak driving, Floquet-Lindblad, and Floquet-Redfield master equations. We identify regimes where the power injected by the periodic driving is used to pump heat from the cold to the hot reservoir and derive analytic sufficient conditions for them based on a cycle analysis of the Floquet-Lindblad master equation. In those regimes, we also argue for which parameters collective enhancements like a quadratic scaling of the cooling current with N can be expected and support our arguments by numerical simulations."}],"status":"public","external_id":{"arxiv":["2310.18126"],"isi":["001226579400001"]},"publication":"Physical Review Applied","date_created":"2024-05-05T22:01:04Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.18126","open_access":"1"}],"type":"journal_article","date_updated":"2025-09-04T13:51:06Z","arxiv":1,"intvolume":"        21","author":[{"full_name":"Kolisnyk, Dmytro","id":"530a7320-5355-11ee-ae5a-82a46997aaa7","first_name":"Dmytro","last_name":"Kolisnyk"},{"last_name":"Queißer","first_name":"Friedemann","full_name":"Queißer, Friedemann"},{"first_name":"Gernot","last_name":"Schaller","full_name":"Schaller, Gernot"},{"full_name":"Schützhold, Ralf","last_name":"Schützhold","first_name":"Ralf"}],"month":"04","issue":"4","volume":21,"publication_status":"published","year":"2024","article_number":"044050","_id":"15360","quality_controlled":"1","date_published":"2024-04-26T00:00:00Z","publisher":"American Physical Society","isi":1,"acknowledgement":"Financial support by the DFG (project ID 278162697 – SFB 1242) is gratefully acknowledged.\r\n","doi":"10.1103/PhysRevApplied.21.044050","publication_identifier":{"eissn":["2331-7019"]},"article_processing_charge":"No","department":[{"_id":"GradSch"}],"day":"26","oa":1,"title":"Floquet analysis of a superradiant many-qutrit refrigerator","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"intvolume":"      2787","date_updated":"2024-05-06T06:39:10Z","type":"book_chapter","scopus_import":"1","oa_version":"None","publication":"Plant Functional Genomics","date_created":"2024-05-05T22:01:04Z","external_id":{"pmid":["38656499"]},"status":"public","abstract":[{"text":"Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"chicago":"Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” In <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>.","short":"A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.), Plant Functional Genomics, Springer Nature, 2024, pp. 305–313.","mla":"Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, vol. 2787, Springer Nature, 2024, pp. 305–13, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>.","ista":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology, vol. 2787, 305–313.","ama":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Maghuly F, ed. <i>Plant Functional Genomics</i>. Vol 2787. MIMB. Springer Nature; 2024:305-313. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>","ieee":"A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf,” in <i>Plant Functional Genomics</i>, vol. 2787, F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313.","apa":"Jayasree, A., Salava, H., Nodzynski, T., &#38; Sravankumar, T. (2024). Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), <i>Plant Functional Genomics</i> (Vol. 2787, pp. 305–313). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>"},"year":"2024","publication_status":"published","volume":2787,"month":"04","series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"author":[{"full_name":"Jayasree, Aswathy","first_name":"Aswathy","last_name":"Jayasree"},{"full_name":"Salava, Hymavathi","first_name":"Hymavathi","last_name":"Salava"},{"full_name":"Nodzynski, Tomasz","last_name":"Nodzynski","first_name":"Tomasz"},{"last_name":"Sravankumar","orcid":"0000-0001-6925-6950","first_name":"Thula","full_name":"Sravankumar, Thula","id":"055b7938-0b72-11ef-94eb-d14136011bb5"}],"pmid":1,"page":"305-313","acknowledgement":"Special thanks to Dr. Marta Zwiewka for the support. Thanks to the Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively. Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility of CEITEC Masaryk University is acknowledged for the technical support.","doi":"10.1007/978-1-0716-3778-4_21","publisher":"Springer Nature","date_published":"2024-04-25T00:00:00Z","_id":"15361","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf","editor":[{"first_name":"Fatemeh","last_name":"Maghuly","full_name":"Maghuly, Fatemeh"}],"day":"25","department":[{"_id":"JiFr"}],"article_processing_charge":"No","publication_identifier":{"isbn":["9781071637777"],"eissn":["1940-6029"]}},{"day":"01","department":[{"_id":"FyKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["1018-4813"],"eissn":["1476-5438"]},"file":[{"content_type":"application/pdf","date_created":"2025-01-09T09:21:25Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"e45fc987f4e9ebafdd0ec4f0e9027de4","success":1,"file_name":"2024_EJHG_Andrianova.pdf","file_id":"18799","date_updated":"2025-01-09T09:21:25Z","file_size":3060724}],"doi":"10.1038/s41431-024-01598-8","acknowledgement":"This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)].","isi":1,"publisher":"Springer Nature","quality_controlled":"1","_id":"15362","date_published":"2024-07-01T00:00:00Z","volume":32,"month":"07","year":"2024","file_date_updated":"2025-01-09T09:21:25Z","publication_status":"published","pmid":1,"page":"837-845","author":[{"full_name":"Andrianova, Maria A.","last_name":"Andrianova","first_name":"Maria A."},{"full_name":"Seplyarskiy, Vladimir B.","last_name":"Seplyarskiy","first_name":"Vladimir B."},{"last_name":"Terradas","first_name":"Mariona","full_name":"Terradas, Mariona"},{"full_name":"Sánchez-Heras, Ana Beatriz","first_name":"Ana Beatriz","last_name":"Sánchez-Heras"},{"full_name":"Mur, Pilar","last_name":"Mur","first_name":"Pilar"},{"full_name":"Soto, José Luis","last_name":"Soto","first_name":"José Luis"},{"first_name":"Gemma","last_name":"Aiza","full_name":"Aiza, Gemma"},{"full_name":"Borràs, Emma","last_name":"Borràs","first_name":"Emma"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Kondrashov, Alexey S.","first_name":"Alexey S.","last_name":"Kondrashov"},{"first_name":"Georgii A.","last_name":"Bazykin","full_name":"Bazykin, Georgii A."},{"full_name":"Valle, Laura","first_name":"Laura","last_name":"Valle"}],"OA_type":"hybrid","project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"},{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"},{"name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127"}],"OA_place":"publisher","intvolume":"        32","ddc":["570"],"date_updated":"2026-04-15T08:51:09Z","language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"citation":{"ista":"Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845.","ieee":"M. A. Andrianova <i>et al.</i>, “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” <i>European Journal of Human Genetics</i>, vol. 32. Springer Nature, pp. 837–845, 2024.","ama":"Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. 2024;32:837-845. doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>","apa":"Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>","short":"M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845.","mla":"Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>, vol. 32, Springer Nature, 2024, pp. 837–45, doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>.","chicago":"Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>."},"type":"journal_article","oa_version":"Published Version","publication":"European Journal of Human Genetics","scopus_import":"1","date_created":"2024-05-05T22:01:04Z","has_accepted_license":"1","status":"public","external_id":{"isi":["001207703200001"],"pmid":["38658779"]},"abstract":[{"lang":"eng","text":"Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate."}]},{"external_id":{"arxiv":["2311.09347"],"isi":["001215855200002"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Two-dimensional semiconductor-superconductor heterostructures form the foundation of numerous nanoscale physical systems. However, measuring the properties of such heterostructures, and characterizing the semiconductor in-situ is challenging. A recent experimental study by [Phys. Rev. Lett. 128, 107701 (2022)] was able to probe the semiconductor within the heterostructure using microwave measurements of the superfluid density. This work revealed a rapid depletion of superfluid density in semiconductor, caused by the in-plane magnetic field which in presence of spin-orbit coupling creates so-called Bogoliubov Fermi surfaces. The experimental work used a simplified theoretical model that neglected the presence of non-magnetic disorder in the semiconductor, hence describing the data only qualitatively. Motivated by experiments, we introduce a theoretical model describing a disordered semiconductor with strong spin-orbit coupling that is proximitized by a superconductor. Our model provides specific predictions for the density of states and superfluid density. Presence of disorder leads to the emergence of a gapless superconducting phase, that may be viewed as a manifestation of Bogoliubov Fermi surface. When applied to real experimental data, our model showcases excellent quantitative agreement, enabling the extraction of material parameters such as mean free path and mobility, and estimating g-tensor after taking into account the orbital contribution of magnetic field. Our model can be used to probe in-situ parameters of other superconductor-semiconductor heterostructures and can be further extended to give access to transport properties."}],"corr_author":"1","type":"journal_article","scopus_import":"1","date_created":"2024-05-06T09:02:18Z","oa_version":"Published Version","publication":"SciPost Physics","language":[{"iso":"eng"}],"citation":{"chicago":"Babkin, Serafim, Andrew P Higginbotham, and Maksym Serbyn. “Proximity-Induced Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic Field.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">https://doi.org/10.21468/scipostphys.16.5.115</a>.","ista":"Babkin S, Higginbotham AP, Serbyn M. 2024. Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics. 16(5), 115.","ama":"Babkin S, Higginbotham AP, Serbyn M. Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. <i>SciPost Physics</i>. 2024;16(5). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">10.21468/scipostphys.16.5.115</a>","ieee":"S. Babkin, A. P. Higginbotham, and M. Serbyn, “Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field,” <i>SciPost Physics</i>, vol. 16, no. 5. SciPost Foundation, 2024.","apa":"Babkin, S., Higginbotham, A. P., &#38; Serbyn, M. (2024). Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">https://doi.org/10.21468/scipostphys.16.5.115</a>","short":"S. Babkin, A.P. Higginbotham, M. Serbyn, SciPost Physics 16 (2024).","mla":"Babkin, Serafim, et al. “Proximity-Induced Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic Field.” <i>SciPost Physics</i>, vol. 16, no. 5, 115, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">10.21468/scipostphys.16.5.115</a>."},"article_type":"original","ddc":["530"],"arxiv":1,"date_updated":"2026-06-03T07:16:00Z","intvolume":"        16","project":[{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"grant_number":"F8609","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems:  Probing topology in circuits and quantum materials","_id":"34a7f947-11ca-11ed-8bc3-c5dc2bbaae25"}],"author":[{"full_name":"Babkin, Serafim","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","last_name":"Babkin","orcid":"0009-0003-7382-8036","first_name":"Serafim"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"publication_status":"published","file_date_updated":"2024-05-07T12:58:47Z","year":"2024","month":"05","volume":16,"issue":"5","article_number":"115","_id":"15367","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","publisher":"SciPost Foundation","isi":1,"acknowledgement":"We acknowledge useful discussions with M. Geier, A. Levchenko, B. Ramshaw, T. Scaffidi, and\r\nJ. Shabani. This research was funded by the Austrian Science Fund (FWF) F 86.\r\nFor the purpose of open access, authors have applied a CC BY public copyright licence to any\r\nAuthor Accepted Manuscript version arising from this submission. MS acknowledges hospitality of KITP supported in part by the National Science Foundation under Grants No. NSF\r\nPHY-1748958 and PHY-2309135. APH acknowledges the support of the NOMIS foundation.","doi":"10.21468/scipostphys.16.5.115","file":[{"date_created":"2024-05-07T12:58:47Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"f999204856417dcf5a736ac8df432b96","success":1,"date_updated":"2024-05-07T12:58:47Z","file_name":"2024_SciPostPhys_Babkin.pdf","file_id":"15369","file_size":2733685}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2542-4653"]},"article_processing_charge":"Yes","title":"Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MaSe"},{"_id":"AnHi"}],"day":"01"},{"publication_identifier":{"eissn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","department":[{"_id":"JaBr"}],"day":"30","oa":1,"title":"Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3663","_id":"15372","quality_controlled":"1","date_published":"2024-04-30T00:00:00Z","publisher":"Springer Nature","acknowledgement":"We thank I. Stohkendl in the Taylor group for insightful discussions. This work was supported in part by Welch Foundation grants F-1808 (to I.J.F.), and F-1938 (to D.W.T.), the National Institutes of Health R01GM124141 (to I.J.F.), R01AI110577 (to K.A.J.), and R35GM138348 (to D.W.T.), and a Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research Grant (to D.W.T.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.","file":[{"file_size":7477013,"success":1,"checksum":"509c65919067a03ef8ad65c7192cd860","date_updated":"2024-05-13T11:46:19Z","file_name":"2024_NatureComm_Hibshman.pdf","file_id":"15386","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2024-05-13T11:46:19Z"}],"doi":"10.1038/s41467-024-47830-3","pmid":1,"author":[{"full_name":"Hibshman, Grace N.","first_name":"Grace N.","last_name":"Hibshman"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753"},{"full_name":"Hooper, Matthew M.","last_name":"Hooper","first_name":"Matthew M."},{"first_name":"Tyler L.","last_name":"Dangerfield","full_name":"Dangerfield, Tyler L."},{"first_name":"Hongshan","last_name":"Zhang","full_name":"Zhang, Hongshan"},{"last_name":"Finkelstein","first_name":"Ilya J.","full_name":"Finkelstein, Ilya J."},{"last_name":"Johnson","first_name":"Kenneth A.","full_name":"Johnson, Kenneth A."},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."}],"month":"04","volume":15,"file_date_updated":"2024-05-13T11:46:19Z","publication_status":"published","year":"2024","citation":{"chicago":"Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>.","ieee":"G. N. Hibshman <i>et al.</i>, “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>","ista":"Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663.","apa":"Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>","short":"G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).","mla":"Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>, vol. 15, 3663, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>."},"article_type":"original","DOAJ_listed":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing."}],"has_accepted_license":"1","status":"public","external_id":{"pmid":["38688943"]},"scopus_import":"1","oa_version":"Published Version","date_created":"2024-05-12T22:01:00Z","publication":"Nature Communications","corr_author":"1","type":"journal_article","date_updated":"2025-05-14T09:33:21Z","ddc":["570"],"intvolume":"        15"},{"day":"01","department":[{"_id":"JaMa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups","oa":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"doi":"10.1016/j.jfa.2024.110475","isi":1,"file":[{"date_updated":"2025-01-09T09:33:56Z","file_id":"18802","file_name":"2024_JourFunctAnalysis_Wirth.pdf","success":1,"checksum":"657c9f77dd30bb31ce43a591f58126a2","file_size":503148,"content_type":"application/pdf","date_created":"2025-01-09T09:33:56Z","access_level":"open_access","relation":"main_file","creator":"dernst"}],"publisher":"Elsevier","date_published":"2024-08-01T00:00:00Z","_id":"15373","quality_controlled":"1","article_number":"110475","volume":287,"issue":"3","month":"08","year":"2024","publication_status":"published","file_date_updated":"2025-01-09T09:33:56Z","author":[{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior"}],"OA_type":"hybrid","OA_place":"publisher","intvolume":"       287","ddc":["510"],"date_updated":"2025-09-08T07:24:07Z","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric Quantum Markov Semigroups.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">https://doi.org/10.1016/j.jfa.2024.110475</a>.","apa":"Wirth, M. (2024). Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">https://doi.org/10.1016/j.jfa.2024.110475</a>","ama":"Wirth M. Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. <i>Journal of Functional Analysis</i>. 2024;287(3). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">10.1016/j.jfa.2024.110475</a>","ista":"Wirth M. 2024. Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups. Journal of Functional Analysis. 287(3), 110475.","ieee":"M. Wirth, “Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups,” <i>Journal of Functional Analysis</i>, vol. 287, no. 3. Elsevier, 2024.","mla":"Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric Quantum Markov Semigroups.” <i>Journal of Functional Analysis</i>, vol. 287, no. 3, 110475, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110475\">10.1016/j.jfa.2024.110475</a>.","short":"M. Wirth, Journal of Functional Analysis 287 (2024)."},"type":"journal_article","corr_author":"1","publication":"Journal of Functional Analysis","date_created":"2024-05-12T22:01:01Z","oa_version":"Published Version","scopus_import":"1","status":"public","has_accepted_license":"1","external_id":{"isi":["001237916800001"]},"abstract":[{"text":"In this article we prove a refined version of the Christensen–Evans theorem for generators of uniformly continuous GNS-symmetric quantum Markov semigroups. We use this result to show the existence of GNS-symmetric extensions of GNS-symmetric quantum Markov semigroups. In particular, this implies that the generators of GNS-symmetric quantum Markov semigroups on finite-dimensional von Neumann algebra can be written in the form specified by Alicki's theorem.","lang":"eng"}]},{"year":"2024","file_date_updated":"2024-05-13T12:11:22Z","publication_status":"published","issue":"5","volume":43,"month":"05","author":[{"orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","first_name":"Marek","last_name":"Randuch"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"},{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"pmid":1,"intvolume":"        43","date_updated":"2025-09-08T07:23:07Z","ddc":["580"],"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"publication":"Cell Reports","oa_version":"Published Version","scopus_import":"1","date_created":"2024-05-12T22:01:01Z","type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is an essential process of cargo uptake operating in all eukaryotes. In animals and yeast, BAR-SH3 domain proteins, endophilins and amphiphysins, function at the conclusion of CME to recruit factors for vesicle scission and uncoating. Arabidopsis thaliana contains the BAR-SH3 domain proteins SH3P1–SH3P3, but their role is poorly understood. Here, we identify SH3Ps as functional homologs of endophilin/amphiphysin. SH3P1–SH3P3 bind to discrete foci at the plasma membrane (PM), and SH3P2 recruits late to a subset of clathrin-coated pits. The SH3P2 PM recruitment pattern is nearly identical to its interactor, a putative uncoating factor, AUXILIN-LIKE1. Notably, SH3P1–SH3P3 are required for most of AUXILIN-LIKE1 recruitment to the PM. This indicates a plant-specific modification of CME, where BAR-SH3 proteins recruit auxilin-like uncoating factors rather than the uncoating phosphatases, synaptojanins. SH3P1–SH3P3 act redundantly in overall CME with the plant-specific endocytic adaptor TPLATE complex but not due to an SH3 domain in its TASH3 subunit."}],"external_id":{"isi":["001240362800001"],"pmid":["38717900"]},"status":"public","has_accepted_license":"1","article_type":"original","citation":{"apa":"Adamowski, M., Randuch, M., Matijevic, I., Narasimhan, M., &#38; Friml, J. (2024). SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2024.114195\">https://doi.org/10.1016/j.celrep.2024.114195</a>","ieee":"M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, and J. Friml, “SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis,” <i>Cell Reports</i>, vol. 43, no. 5. Cell Press, 2024.","ista":"Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. 2024. SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. Cell Reports. 43(5), 114195.","ama":"Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. <i>Cell Reports</i>. 2024;43(5). doi:<a href=\"https://doi.org/10.1016/j.celrep.2024.114195\">10.1016/j.celrep.2024.114195</a>","mla":"Adamowski, Maciek, et al. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors for Clathrin-Mediated Endocytosis.” <i>Cell Reports</i>, vol. 43, no. 5, 114195, Cell Press, 2024, doi:<a href=\"https://doi.org/10.1016/j.celrep.2024.114195\">10.1016/j.celrep.2024.114195</a>.","short":"M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, J. Friml, Cell Reports 43 (2024).","chicago":"Adamowski, Maciek, Marek Randuch, Ivana Matijevic, Madhumitha Narasimhan, and Jiří Friml. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors for Clathrin-Mediated Endocytosis.” <i>Cell Reports</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.celrep.2024.114195\">https://doi.org/10.1016/j.celrep.2024.114195</a>."},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis","day":"28","department":[{"_id":"JiFr"},{"_id":"MaLo"}],"article_processing_charge":"Yes","publication_identifier":{"eissn":["2211-1247"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"content_type":"application/pdf","date_created":"2024-05-13T12:11:22Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2024_CellReports_Adamowski.pdf","file_id":"15387","date_updated":"2024-05-13T12:11:22Z","success":1,"checksum":"a06bb85be4fc765c51554d27ee2da802","file_size":5698598}],"isi":1,"acknowledgement":"The authors wish to acknowledge Dr. Daniel van Damme for mRuby3/pDONRP2rP3 and Prof. Qi-Jun Chen for sharing plasmids used for CRISPR-Cas9 mutagenesis. This work was supported by the Austrian Science Fund (FWF): I 3630-B25.","doi":"10.1016/j.celrep.2024.114195","publisher":"Cell Press","quality_controlled":"1","_id":"15374","date_published":"2024-05-28T00:00:00Z","article_number":"114195"},{"_id":"15375","date_published":"2024-05-01T00:00:00Z","quality_controlled":"1","doi":"10.1093/plcell/koae034","file":[{"date_updated":"2025-04-23T07:43:12Z","file_name":"2024_PlantCell_He.pdf","file_id":"19611","success":1,"checksum":"eed76c848fe3d8fe9a53943181aaa53c","file_size":50791962,"date_created":"2025-04-23T07:43:12Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst"}],"isi":1,"acknowledgement":"This work was funded by ISTA core support (Y.Y. and X.F.) and grants from the National Natural Science Foundation of China (31871443 to L.W. and P.L.; 32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance with microscopy and the ISTA Scientific Computing Facility for high-performance computing resources.","publisher":"Oxford University Press","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1532-298X"]},"day":"01","department":[{"_id":"XiFe"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis","oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” <i>The Plant Cell</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/plcell/koae034\">https://doi.org/10.1093/plcell/koae034</a>.","mla":"He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” <i>The Plant Cell</i>, vol. 36, no. 5, Oxford University Press, 2024, pp. 1829–43, doi:<a href=\"https://doi.org/10.1093/plcell/koae034\">10.1093/plcell/koae034</a>.","short":"S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant Cell 36 (2024) 1829–1843.","apa":"He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koae034\">https://doi.org/10.1093/plcell/koae034</a>","ista":"He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 36(5), 1829–1843.","ama":"He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. <i>The Plant Cell</i>. 2024;36(5):1829-1843. doi:<a href=\"https://doi.org/10.1093/plcell/koae034\">10.1093/plcell/koae034</a>","ieee":"S. He <i>et al.</i>, “Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis,” <i>The Plant Cell</i>, vol. 36, no. 5. Oxford University Press, pp. 1829–1843, 2024."},"article_type":"original","corr_author":"1","type":"journal_article","scopus_import":"1","oa_version":"Published Version","date_created":"2024-05-12T22:01:01Z","publication":"The Plant Cell","has_accepted_license":"1","external_id":{"pmid":["38309957"],"isi":["001180817000001"]},"status":"public","abstract":[{"lang":"eng","text":"In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA."}],"OA_type":"hybrid","OA_place":"publisher","intvolume":"        36","ddc":["580"],"date_updated":"2025-09-08T07:21:17Z","pmid":1,"page":"1829-1843","author":[{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"full_name":"Yu, Yiming","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","last_name":"Yu","first_name":"Yiming"},{"first_name":"Liang","last_name":"Wang","full_name":"Wang, Liang"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"last_name":"Bai","first_name":"Zhengyong","full_name":"Bai, Zhengyong"},{"first_name":"Guohong","last_name":"Li","full_name":"Li, Guohong"},{"full_name":"Li, Pilong","last_name":"Li","first_name":"Pilong"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"volume":36,"issue":"5","month":"05","year":"2024","file_date_updated":"2025-04-23T07:43:12Z","publication_status":"published"},{"oa":1,"title":"Auction-based scheduling","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToHe"}],"day":"05","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031572555"],"issn":["0302-9743"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","conference":{"location":"Luxembourg City, Luxembourg","start_date":"2024-04-06","end_date":"2024-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publisher":"Springer Nature","file":[{"date_created":"2024-05-22T07:09:24Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"dbeb123510997886d11925aedbf9c400","success":1,"date_updated":"2024-05-22T07:09:24Z","file_name":"2024_LNCS_Avni.pdf","file_id":"15414","file_size":508191}],"doi":"10.1007/978-3-031-57256-2_8","isi":1,"acknowledgement":"This work was supported in part by the ERC project ERC-2020-AdG 101020093 and by ISF grant no. 1679/21.","_id":"15376","date_published":"2024-04-05T00:00:00Z","quality_controlled":"1","publication_status":"published","file_date_updated":"2024-05-22T07:09:24Z","year":"2024","month":"04","volume":14572,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","first_name":"Guy"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik"},{"full_name":"Sadhukhan, Suman","first_name":"Suman","last_name":"Sadhukhan"}],"alternative_title":["LNCS"],"page":"153-172","date_updated":"2025-09-08T07:33:43Z","arxiv":1,"ddc":["000"],"intvolume":"     14572","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"abstract":[{"text":"Sequential decision-making tasks often require satisfaction of multiple, partially-contradictory objectives. Existing approaches are monolithic, where a single policy fulfills all objectives. We present auction-based scheduling, a decentralized framework for multi-objective sequential decision making. Each objective is fulfilled using a separate and independent policy. Composition of policies is performed at runtime, where at each step, the policies simultaneously bid from pre-allocated budgets for the privilege of choosing the next action. The framework allows policies to be independently created, modified, and replaced. We study path planning problems on finite graphs with two temporal objectives and present algorithms to synthesize policies together with bidding policies in a decentralized manner. We consider three categories of decentralized synthesis problems, parameterized by the assumptions that the policies make on each other. We identify a class of assumptions called assume-admissible for which synthesis is always possible for graphs whose every vertex has at most two outgoing edges.","lang":"eng"}],"status":"public","external_id":{"arxiv":["2310.11798"],"isi":["001284187100008"]},"has_accepted_license":"1","scopus_import":"1","date_created":"2024-05-12T22:01:02Z","publication":"30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","oa_version":"Published Version","type":"conference","corr_author":"1","citation":{"apa":"Avni, G., Mallik, K., &#38; Sadhukhan, S. (2024). Auction-based scheduling. In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 14572, pp. 153–172). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_8\">https://doi.org/10.1007/978-3-031-57256-2_8</a>","ama":"Avni G, Mallik K, Sadhukhan S. Auction-based scheduling. In: <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 14572. Springer Nature; 2024:153-172. doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_8\">10.1007/978-3-031-57256-2_8</a>","ista":"Avni G, Mallik K, Sadhukhan S. 2024. Auction-based scheduling. 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 14572, 153–172.","ieee":"G. Avni, K. Mallik, and S. Sadhukhan, “Auction-based scheduling,” in <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Luxembourg City, Luxembourg, 2024, vol. 14572, pp. 153–172.","mla":"Avni, Guy, et al. “Auction-Based Scheduling.” <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 14572, Springer Nature, 2024, pp. 153–72, doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_8\">10.1007/978-3-031-57256-2_8</a>.","short":"G. Avni, K. Mallik, S. Sadhukhan, in:, 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2024, pp. 153–172.","chicago":"Avni, Guy, Kaushik Mallik, and Suman Sadhukhan. “Auction-Based Scheduling.” In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 14572:153–72. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_8\">https://doi.org/10.1007/978-3-031-57256-2_8</a>."},"ec_funded":1,"language":[{"iso":"eng"}]},{"intvolume":"     14572","ddc":["000"],"arxiv":1,"date_updated":"2025-09-08T07:34:49Z","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"type":"conference","corr_author":"1","scopus_import":"1","publication":"30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","date_created":"2024-05-12T22:01:02Z","oa_version":"Published Version","external_id":{"arxiv":["2401.07548"],"isi":["001284187100011"]},"has_accepted_license":"1","status":"public","abstract":[{"text":"We provide an algorithmto solve Rabin and Streett games over graphs\r\nwith n vertices,m edges, and k colours that runs in ˜O³mn(k!)1+o(1)´time and\r\nO(nk logk logn) space, where ˜O hides poly-logarithmic factors. Our algorithm\r\nis an improvement by a super quadratic dependence on k! from the currently\r\nbest known run time of O³mn2(k!)2+o(1)´, obtained by converting a Rabin\r\ngameinto a parity game,while simultaneously improving its exponential space\r\nrequirement.\r\nOur main technical ingredient is a characterisation of progress measures for\r\nRabin games using colourful trees and a combinatorial construction of succinctlyrepresented,\r\nuniversal colourful trees. Colourful universal trees are generalisations\r\nof universal trees used by Jurdzi´nski and Lazi´c (2017) to solve parity\r\ngames, as well as of Rabin progress measures of Klarlund and Kozen (1991).\r\nOur algorithm for Rabin games is a progress measure lifting algorithm where\r\nthe lifting is performed on succinct, colourful, universal trees.","lang":"eng"}],"language":[{"iso":"eng"}],"ec_funded":1,"citation":{"apa":"Majumdar, R., Sağlam, I., &#38; Thejaswini, K. S. (2024). Rabin games and colourful universal trees. In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 14572, pp. 213–231). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_11\">https://doi.org/10.1007/978-3-031-57256-2_11</a>","ista":"Majumdar R, Sağlam I, Thejaswini KS. 2024. Rabin games and colourful universal trees. 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. , LNCS, vol. 14572, 213–231.","ieee":"R. Majumdar, I. Sağlam, and K. S. Thejaswini, “Rabin games and colourful universal trees,” in <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 2024, vol. 14572, pp. 213–231.","ama":"Majumdar R, Sağlam I, Thejaswini KS. Rabin games and colourful universal trees. In: <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 14572. Springer Nature; 2024:213-231. doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_11\">10.1007/978-3-031-57256-2_11</a>","mla":"Majumdar, Rupak, et al. “Rabin Games and Colourful Universal Trees.” <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 14572, Springer Nature, 2024, pp. 213–31, doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_11\">10.1007/978-3-031-57256-2_11</a>.","short":"R. Majumdar, I. Sağlam, K.S. Thejaswini, in:, 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2024, pp. 213–231.","chicago":"Majumdar, Rupak, Irmak Sağlam, and K. S. Thejaswini. “Rabin Games and Colourful Universal Trees.” In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 14572:213–31. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_11\">https://doi.org/10.1007/978-3-031-57256-2_11</a>."},"year":"2024","publication_status":"published","file_date_updated":"2024-05-22T07:24:45Z","volume":14572,"month":"04","alternative_title":["LNCS"],"author":[{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"},{"full_name":"Sağlam, Irmak","last_name":"Sağlam","first_name":"Irmak"},{"full_name":"Thejaswini, K. S.","id":"3807fb92-fdc1-11ee-bb4a-b4d8a431c753","first_name":"K. S.","last_name":"Thejaswini"}],"page":"213-231","file":[{"date_created":"2024-05-22T07:24:45Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"492be74f69cd6ea42d38681082d0b521","success":1,"file_id":"15415","file_name":"2024_LNCS_Majumdar.pdf","date_updated":"2024-05-22T07:24:45Z","file_size":462173}],"doi":"10.1007/978-3-031-57256-2_11","acknowledgement":"This work is a part of the project VAMOS that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant agreements No 101020093. Rupak Majumdar was partially supported by the DFG project 389792660 TRR 248-CPEC.","isi":1,"publisher":"Springer Nature","date_published":"2024-04-06T00:00:00Z","_id":"15377","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Rabin games and colourful universal trees","oa":1,"day":"06","department":[{"_id":"ToHe"}],"article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031572555"]}},{"date_published":"2024-09-01T00:00:00Z","_id":"15378","quality_controlled":"1","publisher":"Wiley","file":[{"file_size":566963,"file_id":"18803","file_name":"2024_CommPureApplMath_Erdoes.pdf","date_updated":"2025-01-09T09:36:41Z","success":1,"checksum":"fbcc9cc7bf274f024e4f4afc9c208f96","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2025-01-09T09:36:41Z"}],"acknowledgement":"László Erdős is partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. Hong Chang Ji is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","isi":1,"doi":"10.1002/cpa.22201","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"article_processing_charge":"Yes (via OA deal)","title":"Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian random matrices","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"LaEr"}],"day":"01","status":"public","external_id":{"isi":["001217139900001"],"arxiv":["2301.04981"]},"has_accepted_license":"1","abstract":[{"text":"We consider N×N non-Hermitian random matrices of the form X+A, where A is a general deterministic matrix and N−−√X consists of independent entries with zero mean, unit variance, and bounded densities. For this ensemble, we prove (i) a Wegner estimate, i.e. that the local density of eigenvalues is bounded by N1+o(1) and (ii) that the expected condition number of any bulk eigenvalue is bounded by N1+o(1); both results are optimal up to the factor No(1). The latter result complements the very recent matching lower bound obtained in [15] (arXiv:2301.03549) and improves the N-dependence of the upper bounds in [5,6,32] (arXiv:1906.11819, arXiv:2005.08930, arXiv:2005.08908). Our main ingredient, a near-optimal lower tail estimate for the small singular values of X+A−z, is of independent interest.","lang":"eng"}],"type":"journal_article","corr_author":"1","scopus_import":"1","date_created":"2024-05-12T22:01:02Z","publication":"Communications on Pure and Applied Mathematics","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"chicago":"Erdös, László, and Hong Chang Ji. “Wegner Estimate and Upper Bound on the Eigenvalue Condition Number of Non-Hermitian Random Matrices.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/cpa.22201\">https://doi.org/10.1002/cpa.22201</a>.","short":"L. Erdös, H.C. Ji, Communications on Pure and Applied Mathematics 77 (2024) 3785–3840.","mla":"Erdös, László, and Hong Chang Ji. “Wegner Estimate and Upper Bound on the Eigenvalue Condition Number of Non-Hermitian Random Matrices.” <i>Communications on Pure and Applied Mathematics</i>, vol. 77, no. 9, Wiley, 2024, pp. 3785–840, doi:<a href=\"https://doi.org/10.1002/cpa.22201\">10.1002/cpa.22201</a>.","ista":"Erdös L, Ji HC. 2024. Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 77(9), 3785–3840.","ieee":"L. Erdös and H. C. Ji, “Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian random matrices,” <i>Communications on Pure and Applied Mathematics</i>, vol. 77, no. 9. Wiley, pp. 3785–3840, 2024.","ama":"Erdös L, Ji HC. Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian random matrices. <i>Communications on Pure and Applied Mathematics</i>. 2024;77(9):3785-3840. doi:<a href=\"https://doi.org/10.1002/cpa.22201\">10.1002/cpa.22201</a>","apa":"Erdös, L., &#38; Ji, H. C. (2024). Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian random matrices. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.22201\">https://doi.org/10.1002/cpa.22201</a>"},"article_type":"original","ec_funded":1,"arxiv":1,"ddc":["510"],"date_updated":"2025-09-08T07:25:47Z","intvolume":"        77","OA_place":"publisher","OA_type":"hybrid","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Ji","first_name":"Hong Chang","full_name":"Ji, Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d"}],"page":"3785-3840","publication_status":"published","file_date_updated":"2025-01-09T09:36:41Z","year":"2024","month":"09","volume":77,"issue":"9"},{"_id":"15379","date_published":"2024-07-01T00:00:00Z","quality_controlled":"1","article_number":" 2400006","doi":"10.1002/bies.202400006","acknowledgement":"The authors thank Alexander Scrutton and James M. Krieger for comments on the manuscript. The authors also acknowledge Shraddha Nayak for help with Figure 1B design. This work was supported by grants from the Medical Research Council (MC_U105174197), the BBSRC (BB/N002113/1), and the Wellcome Trust (223194/Z/21/Z) to IHG.","isi":1,"file":[{"file_id":"18801","file_name":"2024_BioEssays_Stockwell.pdf","date_updated":"2025-01-09T09:31:05Z","checksum":"dc8be74156657e8aab12a9d613233ee3","success":1,"file_size":775825,"content_type":"application/pdf","date_created":"2025-01-09T09:31:05Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"publisher":"Wiley","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1521-1878"],"issn":["0265-9247"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","department":[{"_id":"PeJo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Tuning synaptic strength by regulation of AMPA glutamate receptor localization","citation":{"chicago":"Stockwell, Imogen, Jake Watson, and Ingo H. Greger. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” <i>BioEssays</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/bies.202400006\">https://doi.org/10.1002/bies.202400006</a>.","ama":"Stockwell I, Watson J, Greger IH. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. <i>BioEssays</i>. 2024;46(7). doi:<a href=\"https://doi.org/10.1002/bies.202400006\">10.1002/bies.202400006</a>","ista":"Stockwell I, Watson J, Greger IH. 2024. Tuning synaptic strength by regulation of AMPA glutamate receptor localization. BioEssays. 46(7), 2400006.","ieee":"I. Stockwell, J. Watson, and I. H. Greger, “Tuning synaptic strength by regulation of AMPA glutamate receptor localization,” <i>BioEssays</i>, vol. 46, no. 7. Wiley, 2024.","apa":"Stockwell, I., Watson, J., &#38; Greger, I. H. (2024). Tuning synaptic strength by regulation of AMPA glutamate receptor localization. <i>BioEssays</i>. Wiley. <a href=\"https://doi.org/10.1002/bies.202400006\">https://doi.org/10.1002/bies.202400006</a>","short":"I. Stockwell, J. Watson, I.H. Greger, BioEssays 46 (2024).","mla":"Stockwell, Imogen, et al. “Tuning Synaptic Strength by Regulation of AMPA Glutamate Receptor Localization.” <i>BioEssays</i>, vol. 46, no. 7, 2400006, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/bies.202400006\">10.1002/bies.202400006</a>."},"article_type":"review","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2024-05-12T22:01:02Z","publication":"BioEssays","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Long-term potentiation (LTP) of excitatory synapses is a leading model to explain the concept of information storage in the brain. Multiple mechanisms contribute to LTP, but central amongst them is an increased sensitivity of the postsynaptic membrane to neurotransmitter release. This sensitivity is predominantly determined by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A combination of AMPAR structural data, super-resolution imaging of excitatory synapses, and an abundance of electrophysiological studies are providing an ever-clearer picture of how AMPARs are recruited and organized at synaptic junctions. Here, we review the latest insights into this process, and discuss how both cytoplasmic and extracellular receptor elements cooperate to tune the AMPAR response at the hippocampal CA1 synapse.","lang":"eng"}],"has_accepted_license":"1","external_id":{"pmid":["38693811"],"isi":["001214545700001"]},"status":"public","OA_type":"hybrid","intvolume":"        46","OA_place":"publisher","date_updated":"2025-09-08T07:25:02Z","ddc":["570"],"pmid":1,"author":[{"last_name":"Stockwell","first_name":"Imogen","full_name":"Stockwell, Imogen"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823"},{"full_name":"Greger, Ingo H.","first_name":"Ingo H.","last_name":"Greger"}],"issue":"7","volume":46,"month":"07","year":"2024","file_date_updated":"2025-01-09T09:31:05Z","publication_status":"published"},{"publisher":"Springer Nature","doi":"10.1007/s41468-024-00173-w","file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2025-04-23T08:01:36Z","file_size":522831,"date_updated":"2025-04-23T08:01:36Z","file_name":"2024_JourApplCompTopo_BiswasRa.pdf","file_id":"19612","checksum":"0ee15c1493a6413cf356ab2f32c81a9e","success":1}],"acknowledgement":"The authors thank Uli Wagner and Emo Welzl for comments on an earlier version of this paper, and for pointing out related work in the prior literature.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","quality_controlled":"1","_id":"15380","date_published":"2024-09-01T00:00:00Z","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"article_processing_charge":"Yes (via OA deal)","ddc":["510"],"date_updated":"2025-05-14T09:27:57Z","intvolume":"         8","OA_place":"publisher","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"OA_type":"hybrid","has_accepted_license":"1","external_id":{"pmid":["39308789"]},"status":"public","abstract":[{"lang":"eng","text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements."}],"corr_author":"1","type":"journal_article","date_created":"2024-05-12T22:01:03Z","scopus_import":"1","oa_version":"Published Version","publication":"Journal of Applied and Computational Topology","language":[{"iso":"eng"}],"article_type":"original","citation":{"mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Journal of Applied and Computational Topology</i>, vol. 8, Springer Nature, 2024, pp. 557–78, doi:<a href=\"https://doi.org/10.1007/s41468-024-00173-w\">10.1007/s41468-024-00173-w</a>.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal of Applied and Computational Topology 8 (2024) 557–578.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2024). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-024-00173-w\">https://doi.org/10.1007/s41468-024-00173-w</a>","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Journal of Applied and Computational Topology</i>. 2024;8:557-578. doi:<a href=\"https://doi.org/10.1007/s41468-024-00173-w\">10.1007/s41468-024-00173-w</a>","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Journal of Applied and Computational Topology</i>, vol. 8. Springer Nature, pp. 557–578, 2024.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Journal of Applied and Computational Topology. 8, 557–578.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s41468-024-00173-w\">https://doi.org/10.1007/s41468-024-00173-w</a>."},"ec_funded":1,"publication_status":"published","file_date_updated":"2025-04-23T08:01:36Z","year":"2024","month":"09","volume":8,"related_material":{"record":[{"relation":"earlier_version","id":"11658","status":"public"}]},"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890"},{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera Di Montesano","full_name":"Cultrera Di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian"}],"page":"557-578","pmid":1},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"author":[{"full_name":"Rangel Guerrero, Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","first_name":"Dámaris K","last_name":"Rangel Guerrero"},{"last_name":"Balueva","first_name":"Kira","full_name":"Balueva, Kira"},{"first_name":"Uladzislau","last_name":"Barayeu","full_name":"Barayeu, Uladzislau","id":"b515be12-ec90-11ea-b966-d0b5e15613d2"},{"last_name":"Baracskay","first_name":"Peter","full_name":"Baracskay, Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","orcid":"0000-0001-8849-6570","first_name":"Michele"},{"id":"37BB4FB6-F248-11E8-B48F-1D18A9856A87","full_name":"Roth, Chiara N","first_name":"Chiara N","last_name":"Roth"},{"last_name":"Wulff","first_name":"Peer","full_name":"Wulff, Peer"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"page":"2045-2061.e10","year":"2024","file_date_updated":"2025-01-09T09:15:31Z","publication_status":"published","issue":"12","volume":112,"month":"06","scopus_import":"1","oa_version":"Published Version","publication":"Neuron","date_created":"2024-05-12T22:01:03Z","corr_author":"1","type":"journal_article","abstract":[{"text":"Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.","lang":"eng"}],"external_id":{"pmid":["38636524"],"isi":["001300571400001"]},"has_accepted_license":"1","status":"public","citation":{"mla":"Rangel Guerrero, Dámaris K., et al. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>, vol. 112, no. 12, Cell Press, 2024, p. 2045–2061.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>.","short":"D.K. Rangel Guerrero, K. Balueva, U. Barayeu, P. Baracskay, I. Gridchyn, M. Nardin, C.N. Roth, P. Wulff, J.L. Csicsvari, Neuron 112 (2024) 2045–2061.e10.","apa":"Rangel Guerrero, D. K., Balueva, K., Barayeu, U., Baracskay, P., Gridchyn, I., Nardin, M., … Csicsvari, J. L. (2024). Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>","ista":"Rangel Guerrero DK, Balueva K, Barayeu U, Baracskay P, Gridchyn I, Nardin M, Roth CN, Wulff P, Csicsvari JL. 2024. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. Neuron. 112(12), 2045–2061.e10.","ama":"Rangel Guerrero DK, Balueva K, Barayeu U, et al. Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning. <i>Neuron</i>. 2024;112(12):2045-2061.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">10.1016/j.neuron.2024.03.019</a>","ieee":"D. K. Rangel Guerrero <i>et al.</i>, “Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning,” <i>Neuron</i>, vol. 112, no. 12. Cell Press, p. 2045–2061.e10, 2024.","chicago":"Rangel Guerrero, Dámaris K, Kira Balueva, Uladzislau Barayeu, Peter Baracskay, Igor Gridchyn, Michele Nardin, Chiara N Roth, Peer Wulff, and Jozsef L Csicsvari. “Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding and Contextual Learning.” <i>Neuron</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2024.03.019\">https://doi.org/10.1016/j.neuron.2024.03.019</a>."},"article_type":"original","language":[{"iso":"eng"}],"OA_place":"publisher","intvolume":"       112","date_updated":"2025-09-08T07:26:42Z","ddc":["570"],"project":[{"grant_number":"I 3713-B27","call_identifier":"FWF","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning","day":"19","department":[{"_id":"JoCs"}],"_id":"15381","quality_controlled":"1","date_published":"2024-06-19T00:00:00Z","doi":"10.1016/j.neuron.2024.03.019","isi":1,"acknowledgement":"We thank the kind donations from Andrea Varro, Brian Sauer, Edward Boyden, and Peter Jonas. We thank Jago Wallenschus, Kerstin Kronenbitter, and Didier Gremelle for outstanding technical support; Laura Bollepalli for initial viral targeting experiments; Cihan Önal for initial electrophysiology experiments; Yoav Ben-Simon for histological advice; and Anton Nikitenko for contributing to the analysis. We acknowledge support from the Miba Machine Shop, Bioimaging-, Life Science- and Pre-Clinical Facilities at ISTA. This work was supported by the Austrian Science Fund (FWF I3713 to J.C. as part of the FOR 2143 research consortium), the Deutsche Forschungsgemeinschaft (DFG) (WU 503/2-2 to P.W.), and the Medical Research Council, United Kingdom (grant G1100546/2 to P.W.).","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-09T09:15:31Z","file_size":9149079,"success":1,"checksum":"de5b18ff293d42bd90e83a193e889844","date_updated":"2025-01-09T09:15:31Z","file_name":"2024_Neuron_RangelGuerrero.pdf","file_id":"18798"}],"publisher":"Cell Press"},{"keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"related_material":{"record":[{"relation":"used_in_publication","id":"17142","status":"public"}]},"day":"15","department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"month":"05","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","year":"2024","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","file_date_updated":"2024-05-16T09:08:20Z","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"author":[{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","orcid":"0000-0002-8937-410X","first_name":"Laura"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","full_name":"Masson, Tomas","last_name":"Masson","first_name":"Tomas","orcid":"0000-0002-2634-6283"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","first_name":"Tomas A"},{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","file":[{"success":1,"checksum":"9205eb0876f0f08552dbad80d6884b4b","file_id":"15396","file_name":"PatchClamp.zip","date_updated":"2024-05-15T06:09:17Z","file_size":"1149617663","content_type":"application/zip","date_created":"2024-05-15T06:09:17Z","creator":"mjoesch","relation":"main_file","access_level":"open_access"},{"success":1,"file_name":"SiliconProbe.zip","file_id":"15397","date_updated":"2024-05-15T06:09:12Z","file_size":"564903112","content_type":"application/zip","date_created":"2024-05-15T06:09:12Z","creator":"mjoesch","relation":"main_file","access_level":"open_access"},{"file_size":"11685703","date_updated":"2024-05-15T06:09:14Z","file_name":"WesternBlot.zip","file_id":"15398","success":1,"checksum":"49a807bbab06b5fada38f532e2176e2e","access_level":"open_access","relation":"main_file","creator":"mjoesch","content_type":"application/zip","date_created":"2024-05-15T06:09:14Z"},{"access_level":"open_access","creator":"mjoesch","relation":"main_file","content_type":"application/zip","date_created":"2024-05-15T06:09:38Z","file_size":"1335626779","file_name":"Behaviour.zip","file_id":"15399","date_updated":"2024-05-15T06:09:38Z","success":1,"checksum":"beeeeaa43770090f3b291209ed6b0623"},{"access_level":"open_access","creator":"mjoesch","relation":"main_file","content_type":"text/plain","date_created":"2024-05-16T09:08:20Z","file_size":18841,"file_name":"Readme_Data.txt","file_id":"15400","date_updated":"2024-05-16T09:08:20Z","checksum":"8862ad7719388304d1d19f8e7db8bb00","success":1}],"doi":"10.15479/AT:ISTA:15385","publisher":"Institute of Science and Technology Austria","ddc":["570"],"date_updated":"2025-09-08T07:57:11Z","_id":"15385","date_published":"2024-05-15T00:00:00Z","citation":{"apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>."},"corr_author":"1","type":"research_data","oa_version":"Published Version","date_created":"2024-05-13T15:04:04Z","status":"public","has_accepted_license":"1","abstract":[{"text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)","lang":"eng"}]},{"volume":532,"issue":"5","month":"05","year":"2024","publication_status":"published","pmid":1,"author":[{"full_name":"Reiner, Anton","first_name":"Anton","last_name":"Reiner"},{"full_name":"Medina, Loreta","last_name":"Medina","first_name":"Loreta"},{"full_name":"Abellan, Antonio","first_name":"Antonio","last_name":"Abellan"},{"full_name":"Deng, Yunping","last_name":"Deng","first_name":"Yunping"},{"full_name":"Toledo, Claudio A.B.","first_name":"Claudio A.B.","last_name":"Toledo"},{"full_name":"Luksch, Harald","first_name":"Harald","last_name":"Luksch"},{"full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","last_name":"Vega Zuniga"},{"full_name":"Riley, Nell B.","last_name":"Riley","first_name":"Nell B."},{"last_name":"Hodos","first_name":"William","full_name":"Hodos, William"},{"last_name":"Karten","first_name":"Harvey J.","full_name":"Karten, Harvey J."}],"OA_type":"green","OA_place":"repository","intvolume":"       532","date_updated":"2025-09-08T07:29:27Z","language":[{"iso":"eng"}],"citation":{"chicago":"Reiner, Anton, Loreta Medina, Antonio Abellan, Yunping Deng, Claudio A.B. Toledo, Harald Luksch, Tomas A Vega Zuniga, Nell B. Riley, William Hodos, and Harvey J. Karten. “Neurochemistry and Circuit Organization of the Lateral Spiriform Nucleus of Birds: A Uniquely Nonmammalian Direct Pathway Component of the Basal Ganglia.” <i>Journal of Comparative Neurology</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/cne.25620\">https://doi.org/10.1002/cne.25620</a>.","mla":"Reiner, Anton, et al. “Neurochemistry and Circuit Organization of the Lateral Spiriform Nucleus of Birds: A Uniquely Nonmammalian Direct Pathway Component of the Basal Ganglia.” <i>Journal of Comparative Neurology</i>, vol. 532, no. 5, e25620, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/cne.25620\">10.1002/cne.25620</a>.","short":"A. Reiner, L. Medina, A. Abellan, Y. Deng, C.A.B. Toledo, H. Luksch, T.A. Vega Zuniga, N.B. Riley, W. Hodos, H.J. Karten, Journal of Comparative Neurology 532 (2024).","apa":"Reiner, A., Medina, L., Abellan, A., Deng, Y., Toledo, C. A. B., Luksch, H., … Karten, H. J. (2024). Neurochemistry and circuit organization of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of the basal ganglia. <i>Journal of Comparative Neurology</i>. Wiley. <a href=\"https://doi.org/10.1002/cne.25620\">https://doi.org/10.1002/cne.25620</a>","ieee":"A. Reiner <i>et al.</i>, “Neurochemistry and circuit organization of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of the basal ganglia,” <i>Journal of Comparative Neurology</i>, vol. 532, no. 5. Wiley, 2024.","ama":"Reiner A, Medina L, Abellan A, et al. Neurochemistry and circuit organization of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of the basal ganglia. <i>Journal of Comparative Neurology</i>. 2024;532(5). doi:<a href=\"https://doi.org/10.1002/cne.25620\">10.1002/cne.25620</a>","ista":"Reiner A, Medina L, Abellan A, Deng Y, Toledo CAB, Luksch H, Vega Zuniga TA, Riley NB, Hodos W, Karten HJ. 2024. Neurochemistry and circuit organization of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of the basal ganglia. Journal of Comparative Neurology. 532(5), e25620."},"article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11090467"}],"type":"journal_article","scopus_import":"1","date_created":"2024-05-19T22:01:12Z","publication":"Journal of Comparative Neurology","oa_version":"Submitted Version","external_id":{"pmid":["38733146"],"isi":["001217825300001"]},"status":"public","abstract":[{"text":"We used diverse methods to characterize the role of avian lateral spiriform nucleus (SpL) in basal ganglia motor function. Connectivity analysis showed that SpL receives input from globus pallidus (GP), and the intrapeduncular nucleus (INP) located ventromedial to GP, whose neurons express numerous striatal markers. SpL-projecting GP neurons were large and aspiny, while SpL-projecting INP neurons were medium sized and spiny. Connectivity analysis further showed that SpL receives inputs from subthalamic nucleus (STN) and substantia nigra pars reticulata (SNr), and that the SNr also receives inputs from GP, INP, and STN. Neurochemical analysis showed that SpL neurons express ENK, GAD, and a variety of pallidal neuron markers, and receive GABAergic terminals, some of which also contain DARPP32, consistent with GP pallidal and INP striatal inputs. Connectivity and neurochemical analysis showed that the SpL input to tectum prominently ends on GABAA receptor-enriched tectobulbar neurons. Behavioral studies showed that lesions of SpL impair visuomotor behaviors involving tracking and pecking moving targets. Our results suggest that SpL modulates brainstem-projecting tectobulbar neurons in a manner comparable to the demonstrated influence of GP internus on motor thalamus and of SNr on tectobulbar neurons in mammals. Given published data in amphibians and reptiles, it seems likely the SpL circuit represents a major direct pathway-type circuit by which the basal ganglia exerts its motor influence in nonmammalian tetrapods. The present studies also show that avian striatum is divided into three spatially segregated territories with differing connectivity, a medial striato-nigral territory, a dorsolateral striato-GP territory, and the ventrolateral INP motor territory.","lang":"eng"}],"day":"01","department":[{"_id":"MaJö"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Neurochemistry and circuit organization of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of the basal ganglia","oa":1,"article_processing_charge":"No","publication_identifier":{"eissn":["1096-9861"],"issn":["0021-9967"]},"acknowledgement":"We gratefully thank Marion Joni, Tony Laverghetta, Sherry Cuthbertson, Gary Henderson, and Patricia Lindaman for technical assistance. The research presented here has been supported by NIH grants NS-16857, NS-19620, NS-28721, and EY-05298, and The Methodist Hospitals Endowed Professorship in Neuroscience (A. R.), by grant number 09/50623-9 from the Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (C. A. B. T.), by NIH grant EY-00735 (W. H.), and by NIH grants NS-12078 and EY-02145 (H. J. K.).","isi":1,"doi":"10.1002/cne.25620","publisher":"Wiley","_id":"15404","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","article_number":"e25620"},{"_id":"15405","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","article_number":"176","doi":"10.3847/1538-4357/ad3914","acknowledgement":"We thank the referee for the valuable comments on this paper. We thank John Silverman, Madeline Marshall, MingYang Zhuang, Weizhe Liu, and Jinyi Yang for inspiring discussions and suggestions. D.K. is grateful for the support from JSPS KAKENHI grant No. JP21K13956. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope\r\nScience Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are\r\nassociated with program ID #1243. Facility: JWST (NIRCam) Software: astropy (Astropy Collaboration et al. 2013, 2018), psfMC (Mechtley 2014), webbpsf (Perrin et al. 2014), jwst.","file":[{"content_type":"application/pdf","date_created":"2024-05-21T11:13:25Z","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"47b428f6209d8a6f9869031d9cb8dae6","success":1,"date_updated":"2024-05-21T11:13:25Z","file_name":"2024_AstrophysicalJourn_Yue.pdf","file_id":"15410","file_size":4472346}],"isi":1,"publisher":"IOP Publishing","article_processing_charge":"Yes","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6","day":"01","department":[{"_id":"JoMa"}],"publication":"Astrophysical Journal","oa_version":"Published Version","date_created":"2024-05-19T22:01:12Z","scopus_import":"1","type":"journal_article","abstract":[{"text":"We report JWST/NIRCam measurements of quasar host galaxy emissions and supermassive black hole (SMBH) masses for six quasars at 5.9 < z < 7.1 in the Emission-line galaxies and Intergalactic Gas in the Epoch of Reionization (EIGER) project. We obtain deep NIRCam imaging in the F115W, F200W, and F356W bands, as well as F356W grism spectroscopy of the quasars. We use bright unsaturated stars to construct models of the point-spread functions (PSFs) and estimate the errors of these PSFs. We then measure or constrain the fluxes and morphology of the quasar host galaxies by fitting the quasar images as a point source plus an exponential disk. We successfully detect the host galaxies of three quasars, which have host-to-quasar-flux ratios of ∼1%–5%. Spectral energy distribution fitting suggests that these quasar host galaxies have stellar masses of M* ≳ 1010M⊙. For quasars with host galaxy nondetections, we estimate the upper limits of their stellar masses. We use the grism spectra to measure the Hβ line profile and the continuum luminosity, then estimate the SMBH masses for the quasars. Our results indicate that the positive relation between SMBH masses and host galaxy stellar masses already exists at redshift z ≳ 6. The quasars in our sample show a high BH-to-stellar-mass ratio of MBH/M* ∼ 0.15, which is about ∼2 dex higher than local relations. We find that selection effects only contribute partially to the high MBH/M* ratios of high-redshift quasars. This result hints at a possible redshift evolution of the MBH–M* relation.","lang":"eng"}],"external_id":{"isi":["001214916200001"]},"has_accepted_license":"1","status":"public","article_type":"original","citation":{"ama":"Yue M, Eilers AC, Simcoe RA, et al. EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. 2024;966(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3914\">10.3847/1538-4357/ad3914</a>","ieee":"M. Yue <i>et al.</i>, “EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6,” <i>Astrophysical Journal</i>, vol. 966, no. 2. IOP Publishing, 2024.","ista":"Yue M, Eilers AC, Simcoe RA, Mackenzie R, Matthee JJ, Kashino D, Bordoloi R, Lilly SJ, Naidu RP. 2024. EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6. Astrophysical Journal. 966(2), 176.","apa":"Yue, M., Eilers, A. C., Simcoe, R. A., Mackenzie, R., Matthee, J. J., Kashino, D., … Naidu, R. P. (2024). EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad3914\">https://doi.org/10.3847/1538-4357/ad3914</a>","short":"M. Yue, A.C. Eilers, R.A. Simcoe, R. Mackenzie, J.J. Matthee, D. Kashino, R. Bordoloi, S.J. Lilly, R.P. Naidu, Astrophysical Journal 966 (2024).","mla":"Yue, Minghao, et al. “EIGER. V. Characterizing the Host Galaxies of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>, vol. 966, no. 2, 176, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3914\">10.3847/1538-4357/ad3914</a>.","chicago":"Yue, Minghao, Anna Christina Eilers, Robert A. Simcoe, Ruari Mackenzie, Jorryt J Matthee, Daichi Kashino, Rongmon Bordoloi, Simon J. Lilly, and Rohan P. Naidu. “EIGER. V. Characterizing the Host Galaxies of Luminous Quasars at z ≳ 6.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad3914\">https://doi.org/10.3847/1538-4357/ad3914</a>."},"DOAJ_listed":"1","language":[{"iso":"eng"}],"intvolume":"       966","date_updated":"2025-09-08T07:30:17Z","ddc":["520"],"author":[{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"full_name":"Simcoe, Robert A.","first_name":"Robert A.","last_name":"Simcoe"},{"full_name":"Mackenzie, Ruari","last_name":"Mackenzie","first_name":"Ruari"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X"},{"full_name":"Kashino, Daichi","first_name":"Daichi","last_name":"Kashino"},{"last_name":"Bordoloi","first_name":"Rongmon","full_name":"Bordoloi, Rongmon"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."}],"year":"2024","publication_status":"published","file_date_updated":"2024-05-21T11:13:25Z","issue":"2","volume":966,"month":"05"},{"date_updated":"2025-05-14T09:31:15Z","ddc":["530"],"arxiv":1,"intvolume":"         6","abstract":[{"text":"We report on dynamic Shubnikov–de Haas (SdH) oscillations that are measured in the optical response, subterahertz transmittance of two-dimensional systems, and reveal two distinct types of oscillation nodes: “universal” nodes at integer ratios of radiation and cyclotron frequencies and “tunable” nodes at positions sensitive to all parameters of the structure. The nodes in both real and imaginary parts of the measured complex transmittance are analyzed using a dynamic version of the static Lifshitz-Kosevich formula. These results demonstrate that the node structure of the dynamic SdH oscillations provides an all-optical access to quantization- and interaction-induced renormalization effects, in addition to parameters one can obtain from the static SdH oscillations.","lang":"eng"}],"status":"public","external_id":{"arxiv":["2402.05879"]},"has_accepted_license":"1","publication":"Physical Review Research","date_created":"2024-05-19T22:01:12Z","scopus_import":"1","oa_version":"Published Version","type":"journal_article","DOAJ_listed":"1","article_type":"letter_note","citation":{"short":"M.L. Savchenko, J. Gospodarič, A. Shuvaev, I.A. Dmitriev, V. Dziom, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Physical Review Research 6 (2024).","mla":"Savchenko, M. L., et al. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional Electron Systems.” <i>Physical Review Research</i>, vol. 6, no. 2, L022027, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">10.1103/PhysRevResearch.6.L022027</a>.","ista":"Savchenko ML, Gospodarič J, Shuvaev A, Dmitriev IA, Dziom V, Dobretsova AA, Mikhailov NN, Kvon ZD, Pimenov A. 2024. Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. Physical Review Research. 6(2), L022027.","ieee":"M. L. Savchenko <i>et al.</i>, “Optical Shubnikov-de Haas oscillations in two-dimensional electron systems,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024.","ama":"Savchenko ML, Gospodarič J, Shuvaev A, et al. Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">10.1103/PhysRevResearch.6.L022027</a>","apa":"Savchenko, M. L., Gospodarič, J., Shuvaev, A., Dmitriev, I. A., Dziom, V., Dobretsova, A. A., … Pimenov, A. (2024). Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">https://doi.org/10.1103/PhysRevResearch.6.L022027</a>","chicago":"Savchenko, M. L., J. Gospodarič, A. Shuvaev, I. A. Dmitriev, Vlad Dziom, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, and A. Pimenov. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional Electron Systems.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">https://doi.org/10.1103/PhysRevResearch.6.L022027</a>."},"language":[{"iso":"eng"}],"file_date_updated":"2024-05-22T06:39:35Z","publication_status":"published","year":"2024","month":"04","issue":"2","volume":6,"author":[{"last_name":"Savchenko","first_name":"M. L.","full_name":"Savchenko, M. L."},{"full_name":"Gospodarič, J.","last_name":"Gospodarič","first_name":"J."},{"full_name":"Shuvaev, A.","last_name":"Shuvaev","first_name":"A."},{"first_name":"I. A.","last_name":"Dmitriev","full_name":"Dmitriev, I. A."},{"id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","full_name":"Dziom, Vlad","last_name":"Dziom","first_name":"Vlad","orcid":"0000-0002-1648-0999"},{"full_name":"Dobretsova, A. A.","first_name":"A. A.","last_name":"Dobretsova"},{"first_name":"N. N.","last_name":"Mikhailov","full_name":"Mikhailov, N. N."},{"full_name":"Kvon, Z. D.","last_name":"Kvon","first_name":"Z. D."},{"first_name":"A.","last_name":"Pimenov","full_name":"Pimenov, A."}],"publisher":"American Physical Society","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2024-05-22T06:39:35Z","content_type":"application/pdf","file_size":1697856,"success":1,"checksum":"78c8c3cf1bda766e3de0db45f143a367","date_updated":"2024-05-22T06:39:35Z","file_id":"15412","file_name":"2024_PhysicalReviewResearch_Savchenko.pdf"}],"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/I3456,10.55776/I5539]. I.A.D. acknowledges the financial support of the German Research Foundation (DM 1/6-1). The quantum well growth and transport measurements were supported by RSF 23-72-30003. For open access purposes, the authors have applied a CC BY public copyright license to any authoraccepted manuscript version arising from this submission.","doi":"10.1103/PhysRevResearch.6.L022027","article_number":"L022027","date_published":"2024-04-01T00:00:00Z","_id":"15406","quality_controlled":"1","oa":1,"title":"Optical Shubnikov-de Haas oscillations in two-dimensional electron systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ZhAl"}],"day":"01","publication_identifier":{"eissn":["2643-1564"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes"},{"department":[{"_id":"GradSch"}],"day":"01","oa":1,"title":"Quantum-informed recursive optimization algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2691-3399"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"American Physical Society","file":[{"file_size":2016085,"checksum":"76bdf0b4dc06d59d073a57bd6957a96c","success":1,"file_name":"2024_PRXQuantum_Finzgar.pdf","file_id":"15409","date_updated":"2024-05-21T09:35:14Z","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2024-05-21T09:35:14Z","content_type":"application/pdf"}],"acknowledgement":"J.R.F. and A.K. thank Libor Caha and Alexander Kliesch for insightful discussions. The authors thank Lilly Palackal, Maximilian Passek, Carlos Riofrío, and Gili Rosenberg for thorough reviews of the manuscript, and the Amazon Braket, BMW, and QuEra teams for their support. C.M. thanks the Munich Quantum Valley initiative, which is supported by the Bavarian State Government with funds from the Hightech Agenda Bayern Plus. H.G.K. would like to thank Am Platzl 1A for providing the necessary environment for creative thinking. An open-source implementation of QIRO is available online [60].","doi":"10.1103/PRXQuantum.5.020327","article_number":"020327","_id":"15407","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","month":"05","issue":"2","volume":5,"publication_status":"published","file_date_updated":"2024-05-21T09:35:14Z","year":"2024","author":[{"last_name":"Finžgar","first_name":"Jernej Rudi","full_name":"Finžgar, Jernej Rudi"},{"last_name":"Kerschbaumer","first_name":"Aron","full_name":"Kerschbaumer, Aron","id":"ade85a9c-3200-11ee-973b-91c1eb240410"},{"full_name":"Schuetz, Martin J.A.","last_name":"Schuetz","first_name":"Martin J.A."},{"full_name":"Mendl, Christian B.","last_name":"Mendl","first_name":"Christian B."},{"full_name":"Katzgraber, Helmut G.","first_name":"Helmut G.","last_name":"Katzgraber"}],"OA_type":"gold","date_updated":"2025-05-14T09:29:40Z","ddc":["530"],"arxiv":1,"intvolume":"         5","OA_place":"publisher","citation":{"chicago":"Finžgar, Jernej Rudi, Aron Kerschbaumer, Martin J.A. Schuetz, Christian B. Mendl, and Helmut G. Katzgraber. “Quantum-Informed Recursive Optimization Algorithms.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PRXQuantum.5.020327\">https://doi.org/10.1103/PRXQuantum.5.020327</a>.","short":"J.R. Finžgar, A. Kerschbaumer, M.J.A. Schuetz, C.B. Mendl, H.G. Katzgraber, PRX Quantum 5 (2024).","mla":"Finžgar, Jernej Rudi, et al. “Quantum-Informed Recursive Optimization Algorithms.” <i>PRX Quantum</i>, vol. 5, no. 2, 020327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.020327\">10.1103/PRXQuantum.5.020327</a>.","ista":"Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. 2024. Quantum-informed recursive optimization algorithms. PRX Quantum. 5(2), 020327.","ama":"Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. Quantum-informed recursive optimization algorithms. <i>PRX Quantum</i>. 2024;5(2). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.020327\">10.1103/PRXQuantum.5.020327</a>","ieee":"J. R. Finžgar, A. Kerschbaumer, M. J. A. Schuetz, C. B. Mendl, and H. G. Katzgraber, “Quantum-informed recursive optimization algorithms,” <i>PRX Quantum</i>, vol. 5, no. 2. American Physical Society, 2024.","apa":"Finžgar, J. R., Kerschbaumer, A., Schuetz, M. J. A., Mendl, C. B., &#38; Katzgraber, H. G. (2024). Quantum-informed recursive optimization algorithms. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.5.020327\">https://doi.org/10.1103/PRXQuantum.5.020327</a>"},"DOAJ_listed":"1","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"We propose and implement a family of quantum-informed recursive optimization (QIRO) algorithms for combinatorial optimization problems. Our approach leverages quantum resources to obtain information that is used in problem-specific classical reduction steps that recursively simplify the problem. These reduction steps address the limitations of the quantum component (e.g., locality) and ensure solution feasibility in constrained optimization problems. Additionally, we use backtracking techniques to further improve the performance of the algorithm without increasing the requirements on the quantum hardware. We showcase the capabilities of our approach by informing QIRO with correlations from classical simulations of shallow circuits of the quantum approximate optimization algorithm, solving instances of maximum independent set and maximum satisfiability problems with hundreds of variables. We also demonstrate how QIRO can be deployed on a neutral atom quantum processor to find large independent sets of graphs. In summary, our scheme achieves results comparable to classical heuristics even with relatively weak quantum resources. Furthermore, enhancing the quality of these quantum resources improves the performance of the algorithms. Notably, the modular nature of QIRO offers various avenues for modifications, positioning our work as a template for a broader class of hybrid quantum-classical algorithms for combinatorial optimization.","lang":"eng"}],"external_id":{"arxiv":["2308.13607"]},"status":"public","has_accepted_license":"1","date_created":"2024-05-19T22:01:13Z","oa_version":"Published Version","scopus_import":"1","publication":"PRX Quantum","corr_author":"1","type":"journal_article"}]