[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley","article_type":"original","isi":1,"scopus_import":"1","issue":"3","date_created":"2025-03-19T09:45:11Z","OA_place":"publisher","acknowledgement":"This work was supported by funding from the Czech Science Foundation project no. 20-13587S to JP and SV, Charles University Grant Agency projects no. 289523 to KK and no. 393422 to VS, a DOC fellowship of the Austrian Academy of Sciences to AS, and the Austrian Science Fund (FWF): I 6123-B to JF. The authors acknowledge the Imaging Facility of the Institute of Experimental Botany AS CR supported by the MEYS CR (LM2023050 Czech-BioImaging), the Czech Academy of Sciences and IEB AS CR, and Viničná Microscopy Core Facility cofinanced by the Czech-BioImaging large RI project LM2023050. Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by the MEYS CR. The authors would like to thank Ilse Foissner and Margit Höftberger for discussing details of immunostaining protocol, Katarzyna Retzer and Jan Martinek for help with western blots, Anna Kampová for help with phosphoproteome sampling, Anja Holzhausen and MadLAnd for providing Chara braunii strain S276, and Roman Skokan for valuable discussion. Open access publishing facilitated by Univerzita Karlova, as part of the Wiley - CzechELib agreement.","language":[{"iso":"eng"}],"date_published":"2025-05-01T00:00:00Z","pmid":1,"page":"1066-1083","_id":"19423","intvolume":"       246","publication_identifier":{"issn":["1469-8137"]},"type":"journal_article","title":"The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JiFr"}],"author":[{"last_name":"Kurtović","first_name":"K","full_name":"Kurtović, K"},{"full_name":"Vosolsobě, S","last_name":"Vosolsobě","first_name":"S"},{"first_name":"D","last_name":"Nedvěd","full_name":"Nedvěd, D"},{"full_name":"Müller, K","last_name":"Müller","first_name":"K"},{"full_name":"Dobrev, PI","last_name":"Dobrev","first_name":"PI"},{"full_name":"Schmidt, V","first_name":"V","last_name":"Schmidt"},{"last_name":"Piszczek","first_name":"P","full_name":"Piszczek, P"},{"last_name":"Kuhn","first_name":"A","full_name":"Kuhn, A"},{"first_name":"Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b","last_name":"Smoljan","full_name":"Smoljan, Adrijana"},{"full_name":"Fisher, TJ","last_name":"Fisher","first_name":"TJ"},{"full_name":"Weijers, D","last_name":"Weijers","first_name":"D"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"JL","last_name":"Bowman","full_name":"Bowman, JL"},{"first_name":"J","last_name":"Petrášek","full_name":"Petrášek, J"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic roles in land plants, but its function and transport mechanisms in algae remain poorly understood. We therefore aimed to explore the role of IAA in a complex, streptophyte algae Chara braunii.\r\nHere, we described novel responses of C. braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa and CbPINc. We determined their localization in C. braunii using epitope-specific antibodies and tested their function in heterologous land plant models. Further, using phosphoproteomic analysis, we identified IAA-induced phosphorylation events.\r\nThe thallus regeneration assay showed that IAA promotes thallus elongation and side branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence on the plasma membrane of vegetative and generative cells of C. braunii. However, functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin transport, whereas CbPINc does not. The IAA is effective in the acceleration of cytoplasmic streaming and the phosphorylation of evolutionary conserved targets such as homolog of RAF-like kinase.\r\nThese findings suggest that, although canonical PIN-mediated auxin transport mechanisms might not be fully conserved in Chara, IAA is involved in morphogenesis and fast signaling processes."}],"external_id":{"isi":["001438711600001"],"pmid":["40047465"]},"citation":{"chicago":"Kurtović, K, S Vosolsobě, D Nedvěd, K Müller, PI Dobrev, V Schmidt, P Piszczek, et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” <i>New Phytologist</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/nph.70019\">https://doi.org/10.1111/nph.70019</a>.","ista":"Kurtović K, Vosolsobě S, Nedvěd D, Müller K, Dobrev P, Schmidt V, Piszczek P, Kuhn A, Smoljan A, Fisher T, Weijers D, Friml J, Bowman J, Petrášek J. 2025. The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. New Phytologist. 246(3), 1066–1083.","mla":"Kurtović, K., et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” <i>New Phytologist</i>, vol. 246, no. 3, Wiley, 2025, pp. 1066–83, doi:<a href=\"https://doi.org/10.1111/nph.70019\">10.1111/nph.70019</a>.","short":"K. Kurtović, S. Vosolsobě, D. Nedvěd, K. Müller, P. Dobrev, V. Schmidt, P. Piszczek, A. Kuhn, A. Smoljan, T. Fisher, D. Weijers, J. Friml, J. Bowman, J. Petrášek, New Phytologist 246 (2025) 1066–1083.","apa":"Kurtović, K., Vosolsobě, S., Nedvěd, D., Müller, K., Dobrev, P., Schmidt, V., … Petrášek, J. (2025). The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.70019\">https://doi.org/10.1111/nph.70019</a>","ama":"Kurtović K, Vosolsobě S, Nedvěd D, et al. The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii. <i>New Phytologist</i>. 2025;246(3):1066-1083. doi:<a href=\"https://doi.org/10.1111/nph.70019\">10.1111/nph.70019</a>","ieee":"K. Kurtović <i>et al.</i>, “The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii,” <i>New Phytologist</i>, vol. 246, no. 3. Wiley, pp. 1066–1083, 2025."},"year":"2025","has_accepted_license":"1","month":"05","publication":"New Phytologist","date_updated":"2025-09-30T11:11:18Z","ddc":["580"],"doi":"10.1111/nph.70019","status":"public","publication_status":"published","oa":1,"oa_version":"Published Version","OA_type":"hybrid","day":"01","article_processing_charge":"Yes (via OA deal)","volume":246,"file":[{"file_size":12841729,"date_updated":"2025-04-16T08:03:36Z","creator":"dernst","content_type":"application/pdf","file_id":"19571","file_name":"2025_NewPhytologist_Kurtovic.pdf","success":1,"date_created":"2025-04-16T08:03:36Z","relation":"main_file","checksum":"861c9bf47e7a7766ed03e6d85bd4f6dc","access_level":"open_access"}],"file_date_updated":"2025-04-16T08:03:36Z","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_type":"original","publisher":"Cambridge University Press","date_created":"2025-03-20T12:59:14Z","OA_place":"publisher","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"We would like to thank Timo Seppäläinen for some illuminating discussion about random high-dimensional orders and for bringing our attention to [59]. We would also like to thank the referees for helpful feedback. Michael Anastos is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413. Matthew Kwan is supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777, also funded by the European Union. Zhihan Jin and Benny Sudakov are supported by SNSF grant 200021-228014.","date_published":"2025-03-14T00:00:00Z","intvolume":"        13","_id":"19433","article_number":"e55","corr_author":"1","type":"journal_article","arxiv":1,"publication_identifier":{"issn":["2050-5094"]},"title":"Extremal, enumerative and probabilistic results on ordered hypergraph matchings","department":[{"_id":"MaKw"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos"},{"full_name":"Jin, Zhihan","last_name":"Jin","first_name":"Zhihan"},{"full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"abstract":[{"text":"An ordered r-matching is an r-uniform hypergraph matching equipped with an ordering on its vertices. These objects can be viewed as natural generalisations of r-dimensional orders. The theory of ordered 2-matchings is well developed and has connections and applications to extremal and enumerative combinatorics, probability and geometry. On the other hand, in the case  r≥3 much less is known, largely due to a lack of powerful bijective tools. Recently, Dudek, Grytczuk and Ruciński made some first steps towards a general theory of ordered r-matchings, and in this paper we substantially improve several of their results and introduce some new directions of study. Many intriguing open questions remain.","lang":"eng"}],"quality_controlled":"1","citation":{"chicago":"Anastos, Michael, Zhihan Jin, Matthew Alan Kwan, and Benny Sudakov. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2025. <a href=\"https://doi.org/10.1017/fms.2024.144\">https://doi.org/10.1017/fms.2024.144</a>.","mla":"Anastos, Michael, et al. “Extremal, Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” <i>Forum of Mathematics, Sigma</i>, vol. 13, e55, Cambridge University Press, 2025, doi:<a href=\"https://doi.org/10.1017/fms.2024.144\">10.1017/fms.2024.144</a>.","ista":"Anastos M, Jin Z, Kwan MA, Sudakov B. 2025. Extremal, enumerative and probabilistic results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 13, e55.","short":"M. Anastos, Z. Jin, M.A. Kwan, B. Sudakov, Forum of Mathematics, Sigma 13 (2025).","apa":"Anastos, M., Jin, Z., Kwan, M. A., &#38; Sudakov, B. (2025). Extremal, enumerative and probabilistic results on ordered hypergraph matchings. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2024.144\">https://doi.org/10.1017/fms.2024.144</a>","ama":"Anastos M, Jin Z, Kwan MA, Sudakov B. Extremal, enumerative and probabilistic results on ordered hypergraph matchings. <i>Forum of Mathematics, Sigma</i>. 2025;13. doi:<a href=\"https://doi.org/10.1017/fms.2024.144\">10.1017/fms.2024.144</a>","ieee":"M. Anastos, Z. Jin, M. A. Kwan, and B. Sudakov, “Extremal, enumerative and probabilistic results on ordered hypergraph matchings,” <i>Forum of Mathematics, Sigma</i>, vol. 13. Cambridge University Press, 2025."},"year":"2025","external_id":{"isi":["001444429200001"],"arxiv":["2308.12268"]},"has_accepted_license":"1","publication":"Forum of Mathematics, Sigma","month":"03","ec_funded":1,"date_updated":"2025-09-30T11:18:57Z","ddc":["510"],"publication_status":"published","status":"public","doi":"10.1017/fms.2024.144","oa":1,"OA_type":"gold","oa_version":"Published Version","volume":13,"article_processing_charge":"Yes","day":"14","file":[{"content_type":"application/pdf","date_updated":"2025-04-03T11:24:35Z","file_size":630297,"creator":"dernst","relation":"main_file","checksum":"f396270ad78c1ed67095c8e5a66fca26","access_level":"open_access","success":1,"file_id":"19468","file_name":"2025_ForumMathSigma_Anastos.pdf","date_created":"2025-04-03T11:24:35Z"}],"file_date_updated":"2025-04-03T11:24:35Z","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45","grant_number":"101076777"}]},{"article_number":"16","_id":"19436","intvolume":"         5","pmid":1,"date_published":"2025-03-04T00:00:00Z","acknowledgement":"We thank Prof. Ying Li of Nanjing Agricultural University for her help in providing seeds of K2 materials. This work was carried out with the support of National Natural Science Foundation of China (Grant No. 32070608).","language":[{"iso":"eng"}],"scopus_import":"1","OA_place":"publisher","date_created":"2025-03-23T23:01:25Z","article_type":"original","publisher":"Springer Nature","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Dynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants.","lang":"eng"}],"quality_controlled":"1","author":[{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"},{"first_name":"Di","last_name":"Wu","full_name":"Wu, Di"},{"last_name":"Zhang","first_name":"Yating","full_name":"Zhang, Yating"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"full_name":"Gao, Hongbo","first_name":"Hongbo","id":"77c2e73a-eabd-11ef-aee9-8093a2ba7a93","last_name":"Gao"}],"department":[{"_id":"XiFe"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"DNA methylation dynamics in male germline development in Brassica Rapa","publication_identifier":{"eissn":["2730-9401"]},"corr_author":"1","type":"journal_article","publication":"Molecular Horticulture","month":"03","has_accepted_license":"1","external_id":{"pmid":["40033451"],"isi":["001436233900001"]},"year":"2025","citation":{"apa":"Zhang, J., Wu, D., Zhang, Y., Feng, X., &#38; Gao, H. (2025). DNA methylation dynamics in male germline development in Brassica Rapa. <i>Molecular Horticulture</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s43897-024-00137-9\">https://doi.org/10.1186/s43897-024-00137-9</a>","ama":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline development in Brassica Rapa. <i>Molecular Horticulture</i>. 2025;5. doi:<a href=\"https://doi.org/10.1186/s43897-024-00137-9\">10.1186/s43897-024-00137-9</a>","chicago":"Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” <i>Molecular Horticulture</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s43897-024-00137-9\">https://doi.org/10.1186/s43897-024-00137-9</a>.","mla":"Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” <i>Molecular Horticulture</i>, vol. 5, 16, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s43897-024-00137-9\">10.1186/s43897-024-00137-9</a>.","ista":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. 5, 16.","short":"J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).","ieee":"J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics in male germline development in Brassica Rapa,” <i>Molecular Horticulture</i>, vol. 5. Springer Nature, 2025."},"file_date_updated":"2025-03-25T12:15:32Z","file":[{"date_created":"2025-03-25T12:15:32Z","file_name":"2025_MolecularHorticulture_Zhang.pdf","file_id":"19460","success":1,"access_level":"open_access","checksum":"6d1e0e9b0e1902e4a711f81c5c17a070","relation":"main_file","creator":"dernst","file_size":3014980,"date_updated":"2025-03-25T12:15:32Z","content_type":"application/pdf"}],"article_processing_charge":"Yes","day":"04","volume":5,"oa_version":"Published Version","OA_type":"gold","oa":1,"doi":"10.1186/s43897-024-00137-9","status":"public","publication_status":"published","ddc":["580"],"date_updated":"2025-09-30T11:17:08Z","DOAJ_listed":"1"},{"ddc":["530"],"status":"public","publication_status":"published","doi":"10.1103/PhysRevLett.134.096302","date_updated":"2025-09-30T11:17:58Z","volume":134,"article_processing_charge":"Yes (via OA deal)","day":"07","file_date_updated":"2025-03-25T12:37:07Z","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"},{"_id":"8fa7db46-16d5-11f0-9cad-917600954daf","name":"Polarons in Lead Halide Perovskites","grant_number":"12078"}],"file":[{"content_type":"application/pdf","file_size":708750,"date_updated":"2025-03-25T12:37:07Z","creator":"dernst","relation":"main_file","checksum":"1901efd7f95e8fe70cac412f91ea4da3","access_level":"open_access","file_id":"19461","file_name":"2025_PhysReviewLetters_Kluibenschedl.pdf","success":1,"date_created":"2025-03-25T12:37:07Z"}],"oa":1,"OA_type":"hybrid","oa_version":"Published Version","has_accepted_license":"1","year":"2025","citation":{"ieee":"F. Kluibenschedl, G. Koutentakis, R. Al Hyder, and M. Lemeshko, “Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model,” <i>Physical Review Letters</i>, vol. 134, no. 9. American Physical Society, 2025.","apa":"Kluibenschedl, F., Koutentakis, G., Al Hyder, R., &#38; Lemeshko, M. (2025). Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">https://doi.org/10.1103/PhysRevLett.134.096302</a>","ama":"Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. <i>Physical Review Letters</i>. 2025;134(9). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">10.1103/PhysRevLett.134.096302</a>","mla":"Kluibenschedl, Florian, et al. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” <i>Physical Review Letters</i>, vol. 134, no. 9, 096302, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">10.1103/PhysRevLett.134.096302</a>.","ista":"Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. 2025. Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review Letters. 134(9), 096302.","short":"F. Kluibenschedl, G. Koutentakis, R. Al Hyder, M. Lemeshko, Physical Review Letters 134 (2025).","chicago":"Kluibenschedl, Florian, Georgios Koutentakis, Ragheed Al Hyder, and Mikhail Lemeshko. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice Model.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.096302\">https://doi.org/10.1103/PhysRevLett.134.096302</a>."},"external_id":{"pmid":["40131090"],"isi":["001492808800010"],"arxiv":["2407.19993"]},"ec_funded":1,"month":"03","publication":"Physical Review Letters","title":"Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model","corr_author":"1","type":"journal_article","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"arxiv":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We demonstrate the formation of ferroelectric domain-wall polarons in a minimal two-dimensional lattice model of electrons interacting with rotating dipoles. Along the domain wall, the rotors polarize in opposite directions, causing the electron to localize along a particular lattice direction. The rotor-electron coupling is identified as the origin of a structural instability in the crystal that leads to the domain-wall formation via a symmetry-breaking process. Our results provide the first theoretical description of ferroelectric polarons, as discussed in the context of soft semiconductors."}],"department":[{"_id":"MiLe"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian"},{"last_name":"Koutentakis","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios","full_name":"Koutentakis, Georgios"},{"full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publisher":"American Physical Society","article_type":"original","pmid":1,"date_published":"2025-03-07T00:00:00Z","intvolume":"       134","_id":"19437","article_number":"096302","date_created":"2025-03-23T23:01:25Z","issue":"9","OA_place":"publisher","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"We thank, in alphabetical order, Zhanybek Alpichshev, Cesare Franchini, Areg Ghazaryan, Sebastian Maehrlein, and Artem Volosniev for fruitful discussions and comments. G. M. K. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. R. A. received funding from the Austrian Academy of Science ÖWA Grant No. PR1029OEAW03. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON)."},{"title":"Short INDELs and SNPs as markers of evolutionary processes in hybrid zones","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc/4.0/","corr_author":"1","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"abstract":[{"lang":"eng","text":"Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence."}],"quality_controlled":"1","department":[{"_id":"NiBa"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"author":[{"full_name":"Perini, Samuel","first_name":"Samuel","last_name":"Perini"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publisher":"Oxford University Press","article_type":"original","date_published":"2025-03-01T00:00:00Z","pmid":1,"intvolume":"        38","_id":"19438","page":"367-378","issue":"3","date_created":"2025-03-23T23:01:25Z","OA_place":"publisher","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Natural Environment Research Council (NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish Research Council VR (2018-03695) and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions. R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and the annotation. The bioinformatic analyses were performed on resources at the University of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous reviewers for helpful comments on a previous version.","ddc":["570"],"publication_status":"published","status":"public","doi":"10.1093/jeb/voaf002","date_updated":"2025-09-30T11:19:56Z","volume":38,"article_processing_charge":"Yes (in subscription journal)","day":"01","file_date_updated":"2025-04-03T11:53:06Z","file":[{"content_type":"application/pdf","date_updated":"2025-04-03T11:53:06Z","file_size":12826085,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"01408e626a4131bfec5ffc70b0af9129","success":1,"file_name":"2025_JourEvolBiology_Perini.pdf","file_id":"19469","date_created":"2025-04-03T11:53:06Z"}],"oa":1,"OA_type":"hybrid","oa_version":"Published Version","has_accepted_license":"1","year":"2025","citation":{"ieee":"S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs and SNPs as markers of evolutionary processes in hybrid zones,” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3. Oxford University Press, pp. 367–378, 2025.","short":"S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary Biology 38 (2025) 367–378.","mla":"Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3, Oxford University Press, 2025, pp. 367–78, doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>.","ista":"Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. 38(3), 367–378.","chicago":"Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>.","ama":"Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. 2025;38(3):367-378. doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>","apa":"Perini, S., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2025). Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>"},"external_id":{"isi":["001415267900001"],"pmid":["39803902"]},"month":"03","publication":"Journal of Evolutionary Biology"},{"external_id":{"isi":["001427877700001"],"arxiv":["2501.01490"]},"citation":{"ieee":"A. C. Rodriguez <i>et al.</i>, “A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj,” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 2. IOP Publishing, 2025.","chicago":"Rodriguez, Antonio C., Kareem El-Badry, Pasi Hakala, Pablo Rodríguez-Gil, Tong Bao, Ilkham Galiullin, Jacob A. Kurlander, et al. “A Link between White Dwarf Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">https://doi.org/10.1088/1538-3873/adb0f1</a>.","mla":"Rodriguez, Antonio C., et al. “A Link between White Dwarf Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 2, 024202, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">10.1088/1538-3873/adb0f1</a>.","short":"A.C. Rodriguez, K. El-Badry, P. Hakala, P. Rodríguez-Gil, T. Bao, I. Galiullin, J.A. Kurlander, C.J. Law, I. Pelisoli, M.R. Schreiber, K. Burdge, I. Caiazzo, J.V. Roestel, P. Szkody, A.J. Drake, D.A.H. Buckley, S.B. Potter, B. Gaensicke, K. Mori, E.C. Bellm, S.R. Kulkarni, T.A. Prince, M. Graham, M.M. Kasliwal, S. Rose, Y. Sharma, T. Ahumada, S. Anand, A. Viitanen, A. Wold, T.X. Chen, R. Riddle, R. Smith, Publications of the Astronomical Society of the Pacific 137 (2025).","ista":"Rodriguez AC, El-Badry K, Hakala P, Rodríguez-Gil P, Bao T, Galiullin I, Kurlander JA, Law CJ, Pelisoli I, Schreiber MR, Burdge K, Caiazzo I, Roestel JV, Szkody P, Drake AJ, Buckley DAH, Potter SB, Gaensicke B, Mori K, Bellm EC, Kulkarni SR, Prince TA, Graham M, Kasliwal MM, Rose S, Sharma Y, Ahumada T, Anand S, Viitanen A, Wold A, Chen TX, Riddle R, Smith R. 2025. A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. Publications of the Astronomical Society of the Pacific. 137(2), 024202.","apa":"Rodriguez, A. C., El-Badry, K., Hakala, P., Rodríguez-Gil, P., Bao, T., Galiullin, I., … Smith, R. (2025). A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">https://doi.org/10.1088/1538-3873/adb0f1</a>","ama":"Rodriguez AC, El-Badry K, Hakala P, et al. A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj. <i>Publications of the Astronomical Society of the Pacific</i>. 2025;137(2). doi:<a href=\"https://doi.org/10.1088/1538-3873/adb0f1\">10.1088/1538-3873/adb0f1</a>"},"year":"2025","has_accepted_license":"1","publication":"Publications of the Astronomical Society of the Pacific","month":"02","date_updated":"2025-09-30T11:15:10Z","doi":"10.1088/1538-3873/adb0f1","publication_status":"published","status":"public","ddc":["520"],"oa_version":"Published Version","OA_type":"hybrid","oa":1,"file_date_updated":"2025-03-25T10:01:24Z","file":[{"content_type":"application/pdf","file_size":3291933,"date_updated":"2025-03-25T10:01:24Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"42d5aa504479c3fdf2a10165a9e3319f","file_name":"2025_PubAstronomSocPacific_Rodriguez.pdf","file_id":"19455","success":1,"date_created":"2025-03-25T10:01:24Z"}],"article_processing_charge":"Yes (in subscription journal)","day":"01","volume":137,"article_type":"original","publisher":"IOP Publishing","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We wish to dedicate this work to the memory of our colleague and friend Tom Marsh. Tom's enthusiasm to work on this object and rapid efforts to facilitate data collection truly made this project possible.\r\n\r\nA.C.R. acknowledges support from an NSF Graduate Fellowship. A.C.R. thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation; his participation in the program has benefited this work. P.R.-G. acknowledges support by the Spanish Agencia Estatal de Investigación del Ministerio de Ciencia e Innovación (MCIN/AEI) and the European Regional Development Fund (ERDF) under grant PID2021–124879NB–I00. M.R.S. is supported by FONDECYT (grant No. 1221059) and eRO-STEP (SA 2131/15-2 project number 414059771). I.P. acknowledges support from a Royal Society University Research Fellowship (URF/R1/231496). We thank the referee for feedback that improved the clarity of this paper.\r\n\r\nBased on observations made with the Gran Telescopio Canarias (GTC), installed at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofìsica de Canarias, on the island of La Palma. Based on observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory as part of the ZTF project. ZTF is supported by the National Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration including current partners Caltech, IPAC, the Weizmann Institute of Science, the Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan, the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern University and former partners the University of Washington, Los Alamos National Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted by COO, IPAC, and UW.\r\n\r\nSome of the data presented herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit organization operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the Native Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We are also grateful to the staff of Palomar Observatory for their assistance in carrying out observations used in this work.\r\n\r\nPartly based on observations made with the NOT, owned in collaboration by the University of Turku and Aarhus University, and operated jointly by Aarhus University, the University of Turku and the University of Oslo, representing Denmark, Finland and Norway, the University of Iceland and Stockholm University at the Observatorio del Roque de los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias. The data presented here were obtained with ALFOSC, which is provided by the Instituto de Astrofisica de Andalucia (IAA) under a joint agreement with the University of Copenhagen and NOT. The observation with the SALT was obtained under program 2021-2-LSP-001 (PI: D. Buckley). Polish participation in SALT is funded by grant No. MEiN nr 2021/WK/01. D.A.H.B. acknowledges support from the National Research Foundation.\r\n\r\nThis work presents results from the European Space Agency (ESA) space mission Gaia. Gaia data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions, in particular the institutions participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia. This work made use of data supplied by the UK Swift Science Data Centre at the University of Leicester\r\n\r\nE.C.B. and J.K. acknowledge support from the DIRAC Institute in the Department of Astronomy at the University of Washington. The DIRAC Institute is supported through generous gifts from the Charles and Lisa Simonyi Fund for Arts and Sciences, and the Washington Research Foundation.","language":[{"iso":"eng"}],"scopus_import":"1","issue":"2","date_created":"2025-03-23T23:01:26Z","OA_place":"publisher","article_number":"024202","_id":"19439","intvolume":"       137","date_published":"2025-02-01T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["0004-6280"]},"type":"journal_article","title":"A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj","author":[{"full_name":"Rodriguez, Antonio C.","first_name":"Antonio C.","last_name":"Rodriguez"},{"full_name":"El-Badry, Kareem","last_name":"El-Badry","first_name":"Kareem"},{"full_name":"Hakala, Pasi","first_name":"Pasi","last_name":"Hakala"},{"first_name":"Pablo","last_name":"Rodríguez-Gil","full_name":"Rodríguez-Gil, Pablo"},{"full_name":"Bao, Tong","first_name":"Tong","last_name":"Bao"},{"full_name":"Galiullin, Ilkham","last_name":"Galiullin","first_name":"Ilkham"},{"first_name":"Jacob A.","last_name":"Kurlander","full_name":"Kurlander, Jacob A."},{"last_name":"Law","first_name":"Casey J.","full_name":"Law, Casey J."},{"first_name":"Ingrid","last_name":"Pelisoli","full_name":"Pelisoli, Ingrid"},{"full_name":"Schreiber, Matthias R.","last_name":"Schreiber","first_name":"Matthias R."},{"full_name":"Burdge, Kevin","last_name":"Burdge","first_name":"Kevin"},{"full_name":"Caiazzo, Ilaria","orcid":"0000-0002-4770-5388","first_name":"Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","last_name":"Caiazzo"},{"full_name":"Roestel, Jan Van","last_name":"Roestel","first_name":"Jan Van"},{"last_name":"Szkody","first_name":"Paula","full_name":"Szkody, Paula"},{"last_name":"Drake","first_name":"Andrew J.","full_name":"Drake, Andrew J."},{"first_name":"David A.H.","last_name":"Buckley","full_name":"Buckley, David A.H."},{"full_name":"Potter, Stephen B.","first_name":"Stephen B.","last_name":"Potter"},{"full_name":"Gaensicke, Boris","last_name":"Gaensicke","first_name":"Boris"},{"full_name":"Mori, Kaya","first_name":"Kaya","last_name":"Mori"},{"last_name":"Bellm","first_name":"Eric C.","full_name":"Bellm, Eric C."},{"full_name":"Kulkarni, Shrinivas R.","last_name":"Kulkarni","first_name":"Shrinivas R."},{"last_name":"Prince","first_name":"Thomas A.","full_name":"Prince, Thomas A."},{"full_name":"Graham, Matthew","first_name":"Matthew","last_name":"Graham"},{"last_name":"Kasliwal","first_name":"Mansi M.","full_name":"Kasliwal, Mansi M."},{"first_name":"Sam","last_name":"Rose","full_name":"Rose, Sam"},{"first_name":"Yashvi","last_name":"Sharma","full_name":"Sharma, Yashvi"},{"last_name":"Ahumada","first_name":"Tomás","full_name":"Ahumada, Tomás"},{"first_name":"Shreya","last_name":"Anand","full_name":"Anand, Shreya"},{"last_name":"Viitanen","first_name":"Akke","full_name":"Viitanen, Akke"},{"full_name":"Wold, Avery","last_name":"Wold","first_name":"Avery"},{"last_name":"Chen","first_name":"Tracy X.","full_name":"Chen, Tracy X."},{"last_name":"Riddle","first_name":"Reed","full_name":"Riddle, Reed"},{"full_name":"Smith, Roger","first_name":"Roger","last_name":"Smith"}],"department":[{"_id":"IlCa"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"White dwarfs (WDs) are the most abundant compact objects, and recent surveys have suggested that over a third of WDs in accreting binaries host a strong (B  ≳ 1 MG) magnetic field. However, the origin and evolution of WD magnetism remain under debate. Two WD pulsars, AR Sco and J191213.72–441045.1 (J1912), have been found, which are non-accreting binaries hosting rapidly spinning (1.97 minutes and 5.30 minutes, respectively) magnetic WDs. The WD in AR Sco is slowing down on a (math formular) yr timescale. It is believed they will eventually become polars, accreting systems in which a magnetic WD (B  ≈ 10−240 MG) accretes from a Roche lobe-filling donor spinning in sync with the orbit (≳78 minutes). Here, we present multiwavelength data and analysis of Gaia22ayj, which outbursted in 2022 March. We find that Gaia22ayj is a magnetic accreting WD that is rapidly spinning down (math formular\r\n yr) like WD pulsars, but shows clear evidence of accretion, like polars. Strong linear polarization (40%) is detected in Gaia22ayj; such high levels have only been seen in the WD pulsar AR Sco and demonstrate the WD is magnetic. High speed photometry reveals a 9.36 minutes period accompanying a high amplitude (∼2 mag) modulation. We associate this with a WD spin or spin–orbit beat period, not an orbital period as was previously suggested. Fast (60 s) optical spectroscopy reveals a broad \"hump,\" reminiscent of cyclotron emission in polars, between 4000 and 8000 Å. We find an X-ray luminosity of (math formular) in the 0.3–8 keV energy range, while two very large array radio campaigns resulted in a non-detection with a Fr < 15.8 μJy 3σ upper limit. The shared properties of both WD pulsars and polars suggest that Gaia22ayj is a missing link between the two classes of magnetic WD binaries."}]},{"date_published":"2025-03-01T00:00:00Z","_id":"19440","intvolume":"        66","article_number":"e21286","OA_place":"publisher","issue":"2","date_created":"2025-03-23T23:01:26Z","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"The authors would like to express their thanks to the referees of the article for their valuable input towards improving the presentation of our result. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_type":"original","publisher":"Wiley","quality_controlled":"1","abstract":[{"text":"Let μ(G) denote the minimum number of edges whose addition to G results in a Hamiltonian graph, and let μ^(G) denote the minimum number of edges whose addition to G results in a pancyclic graph. We study the distributions of μ(G),μ^(G) in the context of binomial random graphs. Letting d=d(n):=n⋅p, we prove that there exists a function f:R+→[0,1] of order f(d)=12de−d+e−d+O(d6e−3d) such that, if G∼G(n,p) with 20≤d(n)≤0.4logn, then with high probability μ(G)=(1+o(1))⋅f(d)⋅n. Let ni(G) denote the number of degree i vertices in G. A trivial lower bound on μ(G) is given by the expression n0(G)+⌈12n1(G)⌉. In the denser regime of random graphs, we show that if np−13logn−2loglogn→∞ and G∼G(n,p) then, with high probability, μ(G)=n0(G)+⌈12n1(G)⌉. For completion to pancyclicity, we show that if G∼G(n,p) and np≥20 then, with high probability, μ^(G)=μ(G). Finally, we present a polynomial time algorithm such that, if G∼G(n,p) and np≥20, then, with high probability, the algorithm returns a set of edges of size μ(G) whose addition to G results in a pancyclic (and therefore also Hamiltonian) graph.","lang":"eng"}],"department":[{"_id":"MaKw"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"author":[{"full_name":"Alon, Yahav","first_name":"Yahav","last_name":"Alon"},{"full_name":"Anastos, Michael","first_name":"Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos"}],"title":"The completion numbers of hamiltonicity and pancyclicity in random graphs","type":"journal_article","arxiv":1,"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"ec_funded":1,"month":"03","publication":"Random Structures and Algorithms","has_accepted_license":"1","year":"2025","citation":{"chicago":"Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/rsa.21286\">https://doi.org/10.1002/rsa.21286</a>.","ista":"Alon Y, Anastos M. 2025. The completion numbers of hamiltonicity and pancyclicity in random graphs. Random Structures and Algorithms. 66(2), e21286.","short":"Y. Alon, M. Anastos, Random Structures and Algorithms 66 (2025).","mla":"Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>, vol. 66, no. 2, e21286, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/rsa.21286\">10.1002/rsa.21286</a>.","apa":"Alon, Y., &#38; Anastos, M. (2025). The completion numbers of hamiltonicity and pancyclicity in random graphs. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21286\">https://doi.org/10.1002/rsa.21286</a>","ama":"Alon Y, Anastos M. The completion numbers of hamiltonicity and pancyclicity in random graphs. <i>Random Structures and Algorithms</i>. 2025;66(2). doi:<a href=\"https://doi.org/10.1002/rsa.21286\">10.1002/rsa.21286</a>","ieee":"Y. Alon and M. Anastos, “The completion numbers of hamiltonicity and pancyclicity in random graphs,” <i>Random Structures and Algorithms</i>, vol. 66, no. 2. Wiley, 2025."},"external_id":{"isi":["001420226800001"],"arxiv":["2304.03710"]},"volume":66,"day":"01","article_processing_charge":"Yes (in subscription journal)","file":[{"success":1,"file_name":"2025_RandomStruc_Alon.pdf","file_id":"19459","date_created":"2025-03-25T11:46:27Z","relation":"main_file","checksum":"6067747e805fa356d560dc45f2a89918","access_level":"open_access","date_updated":"2025-03-25T11:46:27Z","file_size":549236,"creator":"dernst","content_type":"application/pdf"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"file_date_updated":"2025-03-25T11:46:27Z","oa":1,"OA_type":"hybrid","oa_version":"Published Version","ddc":["510"],"publication_status":"published","status":"public","doi":"10.1002/rsa.21286","date_updated":"2025-09-30T11:15:41Z"},{"month":"03","publication":"ACS Nano","external_id":{"isi":["001443359300001"],"pmid":["40069094"]},"year":"2025","citation":{"ama":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. 2025;19(11):11133-11145. doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>","apa":"Carrasco, C., Martinet, Q., Shen, Z., Lintuvuori, J., Palacci, J. A., &#38; Aubret, A. (2025). Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>","chicago":"Carrasco, Celso, Quentin Martinet, Zaiyi Shen, Juho Lintuvuori, Jérémie A Palacci, and Antoine Aubret. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>.","ista":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. 2025. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. ACS Nano. 19(11), 11133–11145.","mla":"Carrasco, Celso, et al. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>, vol. 19, no. 11, American Chemical Society, 2025, pp. 11133–45, doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>.","short":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J.A. Palacci, A. Aubret, ACS Nano 19 (2025) 11133–11145.","ieee":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J. A. Palacci, and A. Aubret, “Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers,” <i>ACS Nano</i>, vol. 19, no. 11. American Chemical Society, pp. 11133–11145, 2025."},"oa":1,"oa_version":"Submitted Version","OA_type":"green","day":"11","article_processing_charge":"No","volume":19,"project":[{"grant_number":"P35206","name":"Emergent Behavior in Spinning Active Matter","_id":"eb99c9bb-77a9-11ec-83b8-9f8cffa20a35"}],"date_updated":"2025-10-16T10:26:59Z","doi":"10.1021/acsnano.4c18078","status":"public","publication_status":"published","scopus_import":"1","OA_place":"repository","issue":"11","date_created":"2025-03-23T23:01:26Z","acknowledgement":"The authors thank M. Perrin and A. Allard for enlightening discussions. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/P35206]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No. 886024.","language":[{"iso":"eng"}],"date_published":"2025-03-11T00:00:00Z","pmid":1,"page":"11133-11145","_id":"19441","intvolume":"        19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","article_type":"original","isi":1,"department":[{"_id":"JePa"}],"author":[{"last_name":"Carrasco","first_name":"Celso","full_name":"Carrasco, Celso"},{"full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","last_name":"Martinet"},{"full_name":"Shen, Zaiyi","last_name":"Shen","first_name":"Zaiyi"},{"first_name":"Juho","last_name":"Lintuvuori","full_name":"Lintuvuori, Juho"},{"last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"},{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"}],"abstract":[{"lang":"eng","text":"Catalytic microswimmers convert the chemical energy from fuel into motion. They sustain chemical gradients and fluid flows that propel them by phoresis. This leads to unconventional behavior and collective dynamics, such as self-organization into complex structures. Characterizing the nonequilibrium interactions of microswimmers is crucial for advancing our understanding of active systems. However, this remains a challenge owing to the importance of fluctuations at the microscale and the difficulty in disentangling the different contributions to the interactions. Here, we show a massive dependence of the nonequilibrium interactions on the shape of catalytic microswimmers. We perform tracking experiments at high throughput to map interactions between nanocolloidal tracers and dimeric microswimmers of various aspect ratios. Our method leverages dual tracers with differing phoretic mobilities to quantitatively disentangle phoretic motion from hydrodynamic advection. This approach is validated through experiments on single chemically active sites and on immobilized catalytic microswimmers. We further investigate the activity-driven interactions of free microswimmers and directly measure their phoretic interactions. When compared to standard models, our findings highlight the important role of osmotic flows for microswimmers near surfaces and reveal an enhanced contribution of hydrodynamic advection relative to phoretic motion as the size of the microswimmer increases. Our study provides robust measurements of the nonequilibrium interactions from catalytic microswimmers and lays the groundwork for a realistic description of active systems."}],"quality_controlled":"1","main_file_link":[{"url":"https://hal.science/hal-04682818v2","open_access":"1"}],"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"type":"journal_article","title":"Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"1. Climate change is expected to induce shifts in the composition, structure and functioning of Arctic tundra ecosystems. Increases in the frequency and severity of tundra fires have the potential to catalyse vegetation transitions with far-reaching local, regional and global consequences.\r\n2. We propose that post-fire tundra recovery, coupled with climate change, may not necessarily lead to pre-fire conditions. Our hypothesis, based on surveys and literature, suggests two climate–fire driven trajectories. One trajectory results in increased woody vegetation under low fire frequency; the other results in grass dominance under high frequency.\r\n3. Future research should address uncertainties regarding possible tundra ecosystem shifts linked to fires, using methods that encompass greater temporal and spatial scales than previously addressed. More case studies, especially in underrepresented regions and ecosystem types, are essential to broaden the empirical basis for forecasts and potential fire management strategies.\r\n4. Synthesis. Our review synthesises current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems, highlighting potential transitions and alternative ecosystem states and their implications. We discuss challenges in defining and predicting these trajectories as well as future directions."}],"author":[{"first_name":"Ramona Julia","last_name":"Heim","full_name":"Heim, Ramona Julia"},{"last_name":"Rocha","first_name":"Adrian V.","full_name":"Rocha, Adrian V."},{"full_name":"Zemlianskii, Vitalii","last_name":"Zemlianskii","first_name":"Vitalii"},{"full_name":"Barrett, Kirsten","first_name":"Kirsten","last_name":"Barrett"},{"full_name":"Bültmann, Helga","last_name":"Bültmann","first_name":"Helga"},{"full_name":"Breen, Amy","first_name":"Amy","last_name":"Breen"},{"first_name":"Gerald Verner","last_name":"Frost","full_name":"Frost, Gerald Verner"},{"full_name":"Hollingsworth, Teresa Nettleton","last_name":"Hollingsworth","first_name":"Teresa Nettleton"},{"last_name":"Jandt","first_name":"Randi","full_name":"Jandt, Randi"},{"last_name":"Kozlova","first_name":"Maria","full_name":"Kozlova, Maria"},{"full_name":"Kurka, Anastasiya","last_name":"Kurka","first_name":"Anastasiya"},{"full_name":"Jorgenson, Mark Torre","last_name":"Jorgenson","first_name":"Mark Torre"},{"first_name":"Simon M.","last_name":"Landhäusser","full_name":"Landhäusser, Simon M."},{"first_name":"Michael Mark","last_name":"Loranty","full_name":"Loranty, Michael Mark"},{"full_name":"Miller, Eric A.","first_name":"Eric A.","last_name":"Miller"},{"last_name":"Narita","first_name":"Kenji","full_name":"Narita, Kenji"},{"last_name":"Pravdolyubova","first_name":"Evgeniya","id":"0b30719b-13f0-11ed-ab2a-94498bc6a278","full_name":"Pravdolyubova, Evgeniya"},{"full_name":"Hölzel, Norbert","first_name":"Norbert","last_name":"Hölzel"},{"first_name":"Gabriela","last_name":"Schaepman-Strub","full_name":"Schaepman-Strub, Gabriela"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"}],"title":"Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?","type":"journal_article","publication_identifier":{"issn":["0022-0477"],"eissn":["1365-2745"]},"intvolume":"       113","_id":"19442","page":"1042-1056","date_published":"2025-05-01T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"We would like to express our sincere gratitude to all the data providers who carried out fieldwork in different regions of the Arctic and published their data, which we used for our meta-analysis. We recognise the hard work and dedication of these individuals, without whom this paper would not have been possible. We are grateful to the editor and the anonymous reviewer for their time and valuable feedback on this manuscript. We particularly appreciate the detailed and constructive comments provided by reviewer Mara Baudena, which significantly strengthened our work. We also acknowledge the Indigenous peoples and rural communities of the Arctic, whose traditional knowledge, rights, and interests are integral to the stewardship and study of these ecosystems. This work was funded in part by the U.S. National Aeronautics and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled and organized by Projekt DEAL.","date_created":"2025-03-23T23:01:27Z","issue":"5","OA_place":"publisher","scopus_import":"1","isi":1,"article_type":"review","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-12-30T08:08:18Z","file":[{"content_type":"application/pdf","file_size":2662766,"date_updated":"2025-12-30T08:08:18Z","creator":"dernst","relation":"main_file","checksum":"e2785ae265e211b4dc7fc9c5b7744948","access_level":"open_access","file_id":"20890","file_name":"2025_JournEcology_Heim.pdf","success":1,"date_created":"2025-12-30T08:08:18Z"}],"volume":113,"article_processing_charge":"Yes (via OA deal)","day":"01","OA_type":"hybrid","oa_version":"Published Version","oa":1,"status":"public","PlanS_conform":"1","publication_status":"published","doi":"10.1111/1365-2745.70022","ddc":["550","570"],"date_updated":"2025-12-30T08:09:47Z","month":"05","publication":"Journal of Ecology","has_accepted_license":"1","citation":{"ieee":"R. J. Heim <i>et al.</i>, “Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?,” <i>Journal of Ecology</i>, vol. 113, no. 5. Wiley, pp. 1042–1056, 2025.","ama":"Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. 2025;113(5):1042-1056. doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>","apa":"Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen, A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>","ista":"Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV, Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? Journal of Ecology. 113(5), 1042–1056.","short":"R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen, G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson, S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel, G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.","mla":"Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>, vol. 113, no. 5, Wiley, 2025, pp. 1042–56, doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>.","chicago":"Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett, Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>."},"year":"2025","external_id":{"isi":["001443422900001"]}},{"has_accepted_license":"1","external_id":{"pmid":["39947174"],"isi":["001463196100001"]},"citation":{"ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.","apa":"Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>","ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4. doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>","chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4."},"year":"2025","month":"04","publication":"Structure","doi":"10.1016/j.str.2025.01.020","PlanS_conform":"1","publication_status":"published","status":"public","ddc":["570"],"date_updated":"2025-09-30T11:13:02Z","file_date_updated":"2025-08-05T12:15:13Z","file":[{"content_type":"application/pdf","creator":"dernst","date_updated":"2025-08-05T12:15:13Z","file_size":4367530,"access_level":"open_access","checksum":"f346bc357a66a88cca3d0eb95793fb73","relation":"main_file","date_created":"2025-08-05T12:15:13Z","success":1,"file_name":"2025_Structure_Harar.pdf","file_id":"20130"}],"day":"03","article_processing_charge":"Yes (in subscription journal)","volume":33,"oa_version":"Published Version","OA_type":"hybrid","oa":1,"article_type":"original","publisher":"Elsevier","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"820-827.e4","_id":"19443","intvolume":"        33","date_published":"2025-04-03T00:00:00Z","pmid":1,"acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2025-03-23T23:01:27Z","issue":"4","OA_place":"publisher","title":"FakET: Simulating cryo-electron tomograms with neural style transfer","related_material":{"link":[{"relation":"software","url":"https://github.com/paloha/faket/"}]},"publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"corr_author":"1","type":"journal_article","abstract":[{"text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.","lang":"eng"}],"quality_controlled":"1","author":[{"full_name":"Harar, Pavol","first_name":"Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","orcid":"0000-0001-5206-1794","last_name":"Harar"},{"full_name":"Herrmann, Lukas","first_name":"Lukas","last_name":"Herrmann"},{"full_name":"Grohs, Philipp","last_name":"Grohs","first_name":"Philipp"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"AlMi"}]},{"OA_type":"closed access","oa_version":"None","volume":639,"article_processing_charge":"No","day":"13","date_updated":"2025-09-30T11:13:47Z","publication_status":"published","status":"public","doi":"10.1038/s41586-024-08487-6","publication":"Nature","month":"03","citation":{"ieee":"S. P. Pașca <i>et al.</i>, “A framework for neural organoids, assembloids and transplantation studies,” <i>Nature</i>, vol. 639, no. 8054. Springer Nature, pp. 315–320, 2025.","mla":"Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>, vol. 639, no. 8054, Springer Nature, 2025, pp. 315–20, doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>.","short":"S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A. Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M. Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G. Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature 639 (2025) 315–320.","ista":"Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054), 315–320.","chicago":"Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>.","apa":"Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage, F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>","ama":"Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. 2025;639(8054):315-320. doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>"},"year":"2025","external_id":{"isi":["001437461900001"],"pmid":["39653126"]},"department":[{"_id":"GaNo"}],"author":[{"full_name":"Pașca, Sergiu P.","first_name":"Sergiu P.","last_name":"Pașca"},{"full_name":"Arlotta, Paola","first_name":"Paola","last_name":"Arlotta"},{"full_name":"Bateup, Helen S.","last_name":"Bateup","first_name":"Helen S."},{"full_name":"Camp, J. Gray","first_name":"J. Gray","last_name":"Camp"},{"full_name":"Cappello, Silvia","first_name":"Silvia","last_name":"Cappello"},{"full_name":"Gage, Fred H.","last_name":"Gage","first_name":"Fred H."},{"full_name":"Knoblich, Jürgen A.","last_name":"Knoblich","first_name":"Jürgen A."},{"first_name":"Arnold R.","last_name":"Kriegstein","full_name":"Kriegstein, Arnold R."},{"full_name":"Lancaster, Madeline A.","last_name":"Lancaster","first_name":"Madeline A."},{"full_name":"Ming, Guo Li","first_name":"Guo Li","last_name":"Ming"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"},{"last_name":"Okano","first_name":"Hideyuki","full_name":"Okano, Hideyuki"},{"first_name":"Malin","last_name":"Parmar","full_name":"Parmar, Malin"},{"full_name":"Park, In Hyun","first_name":"In Hyun","last_name":"Park"},{"first_name":"Orly","last_name":"Reiner","full_name":"Reiner, Orly"},{"full_name":"Song, Hongjun","last_name":"Song","first_name":"Hongjun"},{"first_name":"Lorenz","last_name":"Studer","full_name":"Studer, Lorenz"},{"full_name":"Takahashi, Jun","first_name":"Jun","last_name":"Takahashi"},{"first_name":"Sally","last_name":"Temple","full_name":"Temple, Sally"},{"full_name":"Testa, Giuseppe","first_name":"Giuseppe","last_name":"Testa"},{"last_name":"Treutlein","first_name":"Barbara","full_name":"Treutlein, Barbara"},{"last_name":"Vaccarino","first_name":"Flora M.","full_name":"Vaccarino, Flora M."},{"first_name":"Pierre","last_name":"Vanderhaeghen","full_name":"Vanderhaeghen, Pierre"},{"last_name":"Young-Pearse","first_name":"Tracy","full_name":"Young-Pearse, Tracy"}],"abstract":[{"text":"As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"title":"A framework for neural organoids, assembloids and transplantation studies","date_created":"2025-03-23T23:01:27Z","issue":"8054","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"The authors thank members of their laboratories who provided feedback on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L. Li, N. Caporale, E. Villa and M. Sutcliffe.","pmid":1,"date_published":"2025-03-13T00:00:00Z","intvolume":"       639","_id":"19444","page":"315-320","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publisher":"Springer Nature","article_type":"original"},{"language":[{"iso":"eng"}],"acknowledgement":"J. M. Křišťan acknowledges the support of the Czech Science Foundation Grant No. 24-12046S. This work was supported by the Grant Agency of the Czech Technical University in Prague, grant No. SGS23/205/OHK3/3T/18. J. Svoboda acknowledges the support of the ERC CoG 863818 (ForM-SMArt) grant.","OA_place":"repository","date_created":"2025-03-23T23:01:27Z","scopus_import":"1","_id":"19445","intvolume":"     15411","alternative_title":["LNCS"],"page":"244-265","date_published":"2025-02-20T00:00:00Z","isi":1,"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"location":"Chengdu, China","name":"WALCOM: International Conference and Workshops on Algorithms and Computation","start_date":"2025-02-28","end_date":"2025-03-02"},"author":[{"full_name":"Křišťan, Jan Matyáš","first_name":"Jan Matyáš","last_name":"Křišťan"},{"orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"In reconfiguration, we are given two solutions to a graph problem, such as Vertex Cover or Dominating Set, with each solution represented by a placement of tokens on vertices of the graph. Our task is to reconfigure one into the other using small steps while ensuring the intermediate configurations of tokens are also valid solutions. The two commonly studied settings are Token Jumping and Token Sliding, which allows moving a single token to an arbitrary or an adjacent vertex, respectively.\r\n\r\nWe introduce new rules that generalize Token Jumping, parameterized by the number of tokens allowed to move at once and by the maximum distance of each move. Our main contribution is identifying minimal rules that allow reconfiguring any possible given solution into any other for Independent Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide an efficient algorithm that finds a corresponding reconfiguration sequence.\r\n\r\nWe further focus on the rule that allows each token to move to an adjacent vertex in a single step. This natural variant turns out to be the minimal rule that guarantees reconfigurability for Vertex Cover. We determine the computational complexity of deciding whether a (shortest) reconfiguration sequence exists under this rule for the three studied problems. While reachability for Vertex Cover is shown to be in P, finding a shortest sequence is shown to be NP-complete. For Independent Set and Dominating Set, even reachability is shown to be PSPACE-complete.","lang":"eng"}],"quality_controlled":"1","type":"conference","arxiv":1,"publication_identifier":{"isbn":["9789819628445"],"eissn":["1611-3349"],"issn":["0302-9743"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2411.12582"}],"title":"Reconfiguration using generalized token jumping","month":"02","publication":"19th International Conference and Workshops on Algorithms and Computation","ec_funded":1,"citation":{"ieee":"J. M. Křišťan and J. Svoboda, “Reconfiguration using generalized token jumping,” in <i>19th International Conference and Workshops on Algorithms and Computation</i>, Chengdu, China, 2025, vol. 15411, pp. 244–265.","chicago":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” In <i>19th International Conference and Workshops on Algorithms and Computation</i>, 15411:244–65. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>.","mla":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” <i>19th International Conference and Workshops on Algorithms and Computation</i>, vol. 15411, Springer Nature, 2025, pp. 244–65, doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>.","short":"J.M. Křišťan, J. Svoboda, in:, 19th International Conference and Workshops on Algorithms and Computation, Springer Nature, 2025, pp. 244–265.","ista":"Křišťan JM, Svoboda J. 2025. Reconfiguration using generalized token jumping. 19th International Conference and Workshops on Algorithms and Computation. WALCOM: International Conference and Workshops on Algorithms and Computation, LNCS, vol. 15411, 244–265.","ama":"Křišťan JM, Svoboda J. Reconfiguration using generalized token jumping. In: <i>19th International Conference and Workshops on Algorithms and Computation</i>. Vol 15411. Springer Nature; 2025:244-265. doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>","apa":"Křišťan, J. M., &#38; Svoboda, J. (2025). Reconfiguration using generalized token jumping. In <i>19th International Conference and Workshops on Algorithms and Computation</i> (Vol. 15411, pp. 244–265). Chengdu, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>"},"year":"2025","external_id":{"arxiv":["2411.12582"],"isi":["001537885900016"]},"OA_type":"green","oa_version":"Preprint","oa":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"volume":15411,"article_processing_charge":"No","day":"20","date_updated":"2025-09-30T11:14:33Z","publication_status":"published","status":"public","doi":"10.1007/978-981-96-2845-2_16"},{"file":[{"file_size":1553502,"date_updated":"2025-03-25T07:49:04Z","creator":"dernst","content_type":"application/pdf","file_id":"19454","file_name":"2025_PNAS_Chiossi.pdf","success":1,"date_created":"2025-03-25T07:49:04Z","relation":"main_file","access_level":"open_access","checksum":"1217207c254553154faa065964990988"}],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"file_date_updated":"2025-03-25T07:49:04Z","day":"10","article_processing_charge":"Yes (in subscription journal)","volume":122,"oa_version":"Published Version","OA_type":"hybrid","oa":1,"doi":"10.1073/pnas.2417025122","publication_status":"published","status":"public","ddc":["570"],"date_updated":"2026-05-06T13:12:01Z","ec_funded":1,"month":"03","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","external_id":{"pmid":["40063792"],"isi":["001459499500001"]},"year":"2025","citation":{"apa":"Chiossi, H. S. C., Nardin, M., Tkačik, G., &#38; Csicsvari, J. L. (2025). Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>","ama":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(11). doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>","mla":"Chiossi, Heloisa S. C., et al. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11, e2417025122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>.","short":"H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the National Academy of Sciences 122 (2025).","ista":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. 2025. Learning reshapes the hippocampal representation hierarchy. Proceedings of the National Academy of Sciences. 122(11), e2417025122.","chicago":"Chiossi, Heloisa S. C., Michele Nardin, Gašper Tkačik, and Jozsef L Csicsvari. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>.","ieee":"H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes the hippocampal representation hierarchy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11. National Academy of Sciences, 2025."},"quality_controlled":"1","abstract":[{"lang":"eng","text":"A key feature of biological and artificial neural networks is the progressive refinement of their neural representations with experience. In neuroscience, this fact has inspired several recent studies in sensory and motor systems. However, less is known about how higher associational cortical areas, such as the hippocampus, modify representations throughout the learning of complex tasks. Here, we focus on associative learning, a process that requires forming a connection between the representations of different variables for appropriate behavioral response. We trained rats in a space-context associative task and monitored hippocampal neural activity throughout the entire learning period, over several days. This allowed us to assess changes in the representations of context, movement direction, and position, as well as their relationship to behavior. We identified a hierarchical representational structure in the encoding of these three task variables that was preserved throughout learning. Nevertheless, we also observed changes at the lower levels of the hierarchy where context was encoded. These changes were local in neural activity space and restricted to physical positions where context identification was necessary for correct decision-making, supporting better context decoding and contextual code compression. Our results demonstrate that the hippocampal code not only accommodates hierarchical relationships between different variables but also enables efficient learning through minimal changes in neural activity space. Beyond the hippocampus, our work reveals a representation learning mechanism that might be implemented in other biological and artificial networks performing similar tasks."}],"author":[{"first_name":"Heloisa","orcid":"0009-0004-2973-278X","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi","full_name":"Chiossi, Heloisa"},{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","last_name":"Nardin","full_name":"Nardin, Michele"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"department":[{"_id":"GaTk"},{"_id":"JoCs"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Learning reshapes the hippocampal representation hierarchy","related_material":{"record":[{"id":"18991","relation":"research_data","status":"public"}],"link":[{"relation":"software","url":"https://github.com/hchiossi/hpc-hierarchy"}]},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"corr_author":"1","type":"journal_article","article_number":"e2417025122","_id":"19453","intvolume":"       122","pmid":1,"date_published":"2025-03-10T00:00:00Z","acknowledgement":"We would like to thank Rebecca Morse for performing the recordings in one of the animals under the supervision of H.S.C.C., Jago Wallenschus for the technical support, especially with maze design, Wiktor Mlynarski for the advice and discussions and Andrea Cumpelik for suggestions during the writing. M.N. was supported by the Howard Hughes Medical Institute. H.S.C.C. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665385.","language":[{"iso":"eng"}],"scopus_import":"1","issue":"11","OA_place":"publisher","date_created":"2025-03-25T07:38:35Z","publisher":"National Academy of Sciences","APC_amount":"3317,75 EUR","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Nature Reviews Molecular Cell Biology","month":"06","external_id":{"pmid":["40155512"],"isi":["001455740100001"]},"year":"2025","citation":{"ieee":"C. Bernecky, “Understanding the machinery that reads the genome,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 26. Springer Nature, 2025.","apa":"Bernecky, C. (2025). Understanding the machinery that reads the genome. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-025-00844-1\">https://doi.org/10.1038/s41580-025-00844-1</a>","ama":"Bernecky C. Understanding the machinery that reads the genome. <i>Nature Reviews Molecular Cell Biology</i>. 2025;26. doi:<a href=\"https://doi.org/10.1038/s41580-025-00844-1\">10.1038/s41580-025-00844-1</a>","chicago":"Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41580-025-00844-1\">https://doi.org/10.1038/s41580-025-00844-1</a>.","short":"C. Bernecky, Nature Reviews Molecular Cell Biology 26 (2025).","ista":"Bernecky C. 2025. Understanding the machinery that reads the genome. Nature Reviews Molecular Cell Biology. 26, 415.","mla":"Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 26, 415, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41580-025-00844-1\">10.1038/s41580-025-00844-1</a>."},"day":"01","article_processing_charge":"No","volume":26,"oa_version":"None","OA_type":"closed access","doi":"10.1038/s41580-025-00844-1","publication_status":"published","status":"public","date_updated":"2025-09-30T11:20:36Z","article_number":"415","_id":"19465","intvolume":"        26","date_published":"2025-06-01T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2025-03-31T10:07:22Z","article_type":"letter_note","publisher":"Springer Nature","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","author":[{"full_name":"Bernecky, Carrie A","last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036"}],"department":[{"_id":"CaBe"}],"title":"Understanding the machinery that reads the genome","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"type":"journal_article","corr_author":"1"},{"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"author":[{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13212"},{"status":"public","relation":"part_of_dissertation","id":"19421"}]},"title":"The cAMP second messenger in auxin signalling","corr_author":"1","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_published":"2025-04-04T00:00:00Z","alternative_title":["ISTA Thesis"],"_id":"19478","page":"118","OA_place":"publisher","date_created":"2025-04-04T07:48:24Z","language":[{"iso":"eng"}],"acknowledgement":"This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B).","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","day":"04","article_processing_charge":"No","file":[{"creator":"hchen","date_updated":"2025-04-08T08:22:37Z","file_size":16344814,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-04-08T08:00:07Z","file_name":"Thesis_0403_Huihuang.docx","file_id":"19526","checksum":"b154973663a1bba505683faab7ae5ead","access_level":"closed","relation":"source_file"},{"date_created":"2025-04-08T08:00:06Z","embargo_to":"local","file_name":"Thesis_0406_PDFA_Huihuang_1.pdf","file_id":"19527","checksum":"0099565f024388830c125ec17375c1a0","access_level":"closed","relation":"main_file","creator":"hchen","date_updated":"2025-04-09T13:53:38Z","file_size":8482147,"content_type":"application/pdf","embargo":"2026-10-08"}],"file_date_updated":"2025-04-09T13:53:38Z","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"},{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"oa_version":"Published Version","ddc":["580"],"publication_status":"published","status":"public","doi":"10.15479/AT-ISTA-19478","date_updated":"2026-04-28T13:42:45Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"04","degree_awarded":"PhD","has_accepted_license":"1","citation":{"apa":"Chen, H. (2025). <i>The cAMP second messenger in auxin signalling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>","ama":"Chen H. The cAMP second messenger in auxin signalling. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>","mla":"Chen, Huihuang. <i>The CAMP Second Messenger in Auxin Signalling</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>.","short":"H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025.","ista":"Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria.","chicago":"Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>.","ieee":"H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025."},"year":"2025","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}]},{"publication":"Annali della Scuola Normale Superiore di Pisa, Classe di Scienze","month":"03","citation":{"ieee":"S. Chan, P. Koymans, C. Pagano, and E. Sofos, “6-torision and integral points on quartic threefolds,” <i>Annali della Scuola Normale Superiore di Pisa, Classe di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale, 2025.","ama":"Chan S, Koymans P, Pagano C, Sofos E. 6-torision and integral points on quartic threefolds. <i>Annali della Scuola Normale Superiore di Pisa, Classe di Scienze</i>. 2025. doi:<a href=\"https://doi.org/10.2422/2036-2145.202412_006\">10.2422/2036-2145.202412_006</a>","apa":"Chan, S., Koymans, P., Pagano, C., &#38; Sofos, E. (2025). 6-torision and integral points on quartic threefolds. <i>Annali Della Scuola Normale Superiore Di Pisa, Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale. <a href=\"https://doi.org/10.2422/2036-2145.202412_006\">https://doi.org/10.2422/2036-2145.202412_006</a>","chicago":"Chan, Stephanie, Peter Koymans, Carlo Pagano, and Efthymios Sofos. “6-Torision and Integral Points on Quartic Threefolds.” <i>Annali Della Scuola Normale Superiore Di Pisa, Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale, 2025. <a href=\"https://doi.org/10.2422/2036-2145.202412_006\">https://doi.org/10.2422/2036-2145.202412_006</a>.","ista":"Chan S, Koymans P, Pagano C, Sofos E. 2025. 6-torision and integral points on quartic threefolds. Annali della Scuola Normale Superiore di Pisa, Classe di Scienze., 18.","short":"S. Chan, P. Koymans, C. Pagano, E. Sofos, Annali Della Scuola Normale Superiore Di Pisa, Classe Di Scienze (2025).","mla":"Chan, Stephanie, et al. “6-Torision and Integral Points on Quartic Threefolds.” <i>Annali Della Scuola Normale Superiore Di Pisa, Classe Di Scienze</i>, 18, Scuola Normale Superiore - Edizioni della Normale, 2025, doi:<a href=\"https://doi.org/10.2422/2036-2145.202412_006\">10.2422/2036-2145.202412_006</a>."},"year":"2025","external_id":{"arxiv":["2403.13359"]},"day":"07","article_processing_charge":"No","OA_type":"green","oa_version":"Preprint","oa":1,"status":"public","publication_status":"epub_ahead","doi":"10.2422/2036-2145.202412_006","date_updated":"2025-05-14T11:40:24Z","_id":"19483","article_number":"18","date_published":"2025-03-07T00:00:00Z","language":[{"iso":"eng"}],"OA_place":"repository","date_created":"2025-04-05T10:49:27Z","article_type":"original","publisher":"Scuola Normale Superiore - Edizioni della Normale","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We prove matching upper and lower bounds for the average of the6-torsionof class groups of quadratic fields. Furthermore, we count the number of integer solutions on an affine quartic threefold.","lang":"eng"}],"author":[{"full_name":"Chan, Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","first_name":"Yik Tung","orcid":"0000-0001-8467-4106","last_name":"Chan"},{"full_name":"Koymans, Peter","last_name":"Koymans","first_name":"Peter"},{"last_name":"Pagano","first_name":"Carlo","full_name":"Pagano, Carlo"},{"first_name":"Efthymios","last_name":"Sofos","full_name":"Sofos, Efthymios"}],"department":[{"_id":"TiBr"}],"title":"6-torision and integral points on quartic threefolds","corr_author":"1","type":"journal_article","arxiv":1,"publication_identifier":{"eissn":["2036-2145"],"issn":["0391-173X"]},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2403.13359","open_access":"1"}]},{"publication":"npj Computational Materials","month":"03","citation":{"chicago":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>.","ista":"Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions. npj Computational Materials. 11, 80.","mla":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>, vol. 11, 80, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>.","short":"B. Cheng, Npj Computational Materials 11 (2025).","apa":"Cheng, B. (2025). Latent Ewald summation for machine learning of long-range interactions. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>","ama":"Cheng B. Latent Ewald summation for machine learning of long-range interactions. <i>npj Computational Materials</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>","ieee":"B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,” <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025."},"year":"2025","external_id":{"arxiv":["2408.15165"],"isi":["001453622900002"]},"has_accepted_license":"1","OA_type":"gold","oa_version":"Published Version","oa":1,"file_date_updated":"2025-04-08T09:34:58Z","file":[{"creator":"dernst","date_updated":"2025-04-08T09:34:58Z","file_size":1608315,"content_type":"application/pdf","date_created":"2025-04-08T09:34:58Z","success":1,"file_id":"19528","file_name":"2025_npjCompMaterials_Cheng.pdf","checksum":"cc99b7407a12139d9b2d8457961935ae","access_level":"open_access","relation":"main_file"}],"volume":11,"article_processing_charge":"Yes","day":"26","date_updated":"2025-09-30T11:31:47Z","DOAJ_listed":"1","publication_status":"published","status":"public","doi":"10.1038/s41524-025-01577-7","ddc":["000"],"language":[{"iso":"eng"}],"acknowledgement":"B. C. thanks David Limmer for providing the water slab dataset, and Carolin Faller for the NaCl dataset.","OA_place":"publisher","date_created":"2025-04-06T22:01:32Z","scopus_import":"1","intvolume":"        11","_id":"19495","article_number":"80","date_published":"2025-03-26T00:00:00Z","isi":1,"article_type":"original","publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"department":[{"_id":"BiCh"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","abstract":[{"text":"Machine learning interatomic potentials (MLIPs) often neglect long-range interactions, such as electrostatic and dispersion forces. In this work, we introduce a straightforward and efficient method to account for long-range interactions by learning a hidden variable from local atomic descriptors and applying an Ewald summation to this variable. We demonstrate that in systems including charged and polar molecular dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can lead to unphysical predictions even when employing message passing. The long-range models effectively eliminate these artifacts, with only about twice the computational cost of short-range MLIPs.","lang":"eng"}],"corr_author":"1","type":"journal_article","arxiv":1,"publication_identifier":{"eissn":["2057-3960"]},"title":"Latent Ewald summation for machine learning of long-range interactions"},{"scopus_import":"1","date_created":"2025-04-06T22:01:32Z","OA_place":"repository","language":[{"iso":"eng"}],"date_published":"2025-05-01T00:00:00Z","article_number":"15","intvolume":"       310","_id":"19496","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","publisher":"Springer Nature","isi":1,"department":[{"_id":"VaKa"}],"author":[{"last_name":"Helfter","id":"7d296fbe-e2c6-11ee-84d3-d5c2945f9a57","first_name":"Mathieu","full_name":"Helfter, Mathieu"}],"abstract":[{"lang":"eng","text":"We introduce the notions of scale for sets and measures on metric space by generalizing the usual notions of dimension. Several versions of scales are introduced such as Hausdorff, packing, box, local and quantization. They are defined for different growth, allowing a refined study of infinite dimensional spaces. We prove general theorems comparing the different versions of scales. They are applied to describe geometries of ergodic decompositions, of the Wiener measure and from functional spaces. The first application solves a problem of Berger on the notions of emergence (2020); the second lies in the geometry of the Wiener measure and extends the work of Dereich–Lifshits (2005); the last refines Kolmogorov–Tikhomirov (1958) study on finitely differentiable functions."}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.05231"}],"publication_identifier":{"eissn":["1432-1823"],"issn":["0025-5874"]},"arxiv":1,"type":"journal_article","corr_author":"1","title":"Scales","month":"05","publication":"Mathematische Zeitschrift","external_id":{"arxiv":["2206.05231"],"isi":["001450830300001"]},"year":"2025","citation":{"ieee":"M. Helfter, “Scales,” <i>Mathematische Zeitschrift</i>, vol. 310. Springer Nature, 2025.","chicago":"Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00209-025-03719-5\">https://doi.org/10.1007/s00209-025-03719-5</a>.","short":"M. Helfter, Mathematische Zeitschrift 310 (2025).","mla":"Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>, vol. 310, 15, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00209-025-03719-5\">10.1007/s00209-025-03719-5</a>.","ista":"Helfter M. 2025. Scales. Mathematische Zeitschrift. 310, 15.","apa":"Helfter, M. (2025). Scales. <i>Mathematische Zeitschrift</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00209-025-03719-5\">https://doi.org/10.1007/s00209-025-03719-5</a>","ama":"Helfter M. Scales. <i>Mathematische Zeitschrift</i>. 2025;310. doi:<a href=\"https://doi.org/10.1007/s00209-025-03719-5\">10.1007/s00209-025-03719-5</a>"},"oa":1,"oa_version":"Preprint","OA_type":"green","article_processing_charge":"No","day":"01","volume":310,"date_updated":"2025-09-30T11:31:00Z","doi":"10.1007/s00209-025-03719-5","status":"public","publication_status":"published"},{"publication":"Classical and Quantum Gravity","month":"04","external_id":{"arxiv":["2412.12726"],"isi":["001448904700001"]},"citation":{"ieee":"Á. Kis-Tóth, Z. Haiman, and Z. Frei, “Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background?,” <i>Classical and Quantum Gravity</i>, vol. 42, no. 7. IOP Publishing, 2025.","apa":"Kis-Tóth, Á., Haiman, Z., &#38; Frei, Z. (2025). Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? <i>Classical and Quantum Gravity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6382/adbda6\">https://doi.org/10.1088/1361-6382/adbda6</a>","ama":"Kis-Tóth Á, Haiman Z, Frei Z. Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? <i>Classical and Quantum Gravity</i>. 2025;42(7). doi:<a href=\"https://doi.org/10.1088/1361-6382/adbda6\">10.1088/1361-6382/adbda6</a>","mla":"Kis-Tóth, Ágnes, et al. “Can Quasars, Triggered by Mergers, Account for NANOGrav’s Stochastic Gravitational Wave Background?” <i>Classical and Quantum Gravity</i>, vol. 42, no. 7, 075007, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-6382/adbda6\">10.1088/1361-6382/adbda6</a>.","ista":"Kis-Tóth Á, Haiman Z, Frei Z. 2025. Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? Classical and Quantum Gravity. 42(7), 075007.","short":"Á. Kis-Tóth, Z. Haiman, Z. Frei, Classical and Quantum Gravity 42 (2025).","chicago":"Kis-Tóth, Ágnes, Zoltán Haiman, and Zsolt Frei. “Can Quasars, Triggered by Mergers, Account for NANOGrav’s Stochastic Gravitational Wave Background?” <i>Classical and Quantum Gravity</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-6382/adbda6\">https://doi.org/10.1088/1361-6382/adbda6</a>."},"year":"2025","oa":1,"oa_version":"Preprint","OA_type":"green","article_processing_charge":"No","day":"04","volume":42,"date_updated":"2025-09-30T11:30:11Z","doi":"10.1088/1361-6382/adbda6","status":"public","publication_status":"published","scopus_import":"1","date_created":"2025-04-06T22:01:32Z","OA_place":"repository","issue":"7","acknowledgement":"We thank Chengcheng Xin and Girish Kulkarni for useful discussions. ZH gratefully acknowledges the hospitality of Eötvös University during an extended sabbatical visit, where this work began. ZH acknowledges support from NSF Grant AST-2006176 and NASA Grants 80NSSC22K0822 and 80NSSC24K0440. ZF acknowledges support from the Hungarian National Research, Development and Innovation Office (NKFIH) through the Institutional Excellence Program No. TKP2021-NKTA-64.","language":[{"iso":"eng"}],"date_published":"2025-04-04T00:00:00Z","article_number":"075007","intvolume":"        42","_id":"19497","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","publisher":"IOP Publishing","isi":1,"department":[{"_id":"ZoHa"}],"author":[{"last_name":"Kis-Tóth","first_name":"Ágnes","full_name":"Kis-Tóth, Ágnes"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","orcid":"0000-0003-3633-5403","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"last_name":"Frei","first_name":"Zsolt","full_name":"Frei, Zsolt"}],"abstract":[{"lang":"eng","text":"The stochastic gravitational wave (GW) background recently discovered by several pulsar timing array experiments is consistent with arising from a population of coalescing super-massive black hole binaries. The amplitude of the background is somewhat higher than expected in most previous population models or from the local mass density observations. Such binaries are expected to be produced in galaxy mergers, which are also thought to trigger bright quasar activity. Under the assumptions that (i) a fraction fbin∼1 of all quasars are associated with mergers, (ii) the typical quasar lifetime is tQ∼108 yr, and (iii) adopting Eddington ratios fEdd∼0.25 for the luminosity of quasars, we compute the GW background associated directly with the empirically measured quasar luminosity function. This approach bypasses the need to model the cosmological evolution of black holes or galaxy mergers from simulations or semi-analytical models. We find the amplitude matching the value measured by NANOGrav. Our results are consistent with most quasars being associated with black hole binaries and being the sources of the GW background, and imply a joint constraint on tQ, fEdd and the typical mass ratio q≡M2/M1. The signal in this case would be dominated by relatively distant ∼109M⊙ sources at z≈2−3, at the peak of quasar activity. Similarly to other models, our results remain in tension with the local super-massive black hole mass density."}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.12726","open_access":"1"}],"publication_identifier":{"eissn":["1361-6382"],"issn":["0264-9381"]},"arxiv":1,"type":"journal_article","title":"Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background?"},{"intvolume":"       122","_id":"19499","article_number":"e2419273122","pmid":1,"date_published":"2025-03-25T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"We thank the reviewers. In particular, they inspired us to analyze the reset and state-preparation problems, to compute optimal qubit mappings, and to apply our method to a quantum error correction scheme that includes both bitflip and phaseflip corrections. We also thank Raimundo Saona and Marek Chalupa for their time spent in insightful discussions. This research was partially supported by the European Research Council CoG 863818 (ForM-SMArt) grant.","OA_place":"publisher","date_created":"2025-04-06T22:01:32Z","issue":"12","scopus_import":"1","isi":1,"article_type":"original","publisher":"National Academy of Sciences","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","abstract":[{"text":"Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional quantum error correction algorithms can be improved depending on the hardware. Given different hardware specifications, we automatically synthesize hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger) state preparation. Using stochastic techniques from computer science, our method presents a computational tool to compute exact accuracy guarantees and synthesize optimal algorithms that are often different from traditional ones. We also show that improvements can be gained with respect to the Qiskit transpiler as we compute the hardware-optimal qubit mapping for the GHZ state-preparation problem.","lang":"eng"}],"author":[{"last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Hardware-optimal quantum algorithms","related_material":{"link":[{"relation":"software","url":"https://github.com/smml1996/algorithm_synthesis"},{"relation":"press_release","url":"https://ista.ac.at/en/news/hardware-optimal-quantum-algorithms/","description":"News on ISTA website"}]},"corr_author":"1","type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"ec_funded":1,"publication":"Proceedings of the National Academy of Sciences","month":"03","has_accepted_license":"1","year":"2025","citation":{"ista":"Muroya Lei S, Chatterjee K, Henzinger TA. 2025. Hardware-optimal quantum algorithms. Proceedings of the National Academy of Sciences. 122(12), e2419273122.","mla":"Muroya Lei, Stefanie, et al. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12, e2419273122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>.","short":"S. Muroya Lei, K. Chatterjee, T.A. Henzinger, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Muroya Lei, Stefanie, Krishnendu Chatterjee, and Thomas A Henzinger. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>.","ama":"Muroya Lei S, Chatterjee K, Henzinger TA. Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(12). doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>","apa":"Muroya Lei, S., Chatterjee, K., &#38; Henzinger, T. A. (2025). Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>","ieee":"S. Muroya Lei, K. Chatterjee, and T. A. Henzinger, “Hardware-optimal quantum algorithms,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12. National Academy of Sciences, 2025."},"external_id":{"pmid":["40106357"],"isi":["001459435600001"]},"file":[{"content_type":"application/pdf","file_size":6805668,"date_updated":"2025-04-07T11:42:22Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"83501b8a65ee5fdd3f5604fc28eddc22","file_name":"2025_PNAS_Muroya.pdf","file_id":"19524","success":1,"date_created":"2025-04-07T11:42:22Z"}],"file_date_updated":"2025-04-07T11:42:22Z","project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"volume":122,"article_processing_charge":"Yes (in subscription journal)","day":"25","OA_type":"hybrid","oa_version":"Published Version","oa":1,"status":"public","publication_status":"published","doi":"10.1073/pnas.2419273122","ddc":["000"],"date_updated":"2026-04-28T13:41:14Z"}]