[{"ddc":["000","570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"relation":"main_file","checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","access_level":"open_access","file_size":6609770,"date_updated":"2025-08-04T06:25:23Z","file_id":"20104","creator":"dernst","success":1,"date_created":"2025-08-04T06:25:23Z","file_name":"2025_CompStrucBiotechJour_Vedula.pdf","content_type":"application/pdf"}],"publication":"Computational and Structural Biotechnology Journal","publication_identifier":{"eissn":["2001-0370"]},"doi":"10.1016/j.csbj.2025.07.039","date_created":"2025-08-03T22:01:31Z","year":"2025","title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","external_id":{"isi":["001583543100001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold’s structure prediction for almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins or protein parts. Here we demonstrate that structured peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy. This work suggests that this windowed multiple sequence alignment approach can be a useful tool for predicting the structure of fused, chimeric proteins."}],"license":"https://creativecommons.org/licenses/by/4.0/","article_processing_charge":"Yes","page":"3292-3298","related_material":{"record":[{"status":"public","id":"20103","relation":"software"}],"link":[{"relation":"software","url":"https://github.com/sankethvedula/AFChimera"}]},"OA_place":"publisher","volume":27,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"94f2fe44-70fa-11f0-b76b-92922c09452b","full_name":"Vedula, Sanketh","first_name":"Sanketh","last_name":"Vedula"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander","last_name":"Bronstein"},{"full_name":"Marx, Ailie","last_name":"Marx","first_name":"Ailie"}],"citation":{"apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>.","mla":"Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>, vol. 27, Elsevier, 2025, pp. 3292–98, doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>.","short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298.","ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment,” <i>Computational and Structural Biotechnology Journal</i>, vol. 27. Elsevier, pp. 3292–3298, 2025.","ama":"Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. 2025;27:3292-3298. doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>","ista":"Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. Computational and Structural Biotechnology Journal. 27, 3292–3298."},"PlanS_conform":"1","day":"27","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","date_updated":"2025-11-27T14:09:59Z","publisher":"Elsevier","department":[{"_id":"AlBr"}],"date_published":"2025-06-27T00:00:00Z","month":"06","language":[{"iso":"eng"}],"DOAJ_listed":"1","file_date_updated":"2025-08-04T06:25:23Z","oa":1,"isi":1,"scopus_import":"1","_id":"20100","acknowledgement":"AM acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. AMB is supported by the Schmidt Chair in Artificial Intelligence.","type":"journal_article","oa_version":"Published Version","intvolume":"        27","article_type":"original"},{"citation":{"chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>.","apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).","ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025.","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>"},"PlanS_conform":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","day":"01","status":"public","isi":1,"file_date_updated":"2025-12-30T09:25:17Z","oa":1,"date_published":"2025-11-01T00:00:00Z","month":"11","language":[{"iso":"eng"}],"date_updated":"2025-12-30T09:25:45Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","oa_version":"Published Version","intvolume":"        34","article_type":"original","type":"journal_article","acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","scopus_import":"1","_id":"20102","quality_controlled":"1","file":[{"file_id":"20906","date_updated":"2025-12-30T09:25:17Z","file_size":2767745,"access_level":"open_access","checksum":"ec01edda64cfbc6cbc8adf300f719644","relation":"main_file","content_type":"application/pdf","file_name":"2025_MolecEcology_Raffini.pdf","date_created":"2025-12-30T09:25:17Z","success":1,"creator":"dernst"}],"has_accepted_license":"1","ddc":["570"],"date_created":"2025-08-03T22:01:31Z","year":"2025","article_number":"e70025","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"doi":"10.1111/mec.70025","issue":"21","publication":"Molecular Ecology","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001538172800001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems."}],"title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","author":[{"full_name":"Raffini, Francesca","first_name":"Francesca","last_name":"Raffini"},{"first_name":"Aurélien","last_name":"De Jode","full_name":"De Jode, Aurélien"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M"},{"first_name":"Juan","last_name":"Galindo","full_name":"Galindo, Juan"},{"full_name":"Rolán-Alvarez, Emilio","first_name":"Emilio","last_name":"Rolán-Alvarez"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":34,"OA_place":"publisher"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7910/DVN/DYEBVM"}],"has_accepted_license":"1","ddc":["000"],"citation":{"ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’” Harvard Dataverse, 2025.","short":"S. Vedula, A.M. Bronstein, A. Marx, (2025).","ista":"Vedula S, Bronstein AM, Marx A. 2025. Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment’, Harvard Dataverse, <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>.","ama":"Vedula S, Bronstein AM, Marx A. Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” 2025. doi:<a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’” Harvard Dataverse, 2025. <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">https://doi.org/10.7910/DVN/DYEBVM</a>.","apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Harvard Dataverse. <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">https://doi.org/10.7910/DVN/DYEBVM</a>","mla":"Vedula, Sanketh, et al. <i>Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.”</i> Harvard Dataverse, 2025, doi:<a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>."},"doi":"10.7910/DVN/DYEBVM","day":"27","status":"public","year":"2025","date_created":"2025-08-04T06:18:55Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"title":"Replication Data for: \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\"","month":"06","date_published":"2025-06-27T00:00:00Z","department":[{"_id":"AlBr"}],"publisher":"Harvard Dataverse","date_updated":"2025-11-27T14:09:58Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","article_processing_charge":"No","oa":1,"abstract":[{"text":"Official implementation, windowed MSAs, and the predictions as reported in the manuscript titled \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\". (2025-06-27)","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"20100"}]},"_id":"20103","author":[{"first_name":"Sanketh","last_name":"Vedula","id":"94f2fe44-70fa-11f0-b76b-92922c09452b","full_name":"Vedula, Sanketh"},{"last_name":"Bronstein","first_name":"Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","type":"research_data_reference"},{"article_processing_charge":"No","abstract":[{"text":"This repository contains the data and scripts required to reproduce the results of the manuscript \"Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages\" submitted to the Environmental Research Climate Journal (ERCL). ","lang":"eng"}],"oa":1,"date_published":"2025-05-21T00:00:00Z","month":"05","title":"Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages","date_updated":"2025-08-04T07:46:33Z","publisher":"Zenodo","department":[{"_id":"CaMu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yi-Ling","last_name":"Hwong","orcid":"0000-0001-9281-3479","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","full_name":"Hwong, Yi-Ling"},{"full_name":"Byers, Edward","first_name":"Edward","last_name":"Byers"},{"full_name":"Werning, Michaela","first_name":"Michaela","last_name":"Werning"},{"last_name":"Quilcaille","first_name":"Yann","full_name":"Quilcaille, Yann"}],"oa_version":"Published Version","type":"research_data_reference","OA_place":"repository","related_material":{"record":[{"relation":"used_in_publication","id":"20098","status":"public"}]},"_id":"20107","citation":{"mla":"Hwong, Yi-Ling, et al. <i>Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>.","chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.13988679\">https://doi.org/10.5281/ZENODO.13988679</a>.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13988679\">https://doi.org/10.5281/ZENODO.13988679</a>","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>.","ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages. 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025)."},"corr_author":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.15409324","open_access":"1"}],"ddc":["550"],"date_created":"2025-08-04T07:34:39Z","year":"2025","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"OA_type":"green","doi":"10.5281/ZENODO.13988679","status":"public","day":"21"},{"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Xu, Faqing","first_name":"Faqing","last_name":"Xu"},{"full_name":"Yu, Yongqiang","last_name":"Yu","first_name":"Yongqiang"},{"full_name":"Guan, Bin","id":"56aad729-cca2-11ed-a45a-9b4138991a48","first_name":"Bin","last_name":"Guan"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"first_name":"Zhihong","last_name":"Xu","full_name":"Xu, Zhihong"},{"full_name":"Xue, Hongwei","last_name":"Xue","first_name":"Hongwei"}],"OA_place":"publisher","volume":44,"title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"Auxin regulates various aspects of plant growth and development by modulating the transcription of target genes through the degradation of auxin/indole-3-acetic acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1), a positive regulator of proteasome activity, has been implicated in auxin-mediated proteasome suppression; however, the mechanism by which auxin modulates PTRE1 function remains unclear. Here, we demonstrate that auxin promotes the interaction between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis, ultimately resulting in suppressed auxin-mediated transcriptional regulation. Our findings uncover a previously uncharacterized regulatory axis in auxin signaling that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which fine-tunes Aux/IAA protein homeostasis and auxin responses."}],"publication_status":"published","external_id":{"pmid":["40714631"],"isi":["001542038500001"]},"issue":"8","doi":"10.1016/j.celrep.2025.116056","publication_identifier":{"eissn":["2211-1247"]},"publication":"Cell Reports","year":"2025","date_created":"2025-08-04T13:39:11Z","article_number":"116056","has_accepted_license":"1","ddc":["580"],"quality_controlled":"1","file":[{"creator":"dernst","success":1,"file_name":"2025_CellReports_Xu.pdf","content_type":"application/pdf","date_created":"2025-08-05T06:15:09Z","date_updated":"2025-08-05T06:15:09Z","file_size":24178018,"checksum":"3c43e040a4a7a65ec67ae1d2bb81261a","relation":"main_file","access_level":"open_access","file_id":"20120"}],"_id":"20116","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":"        44","type":"journal_article","acknowledgement":"The study was supported by the National Natural Science Foundation of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai Jiao Tong University) for kind help with the laser confocal microscope observation and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional mutants.","month":"07","language":[{"iso":"eng"}],"date_published":"2025-07-24T00:00:00Z","publisher":"Elsevier","department":[{"_id":"JiFr"}],"date_updated":"2025-09-30T14:13:45Z","isi":1,"oa":1,"DOAJ_listed":"1","file_date_updated":"2025-08-05T06:15:09Z","day":"24","status":"public","OA_type":"gold","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"},"citation":{"short":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).","ieee":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","ama":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>","ista":"Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. Cell Reports. 44(8), 116056.","chicago":"Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>.","apa":"Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., &#38; Xue, H. (2025). Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">https://doi.org/10.1016/j.celrep.2025.116056</a>","mla":"Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” <i>Cell Reports</i>, vol. 44, no. 8, 116056, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116056\">10.1016/j.celrep.2025.116056</a>."}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","day":"16","status":"public","citation":{"mla":"Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>, vol. 188, no. 21, Elsevier, 2025, p. 5862–5877.e23, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>.","apa":"Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>","chicago":"Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>.","ama":"Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. 2025;188(21):5862-5877.e23. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>","ista":"Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ, Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 188(21), 5862–5877.e23.","ieee":"Z. Zhang <i>et al.</i>, “Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites,” <i>Cell</i>, vol. 188, no. 21. Elsevier, p. 5862–5877.e23, 2025.","short":"Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez, R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin, D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23."},"PlanS_conform":"1","type":"journal_article","acknowledgement":"We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of Southampton. This work was supported by Royal Society grant RGS\\R2\\222312 to F.L.N.; Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.; Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P. In addition to MSKCC cryo-EM resources, some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and Simons Foundation (SF349247) and NY State Assembly grants. This research used NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II, operated for the DOE Office of Science by Brookhaven National Laboratory under contract no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the NIH, the National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program of the NIH (National Library of Medicine).","oa_version":"Published Version","intvolume":"       188","article_type":"original","scopus_import":"1","_id":"20143","file_date_updated":"2025-12-29T14:15:25Z","oa":1,"isi":1,"date_updated":"2025-12-29T14:15:58Z","publisher":"Elsevier","department":[{"_id":"JaBr"}],"date_published":"2025-10-16T00:00:00Z","month":"10","language":[{"iso":"eng"}],"date_created":"2025-08-07T05:00:04Z","year":"2025","publication":"Cell","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"doi":"10.1016/j.cell.2025.07.002","issue":"21","file":[{"checksum":"b944de5fbd7455f58e1ff338ad352239","relation":"main_file","access_level":"open_access","date_updated":"2025-12-29T14:15:25Z","file_size":32104588,"file_id":"20875","creator":"dernst","success":1,"date_created":"2025-12-29T14:15:25Z","file_name":"2025_Cell_Zhang.pdf","content_type":"application/pdf"}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1","volume":188,"OA_place":"publisher","author":[{"first_name":"Zhiying","last_name":"Zhang","full_name":"Zhang, Zhiying"},{"full_name":"Todeschini, Thomas C.","last_name":"Todeschini","first_name":"Thomas C."},{"first_name":"Yi","last_name":"Wu","full_name":"Wu, Yi"},{"full_name":"Kogay, Roman","last_name":"Kogay","first_name":"Roman"},{"first_name":"Ameena","last_name":"Naji","full_name":"Naji, Ameena"},{"first_name":"Joaquin","last_name":"Cardenas Rodriguez","full_name":"Cardenas Rodriguez, Joaquin"},{"full_name":"Mondi, Rupavidhya","first_name":"Rupavidhya","last_name":"Mondi"},{"full_name":"Kaganovich, Daniel","first_name":"Daniel","last_name":"Kaganovich"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"last_name":"Bravo","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly"},{"full_name":"Teplova, Marianna","first_name":"Marianna","last_name":"Teplova"},{"full_name":"Amen, Triana","last_name":"Amen","first_name":"Triana"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"},{"last_name":"Patel","first_name":"Dinshaw J.","full_name":"Patel, Dinshaw J."},{"last_name":"Nobrega","first_name":"Franklin L.","full_name":"Nobrega, Franklin L."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","external_id":{"pmid":["40730155"],"isi":["001603560700005"]},"abstract":[{"text":"Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","page":"5862-5877.e23","title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites"},{"article_processing_charge":"No","oa":1,"abstract":[{"text":"This criteria catalogue and the accompanying assessment questions were developed by a working group of KEMÖ (Kooperation E-Medien Österreich, the Austrian Academic Library Consortium). They are intended to support research institutions and organisations in the evaluation of Open Science Infrastructures. The 20 criteria outlined in the catalogue provide a structured basis for making informed decisions regarding the financial support of these infrastructures.\r\n\r\nThe assessment questions are intended to be completed by Open Science Infrastructures and can be shared with them accordingly.","lang":"eng"}],"publication_status":"published","title":"Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures","language":[{"iso":"eng"}],"month":"08","date_published":"2025-08-07T00:00:00Z","publisher":"Zenodo","department":[{"_id":"E-Lib"}],"date_updated":"2025-08-11T07:20:03Z","author":[{"last_name":"Gredler","first_name":"Paul","full_name":"Gredler, Paul"},{"full_name":"Kaier, Christian","last_name":"Kaier","first_name":"Christian"},{"first_name":"Patrick","last_name":"Danowski","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Zoyer","full_name":"Zoyer, Michael"},{"full_name":"Rieck, Katharina","last_name":"Rieck","first_name":"Katharina"},{"last_name":"Ferus","first_name":"Andreas","full_name":"Ferus, Andreas"},{"last_name":"Rosenberger","first_name":"Elisabeth","full_name":"Rosenberger, Elisabeth"},{"full_name":"Löffler, Alexander","last_name":"Löffler","first_name":"Alexander"},{"first_name":"Lisa","last_name":"Hofer","full_name":"Hofer, Lisa"},{"last_name":"Still","first_name":"Laura","full_name":"Still, Laura"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"working_paper","OA_place":"publisher","_id":"20146","citation":{"ista":"Gredler P, Kaier C, Danowski P, Zoyer M, Rieck K, Ferus A, Rosenberger E, Löffler A, Hofer L, Still L. 2025. Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures, Zenodo,p.","ama":"Gredler P, Kaier C, Danowski P, et al. <i>Catalogue of Criteria for Assessing the Funding Eligibility of Open Science Infrastructures</i>. Zenodo; 2025. doi:<a href=\"https://doi.org/10.5281/zenodo.15269364\">10.5281/zenodo.15269364</a>","short":"P. Gredler, C. Kaier, P. Danowski, M. Zoyer, K. Rieck, A. Ferus, E. Rosenberger, A. Löffler, L. Hofer, L. Still, Catalogue of Criteria for Assessing the Funding Eligibility of Open Science Infrastructures, Zenodo, 2025.","ieee":"P. Gredler <i>et al.</i>, <i>Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures</i>. Zenodo, 2025.","mla":"Gredler, Paul, et al. <i>Catalogue of Criteria for Assessing the Funding Eligibility of Open Science Infrastructures</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/zenodo.15269364\">10.5281/zenodo.15269364</a>.","chicago":"Gredler, Paul, Christian Kaier, Patrick Danowski, Michael Zoyer, Katharina Rieck, Andreas Ferus, Elisabeth Rosenberger, Alexander Löffler, Lisa Hofer, and Laura Still. <i>Catalogue of Criteria for Assessing the Funding Eligibility of Open Science Infrastructures</i>. Zenodo, 2025. <a href=\"https://doi.org/10.5281/zenodo.15269364\">https://doi.org/10.5281/zenodo.15269364</a>.","apa":"Gredler, P., Kaier, C., Danowski, P., Zoyer, M., Rieck, K., Ferus, A., … Still, L. (2025). <i>Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures</i>. Zenodo. <a href=\"https://doi.org/10.5281/zenodo.15269364\">https://doi.org/10.5281/zenodo.15269364</a>"},"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.15269364"}],"ddc":["020"],"year":"2025","date_created":"2025-08-07T11:10:14Z","OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.5281/zenodo.15269364","day":"07","status":"public"},{"corr_author":"1","file":[{"checksum":"fda8a1070667c3562263f4867609b41b","relation":"main_file","access_level":"open_access","date_updated":"2025-08-27T12:59:10Z","file_size":63885565,"file_id":"20232","creator":"prodrigu","success":1,"date_created":"2025-08-27T12:59:10Z","file_name":"2025_ReisRodrigues_Patricia_Thesis.pdf","content_type":"application/pdf"},{"creator":"prodrigu","date_created":"2025-08-27T13:00:30Z","file_name":"2025_ReisRodrigues_Patricia_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"e8b65affcbce846a926454df4b2867b9","relation":"source_file","date_updated":"2025-08-27T13:02:28Z","file_size":50483434,"file_id":"20233"}],"has_accepted_license":"1","ddc":["570"],"year":"2025","date_created":"2025-08-08T09:18:02Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT-ISTA-20149","page":"114","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"text":"Immune responses depend on the coordinated and efficient migration of leukocytes. These\r\ncells, which are embedded and tightly confined within tissues, must navigate and traverse\r\ndiverse and complex three-dimensional environments. Leukocytes adapt their locomotory\r\nbehavior to the mechanical, geometrical, and biochemical characteristics of their\r\nsurroundings. In low-density environments, where the pore size of the interstitial matrix\r\nallows free passage, these cells position the nucleus directly behind the lamellipodium, the\r\nprotrusive actin structure that forms the leading front of the cell. In this configuration, they\r\nuse the nucleus as a gauge to identify the path of least resistance.\r\nHere, we show that in high-density environments, where the pore size precludes free passage\r\nof the cell body, leukocytes reposition the microtubule-organizing center (MTOC) and\r\nassociated organelles in front of the nucleus. In this configuration, they use actin structures\r\nprotruding orthogonally to the direction of migration in order to open a path for the cell body.\r\nWe identify two distinct actin populations that serve this purpose at different subcellular\r\nlocalizations. At the leading edge, local indentation of the plasma membrane leads to\r\nrecruitment of the Wiskott-Aldrich syndrome protein (WASp), which, via Arp2/3, results in\r\nthe formation of individual actin foci. At the cell body, actin polymerization is triggered by\r\nDOCK8, a Cdc42 exchange factor, resulting in the formation of a central actin pool.\r\nWe demonstrate that the central and peripheral actin pools are functionally communicating\r\nand that depletion of the central actin pool leads to increased actin accumulation at the cell\r\nfront, resulting in excessive extension of the leading edge.","lang":"eng"}],"publication_status":"published","title":"Coordination of protrusive forces in immune cell migration ","degree_awarded":"PhD","supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Dos Reis Rodrigues","first_name":"Patricia","full_name":"Dos Reis Rodrigues, Patricia","orcid":"0000-0003-1681-508X","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F"}],"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"id":"10703","relation":"part_of_dissertation","status":"public"},{"id":"20082","relation":"part_of_dissertation","status":"public"}]},"citation":{"mla":"Dos Reis Rodrigues, Patricia. <i>Coordination of Protrusive Forces in Immune Cell Migration </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>.","chicago":"Dos Reis Rodrigues, Patricia. “Coordination of Protrusive Forces in Immune Cell Migration .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>.","apa":"Dos Reis Rodrigues, P. (2025). <i>Coordination of protrusive forces in immune cell migration </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20149\">https://doi.org/10.15479/AT-ISTA-20149</a>","ista":"Dos Reis Rodrigues P. 2025. Coordination of protrusive forces in immune cell migration . Institute of Science and Technology Austria.","ama":"Dos Reis Rodrigues P. Coordination of protrusive forces in immune cell migration . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20149\">10.15479/AT-ISTA-20149</a>","ieee":"P. Dos Reis Rodrigues, “Coordination of protrusive forces in immune cell migration ,” Institute of Science and Technology Austria, 2025.","short":"P. Dos Reis Rodrigues, Coordination of Protrusive Forces in Immune Cell Migration , Institute of Science and Technology Austria, 2025."},"project":[{"name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"alternative_title":["ISTA Thesis"],"day":"08","status":"public","oa":1,"file_date_updated":"2025-08-27T13:02:28Z","month":"08","language":[{"iso":"eng"}],"date_published":"2025-08-08T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-28T13:26:50Z","oa_version":"Published Version","type":"dissertation","acknowledgement":"I would like to acknowledge the\r\nfinancial support of the European Research Council through the ERC-SyG grant “Pushing from\r\nwithin: Control of cell shape, integrity and motility by cytoskeletal pushing forces”\r\n(01071793), which made this research possible. ","_id":"20149"},{"PlanS_conform":"1","citation":{"mla":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>, vol. 48, no. 9, Elsevier, 2025, pp. 645–54, doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>.","apa":"Hetzer, M., &#38; Toda, T. (2025). Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>","chicago":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>.","ama":"Hetzer M, Toda T. Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. 2025;48(9):645-654. doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>","ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 645–654.","ieee":"M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” <i>Trends in Neurosciences</i>, vol. 48, no. 9. Elsevier, pp. 645–654, 2025.","short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654."},"status":"public","day":"01","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"MaHe"}],"publisher":"Elsevier","date_updated":"2025-12-29T13:47:58Z","month":"09","language":[{"iso":"eng"}],"date_published":"2025-09-01T00:00:00Z","oa":1,"file_date_updated":"2025-12-29T13:47:27Z","isi":1,"_id":"20154","scopus_import":"1","type":"journal_article","acknowledgement":"The work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872 – T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG, 101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank Dr Laura J. Harrison for editing assistance.","article_type":"original","oa_version":"Published Version","intvolume":"        48","ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-12-29T13:47:27Z","content_type":"application/pdf","file_name":"2025_TrendsNeurosciences_Hetzer.pdf","access_level":"open_access","checksum":"90942491b499f70b0bf48b8aec2e7387","relation":"main_file","file_size":327847,"date_updated":"2025-12-29T13:47:27Z","file_id":"20873"}],"corr_author":"1","publication":"Trends in Neurosciences","issue":"9","publication_identifier":{"issn":["0166-2236"],"eissn":["1878-108X"]},"doi":"10.1016/j.tins.2025.07.004","year":"2025","date_created":"2025-08-10T22:01:29Z","title":"Long-lived cellular molecules in the brain","abstract":[{"lang":"eng","text":"In long-lived mammals, including humans, brain cell homeostasis is critical for maintaining brain function throughout life. Most neurons are generated during development and must maintain their cellular identity and plasticity to preserve brain function. Although extensive studies indicate the importance of recycling and regenerating cellular molecules to maintain cellular homeostasis, recent evidence has shown that some proteins and RNAs do not turn over for months and even years. We propose that these long-lived cellular molecules may be the basis for maintaining brain function in the long term, but also a potential convergent target of brain aging. We highlight key discoveries and challenges, and propose potential directions to unravel the mystery of brain cell longevity."}],"external_id":{"isi":["001568965400001"],"pmid":["40744775"]},"publication_status":"published","page":"645-654","article_processing_charge":"Yes (in subscription journal)","pmid":1,"volume":48,"OA_place":"publisher","author":[{"first_name":"Martin W","last_name":"Hetzer","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"last_name":"Toda","first_name":"Tomohisa","full_name":"Toda, Tomohisa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2025","date_created":"2025-08-10T22:01:29Z","issue":"4","doi":"10.1137/24M1700351","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"publication":"SIAM Journal on Mathematical Analysis","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.14506","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Brigati","first_name":"Giovanni","full_name":"Brigati, Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1"},{"full_name":"Stoltz, Gabriel","last_name":"Stoltz","first_name":"Gabriel"}],"volume":57,"OA_place":"repository","page":"3587-3622","article_processing_charge":"No","abstract":[{"text":"We study time averages for the norm of solutions to kinetic Fokker–Planck equations associated with general Hamiltonians. We provide fully explicit and constructive decay estimates for systems subject to a confining potential, allowing fat-tail, subexponential and (super-)exponential local equilibria, which also include the classic Maxwellian case. The key step in our estimates is a modified Poincaré inequality, obtained via a Lions–Poincaré inequality and an averaging lemma.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001550830900006"],"arxiv":["2302.14506"]},"title":"How to construct explicit decay rates for kinetic Fokker–Planck equations?","OA_type":"green","ec_funded":1,"day":"01","status":"public","citation":{"mla":"Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates for Kinetic Fokker–Planck Equations?” <i>SIAM Journal on Mathematical Analysis</i>, vol. 57, no. 4, Society for Industrial and Applied Mathematics, 2025, pp. 3587–622, doi:<a href=\"https://doi.org/10.1137/24M1700351\">10.1137/24M1700351</a>.","apa":"Brigati, G., &#38; Stoltz, G. (2025). How to construct explicit decay rates for kinetic Fokker–Planck equations? <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/24M1700351\">https://doi.org/10.1137/24M1700351</a>","chicago":"Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates for Kinetic Fokker–Planck Equations?” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2025. <a href=\"https://doi.org/10.1137/24M1700351\">https://doi.org/10.1137/24M1700351</a>.","ama":"Brigati G, Stoltz G. How to construct explicit decay rates for kinetic Fokker–Planck equations? <i>SIAM Journal on Mathematical Analysis</i>. 2025;57(4):3587-3622. doi:<a href=\"https://doi.org/10.1137/24M1700351\">10.1137/24M1700351</a>","ista":"Brigati G, Stoltz G. 2025. How to construct explicit decay rates for kinetic Fokker–Planck equations? SIAM Journal on Mathematical Analysis. 57(4), 3587–3622.","short":"G. Brigati, G. Stoltz, SIAM Journal on Mathematical Analysis 57 (2025) 3587–3622.","ieee":"G. Brigati and G. Stoltz, “How to construct explicit decay rates for kinetic Fokker–Planck equations?,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 57, no. 4. Society for Industrial and Applied Mathematics, pp. 3587–3622, 2025."},"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"article_type":"original","oa_version":"Preprint","intvolume":"        57","type":"journal_article","acknowledgement":"The first author was funded by the European Union's Horizon 2020 research andinnovation program under the Marie Sklodowska-Curie grant agreements 754362 and 101034413,and partially by Project EFI (ANR-17-CE40-0030) of the French National Research Agency (ANR).The work of the second author was partially funded by the European Research Council (ERC) underthe European Union's Horizon 2020 research and innovation programme (grant agreement 810367),and by the Agence Nationale de la Recherche under grants ANR-19-CE40-0010 (QuAMProcs) andANR-21-CE40-0006 (SINEQ).","_id":"20155","scopus_import":"1","isi":1,"oa":1,"month":"08","language":[{"iso":"eng"}],"date_published":"2025-08-01T00:00:00Z","department":[{"_id":"JaMa"}],"publisher":"Society for Industrial and Applied Mathematics","arxiv":1,"date_updated":"2025-11-05T13:51:40Z"},{"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved many times throughout the tree of life, and understanding what has shaped their unusual morphological, sequence, and regulatory features has been a long-standing goal. Most early insights into insect sex chromosome biology came from a few model species, such as the fruit fly Drosophila melanogaster, which limited broad-scale evolutionary inferences. More recently, extensive comparative genomics studies have uncovered several unexpected patterns, which we highlight in this review. First, we describe the conservation of the ancestral X chromosome over 450 million years but also its recurrent turnover (i.e. its reversal to an autosome when a new X chromosome arose) in at least one order. We then summarize classical and more recent findings on how insects modulate the expression of X-linked genes following the degradation of the Y chromosome and how the diverse mechanisms of dosage compensation identified may elucidate important principles of sex chromosome regulatory evolution."}],"external_id":{"isi":["001582424100001"]},"publication_status":"published","article_processing_charge":"Yes (via OA deal)","title":"Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation","volume":72,"OA_place":"publisher","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2025-12-30T13:14:20Z","file_size":897079,"access_level":"open_access","relation":"main_file","checksum":"262640abc34277686b56eb60102976f6","file_id":"20917","success":1,"creator":"dernst","file_name":"2025_CurrOpinionInsectScience_Toups.pdf","content_type":"application/pdf","date_created":"2025-12-30T13:14:20Z"}],"quality_controlled":"1","corr_author":"1","ddc":["570"],"has_accepted_license":"1","article_number":"101411","year":"2025","date_created":"2025-08-17T22:01:35Z","publication":"Current Opinion in Insect Science","publication_identifier":{"issn":["2214-5745"],"eissn":["2214-5753"]},"doi":"10.1016/j.cois.2025.101411","oa":1,"file_date_updated":"2025-12-30T13:14:20Z","isi":1,"publisher":"Elsevier","department":[{"_id":"BeVi"}],"date_updated":"2025-12-30T13:14:38Z","month":"12","language":[{"iso":"eng"}],"date_published":"2025-12-01T00:00:00Z","type":"journal_article","acknowledgement":"This work was supported by an Austrian Research Fund (FWF) grant to B.V. (PAT 8748323) and by the Louisiana Board of Regents Research Competitiveness Subprogram (LEQSF(2025-28)-RD-A-20) to MAT.","article_type":"review","oa_version":"Published Version","intvolume":"        72","_id":"20182","scopus_import":"1","project":[{"name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"}],"PlanS_conform":"1","citation":{"short":"M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (2025).","ieee":"M. A. Toups and B. Vicoso, “Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation,” <i>Current Opinion in Insect Science</i>, vol. 72. Elsevier, 2025.","ista":"Toups MA, Vicoso B. 2025. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. Current Opinion in Insect Science. 72, 101411.","ama":"Toups MA, Vicoso B. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. 2025;72. doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2025). Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>","mla":"Toups, Melissa A., and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>, vol. 72, 101411, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>."},"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01"},{"title":"Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo","publication_status":"published","external_id":{"pmid":["40759648"]},"abstract":[{"lang":"eng","text":"The unequal segregation of organelles has been proposed to be an intrinsic mechanism that contributes to cell fate divergence during asymmetric cell division; however, in vivo evidence is sparse. Using super-resolution microscopy, we analysed the segregation of organelles during the division of the neuroblast QL.p in C. elegans larvae. QL.p divides to generate a daughter that survives, QL.pa, and a daughter that dies, QL.pp. We found that mitochondria segregate unequally by density and morphology and that this is dependent on mitochondrial dynamics. Furthermore, we found that mitochondrial density in QL.pp correlates with the time it takes QL.pp to die. We propose that low mitochondrial density in QL.pp promotes the cell death fate and ensures that QL.pp dies in a highly reproducible and timely manner. Our results provide in vivo evidence that the unequal segregation of mitochondria can contribute to cell fate divergence during asymmetric cell division in a developing animal."}],"article_processing_charge":"Yes","pmid":1,"volume":16,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Segos","first_name":"Ioannis","full_name":"Segos, Ioannis"},{"first_name":"Jens","last_name":"Van Eeckhoven","full_name":"Van Eeckhoven, Jens"},{"last_name":"Berger","first_name":"Simon","full_name":"Berger, Simon"},{"last_name":"Mishra","first_name":"Nikhil","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E"},{"last_name":"Lambie","first_name":"Eric J.","full_name":"Lambie, Eric J."},{"last_name":"Conradt","first_name":"Barbara","full_name":"Conradt, Barbara"}],"ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"20261","file_size":3775190,"date_updated":"2025-09-01T09:46:44Z","access_level":"open_access","relation":"main_file","checksum":"f28e73963ea1f55876d0d1afca0f706a","file_name":"2025_NatureComm_Segos.pdf","content_type":"application/pdf","date_created":"2025-09-01T09:46:44Z","success":1,"creator":"dernst"}],"publication":"Nature Communications","doi":"10.1038/s41467-025-62484-5","publication_identifier":{"eissn":["2041-1723"]},"article_number":"7174","date_created":"2025-08-17T22:01:35Z","year":"2025","date_updated":"2025-09-01T09:47:29Z","department":[{"_id":"CaHe"}],"publisher":"Springer Nature","date_published":"2025-08-04T00:00:00Z","language":[{"iso":"eng"}],"month":"08","file_date_updated":"2025-09-01T09:46:44Z","DOAJ_listed":"1","oa":1,"scopus_import":"1","_id":"20183","acknowledgement":"We thank members of the Conradt lab, the Center for Cell and Molecular Dynamics (https://www.uclccmd.co.uk/) and T. Schedl for discussions and comments on the manuscript. We thank L. McGuinness for excellent technical support. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank Alex Hajnal (University of Zurich, Switzerland) and Andrew deMello (ETH Zurich, Switzerland) for their support of S.B. This work was supported by a predoctoral fellowship from the Studienstiftung des deutschen Volkes to NM, funds from UCL (Division of Biosciences, UCL LSM Capital Equipment Fund) to B.C., and a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to B.C. (RSWF\\R1\\180008), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 and BB/V015648/1to B.C.).","type":"journal_article","intvolume":"        16","oa_version":"Published Version","article_type":"original","citation":{"mla":"Segos, Ioannis, et al. “Unequal Segregation of Mitochondria during Asymmetric Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” <i>Nature Communications</i>, vol. 16, 7174, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-62484-5\">10.1038/s41467-025-62484-5</a>.","chicago":"Segos, Ioannis, Jens Van Eeckhoven, Simon Berger, Nikhil Mishra, Eric J. Lambie, and Barbara Conradt. “Unequal Segregation of Mitochondria during Asymmetric Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-62484-5\">https://doi.org/10.1038/s41467-025-62484-5</a>.","apa":"Segos, I., Van Eeckhoven, J., Berger, S., Mishra, N., Lambie, E. J., &#38; Conradt, B. (2025). Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-62484-5\">https://doi.org/10.1038/s41467-025-62484-5</a>","ama":"Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-62484-5\">10.1038/s41467-025-62484-5</a>","ista":"Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. 2025. Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo. Nature Communications. 16, 7174.","short":"I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E.J. Lambie, B. Conradt, Nature Communications 16 (2025).","ieee":"I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E. J. Lambie, and B. Conradt, “Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"PlanS_conform":"1","status":"public","day":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold"},{"PlanS_conform":"1","citation":{"chicago":"Castell, Sofía D., Consuelo M. Fernandez, Ignacio N. Tumas, Lucía M. Margara, Maria C Miserendino, Danilo G. Ceschin, Roberto J. Pezza, and Mariela R. Monti. “The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas Aeruginosa.” <i>Communications Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s42003-025-08589-5\">https://doi.org/10.1038/s42003-025-08589-5</a>.","apa":"Castell, S. D., Fernandez, C. M., Tumas, I. N., Margara, L. M., Miserendino, M. C., Ceschin, D. G., … Monti, M. R. (2025). The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-025-08589-5\">https://doi.org/10.1038/s42003-025-08589-5</a>","mla":"Castell, Sofía D., et al. “The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas Aeruginosa.” <i>Communications Biology</i>, vol. 8, 1148, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s42003-025-08589-5\">10.1038/s42003-025-08589-5</a>.","short":"S.D. Castell, C.M. Fernandez, I.N. Tumas, L.M. Margara, M.C. Miserendino, D.G. Ceschin, R.J. Pezza, M.R. Monti, Communications Biology 8 (2025).","ieee":"S. D. Castell <i>et al.</i>, “The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa,” <i>Communications Biology</i>, vol. 8. Springer Nature, 2025.","ista":"Castell SD, Fernandez CM, Tumas IN, Margara LM, Miserendino MC, Ceschin DG, Pezza RJ, Monti MR. 2025. The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications Biology. 8, 1148.","ama":"Castell SD, Fernandez CM, Tumas IN, et al. The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa. <i>Communications Biology</i>. 2025;8. doi:<a href=\"https://doi.org/10.1038/s42003-025-08589-5\">10.1038/s42003-025-08589-5</a>"},"status":"public","day":"02","OA_type":"gold","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"PaSc"},{"_id":"GradSch"}],"publisher":"Springer Nature","date_updated":"2025-09-30T14:18:46Z","month":"08","language":[{"iso":"eng"}],"date_published":"2025-08-02T00:00:00Z","oa":1,"DOAJ_listed":"1","isi":1,"_id":"20184","scopus_import":"1","type":"journal_article","acknowledgement":"This work was supported by the Secretaría de Ciencia y Técnica (33620230100926CB), Universidad Nacional de Córdoba; and the Agencia Nacional de Promoción Científica y Técnica (PICT 2018-4527).\r\n\r\n","article_type":"original","oa_version":"Published Version","intvolume":"         8","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1038/s42003-025-08589-5","open_access":"1"}],"has_accepted_license":"1","quality_controlled":"1","publication":"Communications Biology","doi":"10.1038/s42003-025-08589-5","publication_identifier":{"eissn":["2399-3642"]},"article_number":"1148","year":"2025","date_created":"2025-08-17T22:01:35Z","title":"The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa","abstract":[{"text":"Specialized DNA polymerases facilitate various cellular processes. Despite extensive research, the mutagenic effects of these error-prone enzymes on genomes are not fully understood. Here we show that Pol IV promotes genomic instability in Pseudomonas aeruginosa by misincorporating oxidized guanine nucleotides. This activity led to a distinctive mutational signature, characterized by A-to-C transversions occurring preferentially at AT sites flanked by a 5’G and/or 3’C. Furthermore, Pol IV preferentially targeted pathogenicity genes located at specific chromosomal locations near the replication termination region and rRNA-encoding operons. Half of the mutation events catalyzed by Pol IV impaired gene function. This can be attributed to the bias of Pol IV for mutating codons with its preferred sequence contexts, leading to substitutions to unreactive alanine and glycine residues. Remarkably, mutation signatures identified for Pol IV were found in clinical isolate genomes of P. aeruginosa, providing compelling evidence for its role in genetic diversification during pathogen adaptation.","lang":"eng"}],"external_id":{"pmid":["40753298"],"isi":["001541878500001"]},"publication_status":"published","article_processing_charge":"Yes","pmid":1,"OA_place":"publisher","volume":8,"author":[{"full_name":"Castell, Sofía D.","last_name":"Castell","first_name":"Sofía D."},{"first_name":"Consuelo M.","last_name":"Fernandez","full_name":"Fernandez, Consuelo M."},{"full_name":"Tumas, Ignacio N.","first_name":"Ignacio N.","last_name":"Tumas"},{"first_name":"Lucía M.","last_name":"Margara","full_name":"Margara, Lucía M."},{"id":"273e0cbd-72f0-11ef-b75a-f9f932e292fa","full_name":"Miserendino, Maria C","last_name":"Miserendino","first_name":"Maria C"},{"last_name":"Ceschin","first_name":"Danilo G.","full_name":"Ceschin, Danilo G."},{"last_name":"Pezza","first_name":"Roberto J.","full_name":"Pezza, Roberto J."},{"full_name":"Monti, Mariela R.","last_name":"Monti","first_name":"Mariela R."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"day":"07","status":"public","OA_type":"hybrid","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"PlanS_conform":"1","citation":{"ista":"Tsodikovich D. 2025. Local rigidity for symplectic billiards. Journal of Geometric Analysis. 35(10), 306.","ama":"Tsodikovich D. Local rigidity for symplectic billiards. <i>Journal of Geometric Analysis</i>. 2025;35(10). doi:<a href=\"https://doi.org/10.1007/s12220-025-02148-4\">10.1007/s12220-025-02148-4</a>","short":"D. Tsodikovich, Journal of Geometric Analysis 35 (2025).","ieee":"D. Tsodikovich, “Local rigidity for symplectic billiards,” <i>Journal of Geometric Analysis</i>, vol. 35, no. 10. Springer Nature, 2025.","mla":"Tsodikovich, Daniel. “Local Rigidity for Symplectic Billiards.” <i>Journal of Geometric Analysis</i>, vol. 35, no. 10, 306, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s12220-025-02148-4\">10.1007/s12220-025-02148-4</a>.","apa":"Tsodikovich, D. (2025). Local rigidity for symplectic billiards. <i>Journal of Geometric Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12220-025-02148-4\">https://doi.org/10.1007/s12220-025-02148-4</a>","chicago":"Tsodikovich, Daniel. “Local Rigidity for Symplectic Billiards.” <i>Journal of Geometric Analysis</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s12220-025-02148-4\">https://doi.org/10.1007/s12220-025-02148-4</a>."},"project":[{"call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707"}],"_id":"20185","scopus_import":"1","article_type":"original","intvolume":"        35","oa_version":"Published Version","type":"journal_article","acknowledgement":"The author would like to thank Corentin Fierobe, Vadim Kaloshin, Illya Koval and Yunzhe Li for useful discussions. The author would also like to thank the referee for useful remarks. Open access funding provided by Institute of Science and Technology (IST Austria). European Research Council (885707) Mr Daniel Tsodikovich","month":"08","language":[{"iso":"eng"}],"date_published":"2025-08-07T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"VaKa"}],"arxiv":1,"date_updated":"2025-12-30T09:29:27Z","isi":1,"oa":1,"file_date_updated":"2025-12-30T09:28:58Z","issue":"10","doi":"10.1007/s12220-025-02148-4","publication_identifier":{"issn":["1050-6926"]},"publication":"Journal of Geometric Analysis","year":"2025","date_created":"2025-08-17T22:01:35Z","article_number":"306","has_accepted_license":"1","ddc":["510"],"corr_author":"1","file":[{"date_created":"2025-12-30T09:28:58Z","file_name":"2025_JourGeomAnalysis_Tsodikovich.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"20907","access_level":"open_access","checksum":"ed86500742b3fd93db3287558a630383","relation":"main_file","file_size":484344,"date_updated":"2025-12-30T09:28:58Z"}],"quality_controlled":"1","author":[{"first_name":"Daniel","last_name":"Tsodikovich","id":"04531810-fb3e-11ef-87f0-800a4ce333db","full_name":"Tsodikovich, Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":35,"OA_place":"publisher","title":"Local rigidity for symplectic billiards","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We show a local rigidity result for the integrability of symplectic billiards. We prove that any domain which is close to an ellipse, and for which the symplectic billiard map is rationally integrable must be an ellipse as well. This is in spirit of the result of [2] for Birkhoff billiards."}],"external_id":{"isi":["001546433200002"],"arxiv":["2501.08849"]},"publication_status":"published"},{"project":[{"name":"Interface Theory for Security and Privacy","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","grant_number":"F8502"}],"citation":{"short":"T.H. Hsu, A.A. Oliveira da Costa, A. Wintenberg, E. Bartocci, B. Bonakdarpour, Acta Informatica 62 (2025).","ieee":"T. H. Hsu, A. A. Oliveira da Costa, A. Wintenberg, E. Bartocci, and B. Bonakdarpour, “Gray-box runtime enforcement of hyperproperties,” <i>Acta Informatica</i>, vol. 62, no. 3. Springer Nature, 2025.","ama":"Hsu TH, Oliveira da Costa AA, Wintenberg A, Bartocci E, Bonakdarpour B. Gray-box runtime enforcement of hyperproperties. <i>Acta Informatica</i>. 2025;62(3). doi:<a href=\"https://doi.org/10.1007/s00236-025-00502-1\">10.1007/s00236-025-00502-1</a>","ista":"Hsu TH, Oliveira da Costa AA, Wintenberg A, Bartocci E, Bonakdarpour B. 2025. Gray-box runtime enforcement of hyperproperties. Acta Informatica. 62(3), 30.","apa":"Hsu, T. H., Oliveira da Costa, A. A., Wintenberg, A., Bartocci, E., &#38; Bonakdarpour, B. (2025). Gray-box runtime enforcement of hyperproperties. <i>Acta Informatica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00236-025-00502-1\">https://doi.org/10.1007/s00236-025-00502-1</a>","chicago":"Hsu, Tzu Han, Ana A Oliveira da Costa, Andrew Wintenberg, Ezio Bartocci, and Borzoo Bonakdarpour. “Gray-Box Runtime Enforcement of Hyperproperties.” <i>Acta Informatica</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00236-025-00502-1\">https://doi.org/10.1007/s00236-025-00502-1</a>.","mla":"Hsu, Tzu Han, et al. “Gray-Box Runtime Enforcement of Hyperproperties.” <i>Acta Informatica</i>, vol. 62, no. 3, 30, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00236-025-00502-1\">10.1007/s00236-025-00502-1</a>."},"PlanS_conform":"1","status":"public","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","date_updated":"2025-09-30T14:20:11Z","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"date_published":"2025-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","file_date_updated":"2025-09-02T05:53:47Z","oa":1,"isi":1,"scopus_import":"1","_id":"20186","acknowledgement":"This project was funded in part by the Austrian Science Fund (FWF) SFB project SpyCoDe F8502, Vienna Science and Technology Fund (WWTF) [10.47379/ICT19018] (ProbInG) and WWTF project ICT22-023 (TAIGER), National Science Foundation (NSF) CPS Award 1837680, NSF award ECCS-2144416 and NSF SaTC Award 2245114. Open access funding provided by Institute of Science and Technology (IST Austria).","type":"journal_article","oa_version":"Published Version","intvolume":"        62","article_type":"original","ddc":["000"],"has_accepted_license":"1","quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-09-02T05:53:47Z","file_name":"2025_ActaInformatica_Hsu.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"90a43350fd4a8c5cb5b1b0e1aea7970d","file_size":6505049,"date_updated":"2025-09-02T05:53:47Z","file_id":"20267"}],"corr_author":"1","publication":"Acta Informatica","doi":"10.1007/s00236-025-00502-1","publication_identifier":{"issn":["0001-5903"],"eissn":["1432-0525"]},"issue":"3","article_number":"30","date_created":"2025-08-17T22:01:36Z","year":"2025","title":"Gray-box runtime enforcement of hyperproperties","external_id":{"isi":["001546115300001"]},"publication_status":"published","abstract":[{"text":"Enforcement of information-flow policies has been extensively studied by language-based approaches over the past few decades. In this paper, we propose an alternative, novel, general, and effective approach using enforcement of hyperproperties– a powerful formalism for expressing and reasoning about a wide range of information-flow security policies. We study black- vs. gray- vs. white-box enforcement of hyperproperties expressed by nondeterministic finite-word hyperautomata (NFH), where the enforcer has null, some, or complete information about the implementation of the system under scrutiny. Given an NFH, in order to generate a runtime enforcer, we reduce the problem to controller synthesis for hyperproperties and subsequently to the satisfiability problem for quantified Boolean formulas (QBFs). The resulting enforcers are transferable with low-overhead. We conduct a rich set of case studies, including information-flow control for JavaScript code, as well as synthesizing obfuscators for control plants.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","volume":62,"author":[{"full_name":"Hsu, Tzu Han","first_name":"Tzu Han","last_name":"Hsu"},{"first_name":"Ana A","last_name":"Oliveira Da Costa","full_name":"Oliveira Da Costa, Ana A","id":"8b282559-50b0-11ef-861e-d6ace0d92e9b"},{"full_name":"Wintenberg, Andrew","last_name":"Wintenberg","first_name":"Andrew"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"last_name":"Bonakdarpour","first_name":"Borzoo","full_name":"Bonakdarpour, Borzoo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"oa_version":"Published Version","intvolume":"       123","article_type":"original","type":"journal_article","acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","scopus_import":"1","_id":"20187","isi":1,"file_date_updated":"2025-09-01T14:09:31Z","oa":1,"date_published":"2025-08-01T00:00:00Z","language":[{"iso":"eng"}],"month":"08","date_updated":"2026-04-07T11:52:02Z","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"publisher":"Wiley","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","day":"01","status":"public","citation":{"ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>.","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>."},"PlanS_conform":"1","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"}],"author":[{"full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic","first_name":"David"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia"},{"first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","first_name":"Linlin","last_name":"Qi"},{"first_name":"Frédérique","last_name":"Tellier","full_name":"Tellier, Frédérique"},{"id":"cced8a85-223e-11ed-af04-b0596c55053b","full_name":"Smoljan, Adrijana","first_name":"Adrijana","last_name":"Smoljan"},{"first_name":"Hana","last_name":"Rakusova","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","full_name":"Rakusova, Hana"},{"first_name":"Petr","last_name":"Valošek","full_name":"Valošek, Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jean Denis","last_name":"Faure","full_name":"Faure, Jean Denis"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","volume":123,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"20362","status":"public"}]},"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001547884300001"],"pmid":["40782342"]},"publication_status":"published","abstract":[{"text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.","lang":"eng"}],"title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","date_created":"2025-08-17T22:01:36Z","year":"2025","article_number":"e70396","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"doi":"10.1111/tpj.70396","issue":"3","publication":"Plant Journal","corr_author":"1","quality_controlled":"1","file":[{"file_id":"20264","checksum":"1cdc3341d2d23101abca72521f1f23cb","relation":"main_file","access_level":"open_access","file_size":5791111,"date_updated":"2025-09-01T14:09:31Z","date_created":"2025-09-01T14:09:31Z","content_type":"application/pdf","file_name":"2025_PlantJournal_Babic.pdf","creator":"dernst","success":1}],"has_accepted_license":"1","ddc":["580"]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","status":"public","day":"01","citation":{"mla":"Jikko, Yuya, et al. “Front-Biased Activation of the Ras-Rab5-Rac1 Loop Coordinates Collective Cell Migration.” <i>Journal of Cell Science</i>, vol. 138, no. 15, 263779, The Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/jcs.263779\">10.1242/jcs.263779</a>.","chicago":"Jikko, Yuya, Eriko Deguchi, Kimiya Matsuda, Naoya Hino, Shinya Tsukiji, Michiyuki Matsuda, and Kenta Terai. “Front-Biased Activation of the Ras-Rab5-Rac1 Loop Coordinates Collective Cell Migration.” <i>Journal of Cell Science</i>. The Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/jcs.263779\">https://doi.org/10.1242/jcs.263779</a>.","apa":"Jikko, Y., Deguchi, E., Matsuda, K., Hino, N., Tsukiji, S., Matsuda, M., &#38; Terai, K. (2025). Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.263779\">https://doi.org/10.1242/jcs.263779</a>","ama":"Jikko Y, Deguchi E, Matsuda K, et al. Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration. <i>Journal of Cell Science</i>. 2025;138(15). doi:<a href=\"https://doi.org/10.1242/jcs.263779\">10.1242/jcs.263779</a>","ista":"Jikko Y, Deguchi E, Matsuda K, Hino N, Tsukiji S, Matsuda M, Terai K. 2025. Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration. Journal of Cell Science. 138(15), 263779.","short":"Y. Jikko, E. Deguchi, K. Matsuda, N. Hino, S. Tsukiji, M. Matsuda, K. Terai, Journal of Cell Science 138 (2025).","ieee":"Y. Jikko <i>et al.</i>, “Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration,” <i>Journal of Cell Science</i>, vol. 138, no. 15. The Company of Biologists, 2025."},"PlanS_conform":"1","type":"journal_article","acknowledgement":"We are grateful to the members of the Matsuda Laboratory for their helpful input, to K. Hirano, T. Uesugi and K. Takakura, who provided technical assistance, and to the Medical Research Support Center of Kyoto University for DNA sequence analysis. This work was supported by the Kyoto University Live Imaging Center. Financial support was provided by Japan Society for the Promotion of Science (JSPS) KAKENHI grants (21H05226 to K.T., 19H00993 and 20H05898 to M.M.), a Japan Science and Technology Agency (JST) CREST grant (JPMJCR1654 to M.M.), and a JST Moonshot Research and Development Program grant (JPMJPS2022 to M.M.). Open Access funding provided by Tokushima University. Deposited in PMC for immediate release.","oa_version":"Published Version","intvolume":"       138","article_type":"original","scopus_import":"1","_id":"20188","file_date_updated":"2025-09-01T10:02:24Z","oa":1,"isi":1,"date_updated":"2025-11-27T14:12:24Z","department":[{"_id":"CaHe"}],"publisher":"The Company of Biologists","date_published":"2025-08-01T00:00:00Z","month":"08","language":[{"iso":"eng"}],"article_number":"263779","date_created":"2025-08-17T22:01:36Z","year":"2025","publication":"Journal of Cell Science","publication_identifier":{"issn":[" 0021-9533"],"eissn":["1477-9137"]},"doi":"10.1242/jcs.263779","issue":"15","quality_controlled":"1","file":[{"file_size":12393297,"date_updated":"2025-09-01T10:02:24Z","access_level":"open_access","checksum":"29f42619dab5ce251a20c769ed4581c0","relation":"main_file","file_id":"20262","success":1,"creator":"dernst","file_name":"2025_JourCellScience_Jikko.pdf","content_type":"application/pdf","date_created":"2025-09-01T10:02:24Z"}],"ddc":["570"],"has_accepted_license":"1","OA_place":"publisher","volume":138,"author":[{"full_name":"Jikko, Yuya","first_name":"Yuya","last_name":"Jikko"},{"first_name":"Eriko","last_name":"Deguchi","full_name":"Deguchi, Eriko"},{"full_name":"Matsuda, Kimiya","last_name":"Matsuda","first_name":"Kimiya"},{"first_name":"Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","full_name":"Hino, Naoya"},{"first_name":"Shinya","last_name":"Tsukiji","full_name":"Tsukiji, Shinya"},{"full_name":"Matsuda, Michiyuki","first_name":"Michiyuki","last_name":"Matsuda"},{"last_name":"Terai","first_name":"Kenta","full_name":"Terai, Kenta"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["40667649"],"isi":["001567723900009"]},"publication_status":"published","abstract":[{"text":"Collective cell migration is coordinated by the front-to-rear intercellular propagation of EGFR-Ras-ERK pathway activation. However, the molecular mechanisms integrating front-to-rear information into this intercellular signaling cascade, particularly the determinants of cellular front-side specification, remain elusive. We visualized the activity of EGFR, Ras, Rac1 and Rab5A (hereafter Rab5) by using FRET biosensors and chemogenetic tools. Whereas EGFR activation was uniformly observed within cells, Ras activation was biased to the front side within cells. The polarized Ras activation depended on Merlin and Rac1, which also showed front-biased activation. Furthermore, Rab5, a crucial regulator of cell migration, demonstrated similar front-biased activation and was found to function downstream of Ras while being necessary for Rac1 activation. Thus, the positive feedback loop consisting of Ras, Rab5 and Rac1 is activated primarily at the front of collectively migrating cells. These findings offer new spatio-temporal insight into processing front–rear information during collective cell migration.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","title":"Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell migration"},{"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031986673"]},"doi":"10.1007/978-3-031-98668-0_14","publication":"37th International Conference on Computer Aided Verification","year":"2025","date_created":"2025-08-17T22:01:36Z","has_accepted_license":"1","conference":{"location":"Zagreb, Croatia","end_date":"2025-07-25","name":"CAV: Computer Aided Verification","start_date":"2025-07-23"},"ddc":["000"],"quality_controlled":"1","file":[{"date_created":"2025-09-02T05:46:10Z","content_type":"application/pdf","file_name":"2025_CAV_Froleyks.pdf","creator":"dernst","success":1,"file_id":"20266","relation":"main_file","checksum":"15ec1bc9b9409d3b2736f4c9d5f42fd1","access_level":"open_access","date_updated":"2025-09-02T05:46:10Z","file_size":1078274}],"author":[{"full_name":"Froleyks, Nils","first_name":"Nils","last_name":"Froleyks"},{"id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","orcid":"0000-0002-4993-773X","full_name":"Yu, Zhengqi","first_name":"Zhengqi","last_name":"Yu"},{"full_name":"Preiner, Mathias","last_name":"Preiner","first_name":"Mathias"},{"last_name":"Biere","first_name":"Armin","full_name":"Biere, Armin"},{"first_name":"Keijo","last_name":"Heljanko","full_name":"Heljanko, Keijo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":15931,"OA_place":"publisher","title":"Introducing certificates to the hardware model checking competition","page":"281-295","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Certification was made mandatory for the first time in the latest hardware model checking competition. In this case study, we investigate the trade-offs of requiring certificates for both passing and failing properties in the competition. Our evaluation shows that participating model checkers were able to produce compact, correct certificates that could be verified with minimal overhead. Furthermore, the certifying winner of the competition outperforms the previous non-certifying state-of-the-art model checker, demonstrating that certification can be adopted without compromising model checking efficiency.","lang":"eng"}],"external_id":{"isi":["001562507100014"]},"publication_status":"published","alternative_title":["LNCS"],"status":"public","day":"01","ec_funded":1,"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"N. Froleyks, E. Yu, M. Preiner, A. Biere, K. Heljanko, in:, 37th International Conference on Computer Aided Verification, Springer Nature, 2025, pp. 281–295.","ieee":"N. Froleyks, E. Yu, M. Preiner, A. Biere, and K. Heljanko, “Introducing certificates to the hardware model checking competition,” in <i>37th International Conference on Computer Aided Verification</i>, Zagreb, Croatia, 2025, vol. 15931, pp. 281–295.","ista":"Froleyks N, Yu E, Preiner M, Biere A, Heljanko K. 2025. Introducing certificates to the hardware model checking competition. 37th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 15931, 281–295.","ama":"Froleyks N, Yu E, Preiner M, Biere A, Heljanko K. Introducing certificates to the hardware model checking competition. In: <i>37th International Conference on Computer Aided Verification</i>. Vol 15931. Springer Nature; 2025:281-295. doi:<a href=\"https://doi.org/10.1007/978-3-031-98668-0_14\">10.1007/978-3-031-98668-0_14</a>","apa":"Froleyks, N., Yu, E., Preiner, M., Biere, A., &#38; Heljanko, K. (2025). Introducing certificates to the hardware model checking competition. In <i>37th International Conference on Computer Aided Verification</i> (Vol. 15931, pp. 281–295). Zagreb, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-98668-0_14\">https://doi.org/10.1007/978-3-031-98668-0_14</a>","chicago":"Froleyks, Nils, Emily Yu, Mathias Preiner, Armin Biere, and Keijo Heljanko. “Introducing Certificates to the Hardware Model Checking Competition.” In <i>37th International Conference on Computer Aided Verification</i>, 15931:281–95. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-98668-0_14\">https://doi.org/10.1007/978-3-031-98668-0_14</a>.","mla":"Froleyks, Nils, et al. “Introducing Certificates to the Hardware Model Checking Competition.” <i>37th International Conference on Computer Aided Verification</i>, vol. 15931, Springer Nature, 2025, pp. 281–95, doi:<a href=\"https://doi.org/10.1007/978-3-031-98668-0_14\">10.1007/978-3-031-98668-0_14</a>."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"_id":"20189","scopus_import":"1","oa_version":"Published Version","intvolume":"     15931","type":"conference","acknowledgement":"This work is supported in part by the ERC-2020-AdG 101020093, the LIT AI Lab funded by the State of Upper Austria, the Research Council of Finland under the project 336092, and a gift from Intel Corporation.\r\nFurthermore we of course also owe a big thank-you to the submitters of model checkers and benchmarks to the competition over all these years. Without their enthusiasm and support neither the competition nor this study would exist.","language":[{"iso":"eng"}],"month":"01","date_published":"2025-01-01T00:00:00Z","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","date_updated":"2025-12-01T12:34:05Z","isi":1,"oa":1,"file_date_updated":"2025-09-02T05:46:10Z"},{"PlanS_conform":"1","citation":{"short":"H. Katz, A.J. Cameron, A. Saxena, L. Barrufet, N. Choustikov, N.J. Cleri, A. De Graaff, R.S. Ellis, R.A.E. Fosbury, K.E. Heintz, M. Maseda, J.J. Matthee, I. Mcconachie, P.A. Oesch, The Open Journal of Astrophysics 8 (2025).","ieee":"H. Katz <i>et al.</i>, “21 Balmer Jump Street: The nebular continuum at high redshift and implications for the bright galaxy problem, UV continuum slopes, and early stellar populations,” <i>The Open Journal of Astrophysics</i>, vol. 8. Maynooth Academic Publishing, 2025.","ama":"Katz H, Cameron AJ, Saxena A, et al. 21 Balmer Jump Street: The nebular continuum at high redshift and implications for the bright galaxy problem, UV continuum slopes, and early stellar populations. <i>The Open Journal of Astrophysics</i>. 2025;8. doi:<a href=\"https://doi.org/10.33232/001c.142570\">10.33232/001c.142570</a>","ista":"Katz H, Cameron AJ, Saxena A, Barrufet L, Choustikov N, Cleri NJ, De Graaff A, Ellis RS, Fosbury RAE, Heintz KE, Maseda M, Matthee JJ, Mcconachie I, Oesch PA. 2025. 21 Balmer Jump Street: The nebular continuum at high redshift and implications for the bright galaxy problem, UV continuum slopes, and early stellar populations. The Open Journal of Astrophysics. 8.","chicago":"Katz, Harley, Alex J. Cameron, Aayush Saxena, Laia Barrufet, Nicholas Choustikov, Nikko J. Cleri, Anna De Graaff, et al. “21 Balmer Jump Street: The Nebular Continuum at High Redshift and Implications for the Bright Galaxy Problem, UV Continuum Slopes, and Early Stellar Populations.” <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing, 2025. <a href=\"https://doi.org/10.33232/001c.142570\">https://doi.org/10.33232/001c.142570</a>.","apa":"Katz, H., Cameron, A. J., Saxena, A., Barrufet, L., Choustikov, N., Cleri, N. J., … Oesch, P. A. (2025). 21 Balmer Jump Street: The nebular continuum at high redshift and implications for the bright galaxy problem, UV continuum slopes, and early stellar populations. <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing. <a href=\"https://doi.org/10.33232/001c.142570\">https://doi.org/10.33232/001c.142570</a>","mla":"Katz, Harley, et al. “21 Balmer Jump Street: The Nebular Continuum at High Redshift and Implications for the Bright Galaxy Problem, UV Continuum Slopes, and Early Stellar Populations.” <i>The Open Journal of Astrophysics</i>, vol. 8, Maynooth Academic Publishing, 2025, doi:<a href=\"https://doi.org/10.33232/001c.142570\">10.33232/001c.142570</a>."},"day":"25","status":"public","OA_type":"diamond","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"JoMa"}],"arxiv":1,"publisher":"Maynooth Academic Publishing","date_updated":"2025-09-30T14:29:33Z","language":[{"iso":"eng"}],"month":"07","date_published":"2025-07-25T00:00:00Z","oa":1,"file_date_updated":"2025-09-30T14:28:25Z","_id":"20192","scopus_import":"1","acknowledgement":"HK thanks Andrey Kravtsov for insightful comments and thoughtful discussions. We sincerely thank the PIs and Co-Is of the JWST programs where spectral data was made publicly available on the DJA. We refer interested readers to the following papers for survey descriptions regarding the spectral data: Bunker et al. (2023a); D’Eugenio et al. (2024); Bezanson et al. (2022); Barrufet et al. (2024); de Graaff et al. (2024); Finkelstein et al. (2024); Glazebrook et al. (2024); Pierel et al. (2024); Siebert et al. (2024); Maseda et al. (2024). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs listed in Table 1. AJC and AS acknowledge funding from the “FirstGalaxies” Advanced Grant from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 789056). ","type":"journal_article","article_type":"original","oa_version":"Published Version","intvolume":"         8","ddc":["520"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"20412","date_updated":"2025-09-30T14:28:25Z","file_size":1836432,"relation":"main_file","checksum":"ba469d132907147f9e86d87f9124dd14","access_level":"open_access","content_type":"application/pdf","file_name":"2025_OpenJourAstrophysics_Katz.pdf","date_created":"2025-09-30T14:28:25Z","creator":"dernst","success":1}],"publication":"The Open Journal of Astrophysics","doi":"10.33232/001c.142570","publication_identifier":{"eissn":["2565-6120"]},"year":"2025","date_created":"2025-08-17T22:01:37Z","title":"21 Balmer Jump Street: The nebular continuum at high redshift and implications for the bright galaxy problem, UV continuum slopes, and early stellar populations","abstract":[{"lang":"eng","text":"We study the physical origin and spectroscopic impact of extreme nebular emission in high-redshift galaxies. The nebular continuum, which can appear during an extreme starburst, is of particular importance as it tends to redden UV slopes and has a significant contribution to the UV luminosities of galaxies. Furthermore, its shape can be used to infer the gas density and temperature of the interstellar medium. First, we provide a theoretical background, showing how different stellar populations (SPS models, initial mass functions (IMFs), and stellar temperatures) and nebular conditions impact observed galaxy spectra. We demonstrate that, for systems with strong nebular continuum emission, 1) UV fluxes can increase by up to 0.7~mag (or more in the case of hot/massive stars) above the stellar continuum, which may help reconcile the surprising abundance of bright high-redshift galaxies and the elevated UV luminosity density at z>10, 2) at high gas densities, UV slopes can redden from \\beta<-2.5 to \\beta\\sim-1, 3) observational measurements of \\xi_{\\rm ion} are gross underestimates, and 4) UV downturns from two-photon emission can masquerade as damped Ly\\alpha systems. Second, we present a dataset of 58 galaxies observed with NIRSpec on JWST at 2.5<z<9.0 that are selected to have strong nebular continuum emission via the detection of the Balmer jump. Five of the 58 spectra are consistent with being dominated by nebular emission, exhibiting both a Balmer jump and a UV downturn consistent with two-photon emission. For some galaxies, this may imply the presence of hot massive stars and a top-heavy IMF. We conclude by exploring the properties of spectroscopically confirmed z>10 galaxies, finding that UV slopes and UV downturns are in some cases redder or steeper than expected from SPS models, which may hint at more exotic (e.g. hotter/more massive stars or AGN) ionizing sources."}],"publication_status":"published","external_id":{"arxiv":["2408.03189"]},"article_processing_charge":"No","OA_place":"publisher","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Harley","last_name":"Katz","full_name":"Katz, Harley"},{"first_name":"Alex J.","last_name":"Cameron","full_name":"Cameron, Alex J."},{"full_name":"Saxena, Aayush","first_name":"Aayush","last_name":"Saxena"},{"first_name":"Laia","last_name":"Barrufet","full_name":"Barrufet, Laia"},{"first_name":"Nicholas","last_name":"Choustikov","full_name":"Choustikov, Nicholas"},{"full_name":"Cleri, Nikko J.","last_name":"Cleri","first_name":"Nikko J."},{"full_name":"De Graaff, Anna","first_name":"Anna","last_name":"De Graaff"},{"last_name":"Ellis","first_name":"Richard S.","full_name":"Ellis, Richard S."},{"last_name":"Fosbury","first_name":"Robert A.E.","full_name":"Fosbury, Robert A.E."},{"full_name":"Heintz, Kasper E.","last_name":"Heintz","first_name":"Kasper E."},{"first_name":"Michael","last_name":"Maseda","full_name":"Maseda, Michael"},{"first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"last_name":"Mcconachie","first_name":"Ian","full_name":"Mcconachie, Ian"},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."}]},{"scopus_import":"1","_id":"20193","acknowledgement":"We thank A. C. Carnall for supporting our use of Bagpipes. We thank Y. Fu for his help on the use of QSOFitMORE. We thank J. Greene, S. Toft, T. Kakimoto and M. Tanaka for fruitful discussions. This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, under NASA contract NAS 5-03127 for JWST. These observations are associated with programmes GO 1967 and GO 3859. Support for these programmes was provided by NASA through a grant from the Space Telescope Science Institute. This work was supported by World Premier International Research Center Initiative, MEXT, Japan. This work used computing resources at Kavli IPMU. M.O., X.D., J.D.S., Y.M., T.I., K. Ito, K.K. and H.U. are supported by the Japan Society for the Promotion of Science (KAKENHI Grant Numbers JP24K22894, JP22K14071, JP18H01251, JP22H01262, JP21H04494, JP20K14531, JP23K13141, JP17H06130 and JP20H01953). M.O. and K. Inayoshi acknowledge support from the National Natural Science Foundation of China (Grant Numbers 12150410307, 12073003, 11721303, 11991052 and 11950410493). K. Inayoshi acknowledges support from the China Manned Space Project (Grant Numbers CMS-CSST-2021-A04 and CMS-CSST-2021-A06). S.E.I.B. is funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under Emmy Noether Grant Number BO 5771/1-1. Z.H., T.T. and M.S. acknowledge support from the NSF (Grant Numbers AST-2006176, AST-1907208 and AST-2006177). A.L. acknowledges funding from MUR (Grant Number PRIN 2022935STW). B.T. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement Number 950533) and from the Israel Science Foundation (Grant Number 1849/19). F. Walter acknowledges support from the ERC (Grant Cosmic_gas). J.-T.S. is supported by the Deutsche Forschungsgemeinschaft (Project Number 518006966). M.T. acknowledges support from the NWO (Grant Number 0.16.VIDI.189.162, ODIN). S.F. acknowledges support from NASA through the NASA Hubble Fellowship (Grant Number HST-HF2-51505.001-A awarded by the Space Telescope Science Institute). K. Iwasawa acknowledges support under Grant Number PID2022-136827NB-C44 funded by MCIN/AEI/10.13039/501100011033 /FEDER, EU. M. Vestergaard gratefully acknowledges financial support from the Independent Research Fund Denmark (Grant Numbers DFF 8021-00130 and 3103-00146). F. Wang acknowledges support from the NSF (Award Number AST-2513040). R.B. is supported by the SNSF through the Ambizione Grant PZ00P2_223532.","type":"journal_article","intvolume":"         9","oa_version":"Preprint","article_type":"original","date_updated":"2025-12-30T13:08:12Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"ZoHa"}],"date_published":"2025-10-01T00:00:00Z","month":"10","language":[{"iso":"eng"}],"oa":1,"isi":1,"status":"public","day":"01","OA_type":"green","citation":{"ieee":"M. Onoue <i>et al.</i>, “A post-starburst pathway for the formation of massive galaxies and black holes at z &#62; 6,” <i>Nature Astronomy</i>, vol. 9. Springer Nature, pp. 1541–1552, 2025.","short":"M. Onoue, X. Ding, J.D. Silverman, Y. Matsuoka, T. Izumi, M.A. Strauss, C. Ward, C.L. Phillips, K. Ito, I.T. Andika, K. Aoki, J. Arita, S. Baba, R. Bieri, S.E.I. Bosman, A.C. Eilers, S. Fujimoto, M. Habouzit, Z. Haiman, M. Imanishi, K. Inayoshi, K. Iwasawa, K. Jahnke, N. Kashikawa, T. Kawaguchi, K. Kohno, C.H. Lee, J. Li, A. Lupi, J. Lyu, T. Nagao, R. Overzier, J.T. Schindler, M. Schramm, M.T. Scoggins, K. Shimasaku, Y. Toba, B. Trakhtenbrot, M. Trebitsch, T. Treu, H. Umehata, B. Venemans, M. Vestergaard, M. Volonteri, F. Walter, F. Wang, J. Yang, H. Zhang, Nature Astronomy 9 (2025) 1541–1552.","ama":"Onoue M, Ding X, Silverman JD, et al. A post-starburst pathway for the formation of massive galaxies and black holes at z &#62; 6. <i>Nature Astronomy</i>. 2025;9:1541-1552. doi:<a href=\"https://doi.org/10.1038/s41550-025-02628-1\">10.1038/s41550-025-02628-1</a>","ista":"Onoue M, Ding X, Silverman JD, Matsuoka Y, Izumi T, Strauss MA, Ward C, Phillips CL, Ito K, Andika IT, Aoki K, Arita J, Baba S, Bieri R, Bosman SEI, Eilers AC, Fujimoto S, Habouzit M, Haiman Z, Imanishi M, Inayoshi K, Iwasawa K, Jahnke K, Kashikawa N, Kawaguchi T, Kohno K, Lee CH, Li J, Lupi A, Lyu J, Nagao T, Overzier R, Schindler JT, Schramm M, Scoggins MT, Shimasaku K, Toba Y, Trakhtenbrot B, Trebitsch M, Treu T, Umehata H, Venemans B, Vestergaard M, Volonteri M, Walter F, Wang F, Yang J, Zhang H. 2025. A post-starburst pathway for the formation of massive galaxies and black holes at z &#62; 6. Nature Astronomy. 9, 1541–1552.","apa":"Onoue, M., Ding, X., Silverman, J. D., Matsuoka, Y., Izumi, T., Strauss, M. A., … Zhang, H. (2025). A post-starburst pathway for the formation of massive galaxies and black holes at z &#62; 6. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-025-02628-1\">https://doi.org/10.1038/s41550-025-02628-1</a>","chicago":"Onoue, Masafusa, Xuheng Ding, John D. Silverman, Yoshiki Matsuoka, Takuma Izumi, Michael A. Strauss, Charlotte Ward, et al. “A Post-Starburst Pathway for the Formation of Massive Galaxies and Black Holes at z &#62; 6.” <i>Nature Astronomy</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41550-025-02628-1\">https://doi.org/10.1038/s41550-025-02628-1</a>.","mla":"Onoue, Masafusa, et al. “A Post-Starburst Pathway for the Formation of Massive Galaxies and Black Holes at z &#62; 6.” <i>Nature Astronomy</i>, vol. 9, Springer Nature, 2025, pp. 1541–52, doi:<a href=\"https://doi.org/10.1038/s41550-025-02628-1\">10.1038/s41550-025-02628-1</a>."},"OA_place":"repository","volume":9,"author":[{"last_name":"Onoue","first_name":"Masafusa","full_name":"Onoue, Masafusa"},{"first_name":"Xuheng","last_name":"Ding","full_name":"Ding, Xuheng"},{"full_name":"Silverman, John D.","first_name":"John D.","last_name":"Silverman"},{"full_name":"Matsuoka, Yoshiki","last_name":"Matsuoka","first_name":"Yoshiki"},{"full_name":"Izumi, Takuma","last_name":"Izumi","first_name":"Takuma"},{"full_name":"Strauss, Michael A.","first_name":"Michael A.","last_name":"Strauss"},{"full_name":"Ward, Charlotte","first_name":"Charlotte","last_name":"Ward"},{"first_name":"Camryn L.","last_name":"Phillips","full_name":"Phillips, Camryn L."},{"last_name":"Ito","first_name":"Kei","full_name":"Ito, Kei"},{"full_name":"Andika, Irham T.","last_name":"Andika","first_name":"Irham T."},{"full_name":"Aoki, Kentaro","first_name":"Kentaro","last_name":"Aoki"},{"last_name":"Arita","first_name":"Junya","full_name":"Arita, Junya"},{"full_name":"Baba, Shunsuke","first_name":"Shunsuke","last_name":"Baba"},{"last_name":"Bieri","first_name":"Rebekka","full_name":"Bieri, Rebekka"},{"full_name":"Bosman, Sarah E.I.","first_name":"Sarah E.I.","last_name":"Bosman"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"full_name":"Fujimoto, Seiji","first_name":"Seiji","last_name":"Fujimoto"},{"first_name":"Melanie","last_name":"Habouzit","full_name":"Habouzit, Melanie"},{"orcid":"0000-0003-3633-5403","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán","last_name":"Haiman"},{"full_name":"Imanishi, Masatoshi","first_name":"Masatoshi","last_name":"Imanishi"},{"full_name":"Inayoshi, Kohei","last_name":"Inayoshi","first_name":"Kohei"},{"full_name":"Iwasawa, Kazushi","last_name":"Iwasawa","first_name":"Kazushi"},{"full_name":"Jahnke, Knud","last_name":"Jahnke","first_name":"Knud"},{"last_name":"Kashikawa","first_name":"Nobunari","full_name":"Kashikawa, Nobunari"},{"full_name":"Kawaguchi, Toshihiro","first_name":"Toshihiro","last_name":"Kawaguchi"},{"last_name":"Kohno","first_name":"Kotaro","full_name":"Kohno, Kotaro"},{"full_name":"Lee, Chien Hsiu","first_name":"Chien Hsiu","last_name":"Lee"},{"first_name":"Junyao","last_name":"Li","full_name":"Li, Junyao"},{"first_name":"Alessandro","last_name":"Lupi","full_name":"Lupi, Alessandro"},{"first_name":"Jianwei","last_name":"Lyu","full_name":"Lyu, Jianwei"},{"first_name":"Tohru","last_name":"Nagao","full_name":"Nagao, Tohru"},{"last_name":"Overzier","first_name":"Roderik","full_name":"Overzier, Roderik"},{"full_name":"Schindler, Jan Torge","last_name":"Schindler","first_name":"Jan Torge"},{"full_name":"Schramm, Malte","first_name":"Malte","last_name":"Schramm"},{"full_name":"Scoggins, Matthew T.","first_name":"Matthew T.","last_name":"Scoggins"},{"first_name":"Kazuhiro","last_name":"Shimasaku","full_name":"Shimasaku, Kazuhiro"},{"last_name":"Toba","first_name":"Yoshiki","full_name":"Toba, Yoshiki"},{"full_name":"Trakhtenbrot, Benny","first_name":"Benny","last_name":"Trakhtenbrot"},{"last_name":"Trebitsch","first_name":"Maxime","full_name":"Trebitsch, Maxime"},{"first_name":"Tommaso","last_name":"Treu","full_name":"Treu, Tommaso"},{"last_name":"Umehata","first_name":"Hideki","full_name":"Umehata, Hideki"},{"first_name":"Bram","last_name":"Venemans","full_name":"Venemans, Bram"},{"first_name":"Marianne","last_name":"Vestergaard","full_name":"Vestergaard, Marianne"},{"first_name":"Marta","last_name":"Volonteri","full_name":"Volonteri, Marta"},{"last_name":"Walter","first_name":"Fabian","full_name":"Walter, Fabian"},{"full_name":"Wang, Feige","last_name":"Wang","first_name":"Feige"},{"full_name":"Yang, Jinyi","last_name":"Yang","first_name":"Jinyi"},{"last_name":"Zhang","first_name":"Haowen","full_name":"Zhang, Haowen"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A post-starburst pathway for the formation of massive galaxies and black holes at z > 6","publication_status":"published","external_id":{"arxiv":["2409.07113"],"isi":["001548138600001"]},"abstract":[{"lang":"eng","text":"Understanding the rapid formation of supermassive black holes in the early Universe requires insights into stellar mass growth in host galaxies. Here we present NIRSpec rest-frame optical spectra and NIRCam imaging from JWST of two galaxies at z > 6, both hosting moderate-luminosity quasars. These galaxies exhibit Balmer absorption lines, like low-redshift post-starburst galaxies. Our analyses of the medium-resolution spectra and multiband photometry show that the bulk of the stellar mass (log(M*/M☉) ≥ 10.6) formed in starburst episodes at redshift 9 and 7. One of the galaxies shows a clear Balmer break and lacks spatially resolved Hα emission. It falls well below the star-formation main sequence at z = 6, indicating quiescence. The other is transitioning to quiescence; together, these massive galaxies are among the most distant post-starburst systems known. The blueshifted wings of the quasar [O iii] emission lines indicate quasar-driven outflow, which possibly influences star formation. Direct stellar velocity dispersion measurements reveal that one galaxy follows the local black hole mass versus σ* relation whereas the other is overmassive. The existence of massive post-starburst galaxies hosting billion-solar-mass black holes in short-lived quasar phases indicates that supermassive black holes and host galaxies played a principal role in each other’s rapid early formation."}],"article_processing_charge":"No","page":"1541-1552","publication":"Nature Astronomy","doi":"10.1038/s41550-025-02628-1","publication_identifier":{"eissn":["2397-3366"]},"date_created":"2025-08-17T22:01:38Z","year":"2025","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2409.07113"}],"quality_controlled":"1"}]