[{"volume":51,"article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","citation":{"ista":"Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L, Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. Reproductive Biomedicine Online. 51(3), 104942.","short":"I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser, R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).","ama":"Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. 2025;51(3). doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>","ieee":"I. Yotova <i>et al.</i>, “LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3. Elsevier, 2025.","chicago":"Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>.","apa":"Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., … Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>","mla":"Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3, 104942, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>."},"publication":"Reproductive Biomedicine Online","date_created":"2025-07-27T22:01:25Z","date_updated":"2025-09-30T14:10:46Z","quality_controlled":"1","language":[{"iso":"eng"}],"article_number":"104942","intvolume":"        51","month":"07","publication_identifier":{"eissn":["1472-6491"],"issn":["1472-6483"]},"_id":"20079","department":[{"_id":"SiHi"}],"isi":1,"day":"17","article_processing_charge":"No","author":[{"first_name":"Iveta","full_name":"Yotova, Iveta","last_name":"Yotova"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Rainer","full_name":"Rainer, Lisa","first_name":"Lisa"},{"last_name":"Kaup","first_name":"Leonie","full_name":"Kaup, Leonie"},{"last_name":"Heine","first_name":"Jana","full_name":"Heine, Jana"},{"full_name":"Sandrieser, Lejla","first_name":"Lejla","last_name":"Sandrieser"},{"first_name":"René","full_name":"Wenzl, René","last_name":"Wenzl"},{"last_name":"Hudson","first_name":"Quanah J.","full_name":"Hudson, Quanah J."}],"publisher":"Elsevier","pmid":1,"date_published":"2025-07-17T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study was combined with functional experiments in the 12Z endometriosis epithelial cell line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial samples were collected by curettage, and ectopic endometrial lesion samples were collected by laparoscopic surgery from 24 control patients and 41 patients with endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown using siRNA, performing proliferation, adhesion, migration and invasion assays, as well as assessing apoptosis and cell cycle changes with flow cytometry assays. In order to assess the relationship between LINC01638 and histone deacetylase class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z cells led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression, and G1 phase arrest. Further analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are down-regulated in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1 was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment combined with LINC01638 knockdown indicated that LINC01638 regulates RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated in the epithelial layer of endometriotic lesions compared with eutopic endometrium, supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic lesions."}],"publication_status":"published","year":"2025","scopus_import":"1","issue":"3","external_id":{"isi":["001549819000002"],"pmid":["40680553"]},"doi":"10.1016/j.rbmo.2025.104942","title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","OA_type":"closed access","oa_version":"None","acknowledgement":"The authors wish to thank all the participants and health professionals involved in this study. In addition, the authors wish to thank technical assistants Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure and resources.\r\nOpen access funding was provided by the Medical University of Vienna."},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","volume":16,"oa":1,"file_date_updated":"2025-07-31T07:28:54Z","date_updated":"2025-09-30T14:08:22Z","quality_controlled":"1","date_created":"2025-07-27T22:01:26Z","citation":{"ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025.","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>.","apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>."},"publication":"Frontiers in Plant Science","type":"journal_article","month":"07","DOAJ_listed":"1","ddc":["580"],"intvolume":"        16","article_number":"1612366","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","_id":"20080","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"isi":1,"publication_identifier":{"eissn":["1664-462X"]},"date_published":"2025-07-04T00:00:00Z","pmid":1,"author":[{"last_name":"Gallemi","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal","full_name":"Gallemi, Marçal"},{"last_name":"Montesinos López","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","full_name":"Montesinos López, Juan C"},{"first_name":"Nikola","full_name":"Zarevski, Nikola","id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","last_name":"Zarevski"},{"last_name":"Pribyl","full_name":"Pribyl, Jan","first_name":"Jan"},{"full_name":"Skládal, Petr","first_name":"Petr","last_name":"Skládal"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"publisher":"Frontiers Media","day":"04","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"file":[{"file_name":"2025_FrontiersPlantSc_Gallemi.pdf","creator":"dernst","relation":"main_file","file_size":3665187,"file_id":"20093","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","success":1,"access_level":"open_access","date_updated":"2025-07-31T07:28:54Z","content_type":"application/pdf","date_created":"2025-07-31T07:28:54Z"}],"year":"2025","scopus_import":"1","publication_status":"published","OA_place":"publisher","abstract":[{"text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction.","lang":"eng"}],"corr_author":"1","status":"public","external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"ec_funded":1,"oa_version":"Published Version","acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","OA_type":"gold","PlanS_conform":"1","doi":"10.3389/fpls.2025.1612366","title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties"},{"date_created":"2025-07-27T22:01:26Z","date_updated":"2026-02-16T11:49:40Z","quality_controlled":"1","citation":{"chicago":"Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Sibson α-Mutual Information and Its Variational Representations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2025. <a href=\"https://doi.org/10.1109/TIT.2025.3587340\">https://doi.org/10.1109/TIT.2025.3587340</a>.","apa":"Esposito, A. R., Gastpar, M., &#38; Issa, I. (2025). Sibson α-mutual information and its variational representations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2025.3587340\">https://doi.org/10.1109/TIT.2025.3587340</a>","mla":"Esposito, Amedeo Roberto, et al. “Sibson α-Mutual Information and Its Variational Representations.” <i>IEEE Transactions on Information Theory</i>, IEEE, 2025, doi:<a href=\"https://doi.org/10.1109/TIT.2025.3587340\">10.1109/TIT.2025.3587340</a>.","ista":"Esposito AR, Gastpar M, Issa I. 2025. Sibson α-mutual information and its variational representations. IEEE Transactions on Information Theory.","short":"A.R. Esposito, M. Gastpar, I. Issa, IEEE Transactions on Information Theory (2025).","ama":"Esposito AR, Gastpar M, Issa I. Sibson α-mutual information and its variational representations. <i>IEEE Transactions on Information Theory</i>. 2025. doi:<a href=\"https://doi.org/10.1109/TIT.2025.3587340\">10.1109/TIT.2025.3587340</a>","ieee":"A. R. Esposito, M. Gastpar, and I. Issa, “Sibson α-mutual information and its variational representations,” <i>IEEE Transactions on Information Theory</i>. IEEE, 2025."},"publication":"IEEE Transactions on Information Theory","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"article_type":"original","department":[{"_id":"MaMo"}],"_id":"20081","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"month":"07","language":[{"iso":"eng"}],"OA_place":"repository","abstract":[{"text":"Information measures can be constructed from Rényi divergences much like mutual information from Kullback-Leibler divergence. One such information measure is known as Sibson α-mutual information and has received renewed attention recently in several contexts: concentration of measure under dependence, statistical learning, hypothesis testing, and estimation theory. In this paper, we survey and extend the state of the art. In particular, we introduce variational representations for Sibson α-mutual information and employ them in each described context to derive novel results. Namely, we produce generalized Transportation-Cost inequalities and Fano-type inequalities. We also present an overview of known applications, spanning from learning theory and Bayesian risk to universal prediction.","lang":"eng"}],"publication_status":"epub_ahead","year":"2025","scopus_import":"1","status":"public","arxiv":1,"publisher":"IEEE","author":[{"id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto","full_name":"Esposito, Amedeo Roberto","last_name":"Esposito"},{"full_name":"Gastpar, Michael","first_name":"Michael","last_name":"Gastpar"},{"last_name":"Issa","first_name":"Ibrahim","full_name":"Issa, Ibrahim"}],"date_published":"2025-07-11T00:00:00Z","day":"11","article_processing_charge":"No","oa_version":"Preprint","doi":"10.1109/TIT.2025.3587340","title":"Sibson α-mutual information and its variational representations","OA_type":"green","external_id":{"arxiv":["2405.08352"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.08352"}]},{"article_number":"035005","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"07","DOAJ_listed":"1","ddc":["550"],"intvolume":"         4","publication_identifier":{"eissn":["2752-5295"]},"has_accepted_license":"1","_id":"20098","department":[{"_id":"CaMu"}],"article_type":"original","volume":4,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","id":"20107","status":"public"}]},"type":"journal_article","publication":"Environmental Research: Climate","citation":{"mla":"Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>, vol. 4, no. 3, 035005, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>.","chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development key to limiting climate change-driven wildfire damages,” <i>Environmental Research: Climate</i>, vol. 4, no. 3. IOP Publishing, 2025.","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development key to limiting climate change-driven wildfire damages. Environmental Research: Climate. 4(3), 035005.","ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. 2025;4(3). doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research: Climate 4 (2025)."},"file_date_updated":"2025-08-04T07:38:14Z","date_updated":"2025-08-04T07:46:33Z","quality_controlled":"1","date_created":"2025-07-31T14:03:16Z","issue":"3","ec_funded":1,"project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"OA_type":"gold","PlanS_conform":"1","doi":"10.1088/2752-5295/adec11","title":"Sustainable development key to limiting climate change-driven wildfire damages","oa_version":"Published Version","acknowledgement":"We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback for this work. YLH is supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413. EB, MW, and YQ are supported by the European Union’s Horizon Europe research and innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank the two anonymous reviewers for providing helpful feedback that greatly improved this manuscript.","day":"15","article_processing_charge":"Yes","file":[{"creator":"dernst","relation":"main_file","file_name":"2025_EnvironResearchClimate_Hwong.pdf","content_type":"application/pdf","date_updated":"2025-08-04T07:38:14Z","date_created":"2025-08-04T07:38:14Z","file_size":2807041,"file_id":"20108","success":1,"checksum":"ca679496767021e792b0378c48fdee8c","access_level":"open_access"}],"date_published":"2025-07-15T00:00:00Z","author":[{"last_name":"Hwong","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479"},{"last_name":"Byers","full_name":"Byers, Edward","first_name":"Edward"},{"full_name":"Werning, Michaela","first_name":"Michaela","last_name":"Werning"},{"first_name":"Yann","full_name":"Quilcaille, Yann","last_name":"Quilcaille"}],"publisher":"IOP Publishing","corr_author":"1","status":"public","year":"2025","scopus_import":"1","abstract":[{"text":"Climate change is causing wildfires to become more frequent and intense. While predicting burned areas using bioclimatic and anthropogenic factors is an active research area, few studies have examined what drives the economic damages of wildfires. Our study aims to fill this gap by analyzing key factors influencing global economic wildfire damages and projecting future damages under three shared socioeconomic pathways (SSPs). We apply regression analyses to identify significant predictors of economic wildfire damages at country levels and use the fitted model to project future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability index (HVI), reflecting socioeconomic conditions, is the strongest predictor of historical wildfire damages, followed by water vapor pressure deficit during the fire season and population density around forested areas. We found high population density to be associated with lower damages. These findings contrast with studies of burned areas, where climate factors are more dominant. Our model projects that by 2070, average global economic wildfire damages will be three times higher under SSP370 than SSP126. Our model also shows that following SSP126 not only reduces wildfire damages but also lessens the inequalities in damage distribution across countries. This pathway’s dual focus on equitable socioeconomic progress and climate action potentially enhances a country’s resilience that helps mitigate wildfire damages. Our analyses also indicate that strong socioeconomic development can offset wildfire damages associated with climate hazards, although this is less certain under SSP370. SSP126’s integrated approach improves both socioeconomic conditions and limits global warming, providing substantial benefits to less developed countries while still reducing damages in developed nations, despite their already low HVI scores. Our work complements existing research on burned areas and underscores the importance of sustainable development and international collaboration in reducing the economic damages of wildfires.","lang":"eng"}],"OA_place":"publisher","publication_status":"published"},{"ddc":["570"],"intvolume":"        44","month":"08","DOAJ_listed":"1","language":[{"iso":"eng"}],"article_number":"116080","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"PeJo"}],"_id":"20099","isi":1,"has_accepted_license":"1","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":44,"oa":1,"article_type":"original","date_created":"2025-08-03T22:01:30Z","file_date_updated":"2025-08-04T06:53:07Z","quality_controlled":"1","date_updated":"2025-09-30T14:12:02Z","publication":"Cell Reports","citation":{"ista":"Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information flow through hippocampal CA3. Cell Reports. 44(8), 116080.","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).","ama":"Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. 2025;44(8). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>","ieee":"J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes information flow through hippocampal CA3,” <i>Cell Reports</i>, vol. 44, no. 8. Elsevier, 2025.","chicago":"Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>.","apa":"Watson, J., Vargas Barroso, V. M., &#38; Jonas, P. M. (2025). Cell-specific wiring routes information flow through hippocampal CA3. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">https://doi.org/10.1016/j.celrep.2025.116080</a>","mla":"Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through Hippocampal CA3.” <i>Cell Reports</i>, vol. 44, no. 8, 116080, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.116080\">10.1016/j.celrep.2025.116080</a>."},"type":"journal_article","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["001544472300002"]},"ec_funded":1,"issue":"8","oa_version":"Published Version","acknowledgement":"We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically reading an earlier version of the manuscript. We also thank Florian Marr and Christina Altmutter for excellent technical assistance, Alois Schlögl for programming and data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.) and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).","PlanS_conform":"1","doi":"10.1016/j.celrep.2025.116080","title":"Cell-specific wiring routes information flow through hippocampal CA3","OA_type":"gold","author":[{"last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","first_name":"Jake"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"publisher":"Elsevier","date_published":"2025-08-01T00:00:00Z","file":[{"relation":"main_file","creator":"dernst","file_name":"2025_CellReports_Watson.pdf","date_created":"2025-08-04T06:53:07Z","date_updated":"2025-08-04T06:53:07Z","content_type":"application/pdf","success":1,"checksum":"556ff9760661ecd23949d75031043b1f","access_level":"open_access","file_size":27695214,"file_id":"20106"}],"day":"01","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"publication_status":"published","OA_place":"publisher","abstract":[{"lang":"eng","text":"The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3."}],"year":"2025","scopus_import":"1","corr_author":"1","status":"public"},{"article_processing_charge":"Yes","day":"27","file":[{"relation":"main_file","creator":"dernst","file_name":"2025_CompStrucBiotechJour_Vedula.pdf","date_created":"2025-08-04T06:25:23Z","content_type":"application/pdf","date_updated":"2025-08-04T06:25:23Z","success":1,"checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","access_level":"open_access","file_size":6609770,"file_id":"20104"}],"date_published":"2025-06-27T00:00:00Z","publisher":"Elsevier","author":[{"last_name":"Vedula","first_name":"Sanketh","full_name":"Vedula, Sanketh","id":"94f2fe44-70fa-11f0-b76b-92922c09452b"},{"first_name":"Alexander","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein"},{"first_name":"Ailie","full_name":"Marx, Ailie","last_name":"Marx"}],"status":"public","scopus_import":"1","year":"2025","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."}],"OA_place":"publisher","publication_status":"published","external_id":{"isi":["001583543100001"]},"OA_type":"gold","title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","doi":"10.1016/j.csbj.2025.07.039","PlanS_conform":"1","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.","oa_version":"Published Version","article_type":"original","oa":1,"volume":27,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"software","id":"20103"}],"link":[{"url":"https://github.com/sankethvedula/AFChimera","relation":"software"}]},"type":"journal_article","publication":"Computational and Structural Biotechnology Journal","citation":{"short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298.","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.","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.","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>."},"quality_controlled":"1","date_updated":"2025-11-27T14:09:59Z","file_date_updated":"2025-08-04T06:25:23Z","date_created":"2025-08-03T22:01:31Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"DOAJ_listed":"1","month":"06","intvolume":"        27","ddc":["000","570"],"publication_identifier":{"eissn":["2001-0370"]},"page":"3292-3298","has_accepted_license":"1","_id":"20100","isi":1,"department":[{"_id":"AlBr"}]},{"tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"language":[{"iso":"eng"}],"month":"07","intvolume":"       645","ddc":["570"],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"439-447","has_accepted_license":"1","department":[{"_id":"GradSch"}],"_id":"20101","article_type":"original","oa":1,"volume":645,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"research_data","id":"20883"}]},"publication":"Nature","citation":{"ieee":"F. Baier <i>et al.</i>, “The neural basis of species-specific defensive behaviour in Peromyscus mice,” <i>Nature</i>, vol. 645. Springer Nature, pp. 439–447, 2025.","ama":"Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. 2025;645:439-447. doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>","short":"F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447.","ista":"Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. 645, 439–447.","mla":"Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>, vol. 645, Springer Nature, 2025, pp. 439–47, doi:<a href=\"https://doi.org/10.1038/s41586-025-09241-2\">10.1038/s41586-025-09241-2</a>.","apa":"Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>","chicago":"Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E. Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09241-2\">https://doi.org/10.1038/s41586-025-09241-2</a>."},"type":"journal_article","date_updated":"2026-01-05T11:38:40Z","quality_controlled":"1","file_date_updated":"2025-12-30T07:39:45Z","date_created":"2025-08-03T22:01:31Z","external_id":{"pmid":["40702175"]},"OA_type":"hybrid","doi":"10.1038/s41586-025-09241-2","title":"The neural basis of species-specific defensive behaviour in Peromyscus mice","acknowledgement":"The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J. Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice on optogenetic experiments; A. Calzoni for help aligning histological sections to a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with the electrophysiology analysis; I. Vlaemick for help with whole cell experiments; R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan Brockman Williamson Fellowship. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute, of which H.E.H. was an Investigator.","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","day":"23","file":[{"file_name":"2025_Nature_Baier.pdf","creator":"dernst","relation":"main_file","file_id":"20884","file_size":53301589,"access_level":"open_access","checksum":"7ea846a7a49b3b2a248f6a27ab13d591","success":1,"content_type":"application/pdf","date_updated":"2025-12-30T07:39:45Z","date_created":"2025-12-30T07:39:45Z"}],"date_published":"2025-07-23T00:00:00Z","pmid":1,"publisher":"Springer Nature","author":[{"last_name":"Baier","full_name":"Baier, Felix","first_name":"Felix"},{"first_name":"Katja","full_name":"Reinhard, Katja","last_name":"Reinhard"},{"full_name":"Nuttin, Bram","first_name":"Bram","last_name":"Nuttin"},{"first_name":"Arnau","full_name":"Sans-Dublanc, Arnau","last_name":"Sans-Dublanc"},{"first_name":"Chen","full_name":"Liu, Chen","last_name":"Liu"},{"last_name":"Tong","full_name":"Tong, Victoria","first_name":"Victoria"},{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie","full_name":"Murmann, Julie Stefanie","last_name":"Murmann"},{"last_name":"Wierda","first_name":"Keimpe","full_name":"Wierda, Keimpe"},{"full_name":"Farrow, Karl","first_name":"Karl","last_name":"Farrow"},{"last_name":"Hoekstra","full_name":"Hoekstra, Hopi E.","first_name":"Hopi E."}],"status":"public","scopus_import":"1","year":"2025","publication_status":"published","OA_place":"publisher","abstract":[{"lang":"eng","text":"Evading imminent threat from predators is critical for animal survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours remains poorly understood1,2,3,4. Here we find that two sister species of deer mice (genus Peromyscus)5 show different responses to the same looming stimulus: Peromyscus maniculatus, which occupies densely vegetated habitats, predominantly escapes, whereas the open field specialist, Peromyscus polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal grey (dPAG) in driving behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus, and their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain."}]},{"date_published":"2025-11-01T00:00:00Z","author":[{"last_name":"Raffini","full_name":"Raffini, Francesca","first_name":"Francesca"},{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Juan","full_name":"Galindo, Juan","last_name":"Galindo"},{"full_name":"Rolán-Alvarez, Emilio","first_name":"Emilio","last_name":"Rolán-Alvarez"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"publisher":"Wiley","article_processing_charge":"Yes (in subscription journal)","day":"01","file":[{"creator":"dernst","relation":"main_file","file_name":"2025_MolecEcology_Raffini.pdf","content_type":"application/pdf","date_updated":"2025-12-30T09:25:17Z","date_created":"2025-12-30T09:25:17Z","file_id":"20906","file_size":2767745,"access_level":"open_access","checksum":"ec01edda64cfbc6cbc8adf300f719644","success":1}],"scopus_import":"1","year":"2025","OA_place":"publisher","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."}],"publication_status":"published","status":"public","external_id":{"isi":["001538172800001"]},"issue":"21","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.","oa_version":"Published Version","OA_type":"hybrid","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","doi":"10.1111/mec.70025","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"volume":34,"quality_controlled":"1","date_updated":"2025-12-30T09:25:45Z","file_date_updated":"2025-12-30T09:25:17Z","date_created":"2025-08-03T22:01:31Z","type":"journal_article","citation":{"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>.","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>","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.","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.","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).","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>"},"publication":"Molecular Ecology","month":"11","intvolume":"        34","ddc":["570"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"e70025","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"20102","isi":1,"department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]}},{"date_updated":"2025-11-27T14:09:58Z","year":"2025","date_created":"2025-08-04T06:18:55Z","OA_place":"repository","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"}],"status":"public","citation":{"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>.","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>","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>.","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).","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>","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>."},"type":"research_data_reference","date_published":"2025-06-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_for_analysis_in","id":"20100","status":"public"}]},"publisher":"Harvard Dataverse","author":[{"full_name":"Vedula, Sanketh","first_name":"Sanketh","id":"94f2fe44-70fa-11f0-b76b-92922c09452b","last_name":"Vedula"},{"last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"}],"article_processing_charge":"No","day":"27","oa":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","has_accepted_license":"1","_id":"20103","department":[{"_id":"AlBr"}],"doi":"10.7910/DVN/DYEBVM","title":"Replication Data for: \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\"","month":"06","ddc":["000"],"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"main_file_link":[{"url":"https://doi.org/10.7910/DVN/DYEBVM","open_access":"1"}]},{"OA_place":"repository","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"}],"date_created":"2025-08-04T07:34:39Z","year":"2025","date_updated":"2025-08-04T07:46:33Z","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>.","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>","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>.","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.","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>","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025).","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>."},"type":"research_data_reference","corr_author":"1","status":"public","author":[{"full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479","last_name":"Hwong"},{"first_name":"Edward","full_name":"Byers, Edward","last_name":"Byers"},{"first_name":"Michaela","full_name":"Werning, Michaela","last_name":"Werning"},{"full_name":"Quilcaille, Yann","first_name":"Yann","last_name":"Quilcaille"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"20098"}]},"publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-05-21T00:00:00Z","oa":1,"day":"21","article_processing_charge":"No","_id":"20107","department":[{"_id":"CaMu"}],"oa_version":"Published Version","has_accepted_license":"1","title":"Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages","doi":"10.5281/ZENODO.13988679","OA_type":"green","ddc":["550"],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"month":"05","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.15409324","open_access":"1"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"OA_type":"gold","doi":"10.1016/j.celrep.2025.116056","title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","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.","oa_version":"Published Version","issue":"8","external_id":{"isi":["001542038500001"],"pmid":["40714631"]},"status":"public","scopus_import":"1","year":"2025","OA_place":"publisher","publication_status":"published","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."}],"article_processing_charge":"Yes","day":"24","file":[{"checksum":"3c43e040a4a7a65ec67ae1d2bb81261a","success":1,"access_level":"open_access","file_size":24178018,"file_id":"20120","date_created":"2025-08-05T06:15:09Z","date_updated":"2025-08-05T06:15:09Z","content_type":"application/pdf","file_name":"2025_CellReports_Xu.pdf","relation":"main_file","creator":"dernst"}],"pmid":1,"date_published":"2025-07-24T00:00:00Z","publisher":"Elsevier","author":[{"last_name":"Xu","full_name":"Xu, Faqing","first_name":"Faqing"},{"full_name":"Yu, Yongqiang","first_name":"Yongqiang","last_name":"Yu"},{"last_name":"Guan","id":"56aad729-cca2-11ed-a45a-9b4138991a48","full_name":"Guan, Bin","first_name":"Bin"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"last_name":"Xu","full_name":"Xu, Zhihong","first_name":"Zhihong"},{"full_name":"Xue, Hongwei","first_name":"Hongwei","last_name":"Xue"}],"publication_identifier":{"eissn":["2211-1247"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","has_accepted_license":"1","department":[{"_id":"JiFr"}],"_id":"20116","isi":1,"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"article_number":"116056","language":[{"iso":"eng"}],"DOAJ_listed":"1","month":"07","intvolume":"        44","ddc":["580"],"type":"journal_article","citation":{"short":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (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.","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.","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>","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>.","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>."},"publication":"Cell Reports","quality_controlled":"1","date_updated":"2025-09-30T14:13:45Z","file_date_updated":"2025-08-05T06:15:09Z","date_created":"2025-08-04T13:39:11Z","article_type":"original","oa":1,"volume":44,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"external_id":{"isi":["001603560700005"],"pmid":["40730155"]},"issue":"21","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","title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","doi":"10.1016/j.cell.2025.07.002","PlanS_conform":"1","OA_type":"hybrid","author":[{"full_name":"Zhang, Zhiying","first_name":"Zhiying","last_name":"Zhang"},{"first_name":"Thomas C.","full_name":"Todeschini, Thomas C.","last_name":"Todeschini"},{"last_name":"Wu","first_name":"Yi","full_name":"Wu, Yi"},{"first_name":"Roman","full_name":"Kogay, Roman","last_name":"Kogay"},{"last_name":"Naji","first_name":"Ameena","full_name":"Naji, Ameena"},{"last_name":"Cardenas Rodriguez","first_name":"Joaquin","full_name":"Cardenas Rodriguez, Joaquin"},{"first_name":"Rupavidhya","full_name":"Mondi, Rupavidhya","last_name":"Mondi"},{"first_name":"Daniel","full_name":"Kaganovich, Daniel","last_name":"Kaganovich"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"first_name":"Marianna","full_name":"Teplova, Marianna","last_name":"Teplova"},{"last_name":"Amen","full_name":"Amen, Triana","first_name":"Triana"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"},{"full_name":"Patel, Dinshaw J.","first_name":"Dinshaw J.","last_name":"Patel"},{"first_name":"Franklin L.","full_name":"Nobrega, Franklin L.","last_name":"Nobrega"}],"publisher":"Elsevier","pmid":1,"date_published":"2025-10-16T00:00:00Z","file":[{"file_name":"2025_Cell_Zhang.pdf","relation":"main_file","creator":"dernst","checksum":"b944de5fbd7455f58e1ff338ad352239","success":1,"access_level":"open_access","file_size":32104588,"file_id":"20875","date_created":"2025-12-29T14:15:25Z","date_updated":"2025-12-29T14:15:25Z","content_type":"application/pdf"}],"article_processing_charge":"Yes (in subscription journal)","day":"16","abstract":[{"lang":"eng","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."}],"publication_status":"published","OA_place":"publisher","scopus_import":"1","year":"2025","status":"public","intvolume":"       188","ddc":["570"],"month":"10","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JaBr"}],"_id":"20143","isi":1,"has_accepted_license":"1","page":"5862-5877.e23","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":188,"article_type":"original","date_created":"2025-08-07T05:00:04Z","date_updated":"2025-12-29T14:15:58Z","quality_controlled":"1","file_date_updated":"2025-12-29T14:15:25Z","citation":{"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>","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.","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.","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>.","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>."},"type":"journal_article","publication":"Cell"},{"month":"08","ddc":["020"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.15269364","open_access":"1"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","_id":"20146","department":[{"_id":"E-Lib"}],"OA_type":"gold","title":"Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures","doi":"10.5281/zenodo.15269364","date_published":"2025-08-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","author":[{"last_name":"Gredler","first_name":"Paul","full_name":"Gredler, Paul"},{"last_name":"Kaier","full_name":"Kaier, Christian","first_name":"Christian"},{"orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","full_name":"Danowski, Patrick","last_name":"Danowski"},{"full_name":"Zoyer, Michael","first_name":"Michael","last_name":"Zoyer"},{"last_name":"Rieck","full_name":"Rieck, Katharina","first_name":"Katharina"},{"full_name":"Ferus, Andreas","first_name":"Andreas","last_name":"Ferus"},{"last_name":"Rosenberger","full_name":"Rosenberger, Elisabeth","first_name":"Elisabeth"},{"last_name":"Löffler","full_name":"Löffler, Alexander","first_name":"Alexander"},{"full_name":"Hofer, Lisa","first_name":"Lisa","last_name":"Hofer"},{"full_name":"Still, Laura","first_name":"Laura","last_name":"Still"}],"article_processing_charge":"No","day":"07","oa":1,"date_updated":"2025-08-11T07:20:03Z","year":"2025","date_created":"2025-08-07T11:10:14Z","publication_status":"published","OA_place":"publisher","abstract":[{"lang":"eng","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."}],"status":"public","type":"working_paper","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.","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.","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>","ieee":"P. Gredler <i>et al.</i>, <i>Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures</i>. Zenodo, 2025.","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>","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>."}},{"corr_author":"1","status":"public","year":"2025","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","OA_place":"publisher","day":"01","article_processing_charge":"Yes (in subscription journal)","file":[{"file_name":"2025_TrendsNeurosciences_Hetzer.pdf","creator":"dernst","relation":"main_file","file_size":327847,"file_id":"20873","checksum":"90942491b499f70b0bf48b8aec2e7387","success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2025-12-29T13:47:27Z","date_created":"2025-12-29T13:47:27Z"}],"pmid":1,"date_published":"2025-09-01T00:00:00Z","publisher":"Elsevier","author":[{"last_name":"Hetzer","first_name":"Martin W","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"last_name":"Toda","full_name":"Toda, Tomohisa","first_name":"Tomohisa"}],"OA_type":"hybrid","PlanS_conform":"1","title":"Long-lived cellular molecules in the brain","doi":"10.1016/j.tins.2025.07.004","oa_version":"Published Version","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.","issue":"9","external_id":{"pmid":["40744775"],"isi":["001568965400001"]},"type":"journal_article","citation":{"short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.","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.","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>.","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>."},"publication":"Trends in Neurosciences","file_date_updated":"2025-12-29T13:47:27Z","quality_controlled":"1","date_updated":"2025-12-29T13:47:58Z","date_created":"2025-08-10T22:01:29Z","article_type":"original","volume":48,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1878-108X"],"issn":["0166-2236"]},"has_accepted_license":"1","page":"645-654","isi":1,"_id":"20154","department":[{"_id":"MaHe"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"09","ddc":["570"],"intvolume":"        48"},{"day":"01","article_processing_charge":"No","arxiv":1,"author":[{"last_name":"Brigati","full_name":"Brigati, Giovanni","first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1"},{"first_name":"Gabriel","full_name":"Stoltz, Gabriel","last_name":"Stoltz"}],"publisher":"Society for Industrial and Applied Mathematics","date_published":"2025-08-01T00:00:00Z","corr_author":"1","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","OA_place":"repository","year":"2025","scopus_import":"1","ec_funded":1,"issue":"4","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.14506"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"external_id":{"isi":["001550830900006"],"arxiv":["2302.14506"]},"doi":"10.1137/24M1700351","title":"How to construct explicit decay rates for kinetic Fokker–Planck equations?","OA_type":"green","oa_version":"Preprint","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).","volume":57,"oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"SIAM Journal on Mathematical Analysis","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>.","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.","short":"G. Brigati, G. Stoltz, SIAM Journal on Mathematical Analysis 57 (2025) 3587–3622.","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."},"date_created":"2025-08-10T22:01:29Z","quality_controlled":"1","date_updated":"2025-11-05T13:51:40Z","language":[{"iso":"eng"}],"intvolume":"        57","month":"08","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"isi":1,"_id":"20155","department":[{"_id":"JaMa"}],"page":"3587-3622"},{"PlanS_conform":"1","doi":"10.1016/j.cois.2025.101411","title":"Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation","OA_type":"hybrid","oa_version":"Published Version","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.","project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323"}],"external_id":{"isi":["001582424100001"]},"corr_author":"1","status":"public","OA_place":"publisher","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."}],"publication_status":"published","year":"2025","scopus_import":"1","file":[{"date_created":"2025-12-30T13:14:20Z","date_updated":"2025-12-30T13:14:20Z","content_type":"application/pdf","checksum":"262640abc34277686b56eb60102976f6","success":1,"access_level":"open_access","file_size":897079,"file_id":"20917","relation":"main_file","creator":"dernst","file_name":"2025_CurrOpinionInsectScience_Toups.pdf"}],"day":"01","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","last_name":"Toups"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"publisher":"Elsevier","date_published":"2025-12-01T00:00:00Z","publication_identifier":{"eissn":["2214-5753"],"issn":["2214-5745"]},"_id":"20182","isi":1,"department":[{"_id":"BeVi"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"article_number":"101411","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ddc":["570"],"intvolume":"        72","month":"12","type":"journal_article","publication":"Current Opinion in Insect Science","citation":{"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>","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>.","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>.","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>","short":"M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (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.","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."},"date_created":"2025-08-17T22:01:35Z","file_date_updated":"2025-12-30T13:14:20Z","quality_controlled":"1","date_updated":"2025-12-30T13:14:38Z","volume":72,"oa":1,"article_type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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>","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.","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.","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>","short":"I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E.J. Lambie, B. Conradt, Nature Communications 16 (2025)."},"publication":"Nature Communications","type":"journal_article","date_updated":"2025-09-01T09:47:29Z","quality_controlled":"1","file_date_updated":"2025-09-01T09:46:44Z","date_created":"2025-08-17T22:01:35Z","article_type":"original","oa":1,"volume":16,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"has_accepted_license":"1","department":[{"_id":"CaHe"}],"_id":"20183","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"7174","language":[{"iso":"eng"}],"DOAJ_listed":"1","month":"08","intvolume":"        16","ddc":["570"],"status":"public","scopus_import":"1","year":"2025","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."}],"publication_status":"published","OA_place":"publisher","article_processing_charge":"Yes","day":"04","file":[{"creator":"dernst","relation":"main_file","file_name":"2025_NatureComm_Segos.pdf","date_updated":"2025-09-01T09:46:44Z","content_type":"application/pdf","date_created":"2025-09-01T09:46:44Z","file_size":3775190,"file_id":"20261","checksum":"f28e73963ea1f55876d0d1afca0f706a","success":1,"access_level":"open_access"}],"pmid":1,"date_published":"2025-08-04T00:00:00Z","author":[{"last_name":"Segos","full_name":"Segos, Ioannis","first_name":"Ioannis"},{"last_name":"Van Eeckhoven","first_name":"Jens","full_name":"Van Eeckhoven, Jens"},{"full_name":"Berger, Simon","first_name":"Simon","last_name":"Berger"},{"last_name":"Mishra","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","orcid":"0000-0002-6425-5788","full_name":"Mishra, Nikhil","first_name":"Nikhil"},{"full_name":"Lambie, Eric J.","first_name":"Eric J.","last_name":"Lambie"},{"last_name":"Conradt","first_name":"Barbara","full_name":"Conradt, Barbara"}],"publisher":"Springer Nature","OA_type":"gold","title":"Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo","doi":"10.1038/s41467-025-62484-5","PlanS_conform":"1","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.).","oa_version":"Published Version","external_id":{"pmid":["40759648"]}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","oa":1,"volume":8,"quality_controlled":"1","date_updated":"2025-09-30T14:18:46Z","date_created":"2025-08-17T22:01:35Z","publication":"Communications Biology","citation":{"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>.","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>","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>.","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.","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>","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).","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."},"type":"journal_article","DOAJ_listed":"1","month":"08","intvolume":"         8","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"article_number":"1148","language":[{"iso":"eng"}],"has_accepted_license":"1","isi":1,"_id":"20184","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"publication_identifier":{"eissn":["2399-3642"]},"pmid":1,"date_published":"2025-08-02T00:00:00Z","author":[{"first_name":"Sofía D.","full_name":"Castell, Sofía D.","last_name":"Castell"},{"last_name":"Fernandez","full_name":"Fernandez, Consuelo M.","first_name":"Consuelo M."},{"last_name":"Tumas","full_name":"Tumas, Ignacio N.","first_name":"Ignacio N."},{"last_name":"Margara","first_name":"Lucía M.","full_name":"Margara, Lucía M."},{"id":"273e0cbd-72f0-11ef-b75a-f9f932e292fa","full_name":"Miserendino, Maria C","first_name":"Maria C","last_name":"Miserendino"},{"full_name":"Ceschin, Danilo G.","first_name":"Danilo G.","last_name":"Ceschin"},{"last_name":"Pezza","full_name":"Pezza, Roberto J.","first_name":"Roberto J."},{"last_name":"Monti","first_name":"Mariela R.","full_name":"Monti, Mariela R."}],"publisher":"Springer Nature","article_processing_charge":"Yes","day":"02","scopus_import":"1","year":"2025","publication_status":"published","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"}],"OA_place":"publisher","status":"public","external_id":{"pmid":["40753298"],"isi":["001541878500001"]},"main_file_link":[{"url":"https://doi.org/10.1038/s42003-025-08589-5","open_access":"1"}],"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","oa_version":"Published Version","OA_type":"gold","doi":"10.1038/s42003-025-08589-5","title":"The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in Pseudomonas aeruginosa","PlanS_conform":"1"},{"has_accepted_license":"1","_id":"20185","department":[{"_id":"VaKa"}],"isi":1,"publication_identifier":{"issn":["1050-6926"]},"month":"08","ddc":["510"],"intvolume":"        35","article_number":"306","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2025-12-30T09:28:58Z","date_updated":"2025-12-30T09:29:27Z","quality_controlled":"1","date_created":"2025-08-17T22:01:35Z","publication":"Journal of Geometric Analysis","type":"journal_article","citation":{"ieee":"D. Tsodikovich, “Local rigidity for symplectic billiards,” <i>Journal of Geometric Analysis</i>, vol. 35, no. 10. Springer Nature, 2025.","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).","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>.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","volume":35,"oa":1,"oa_version":"Published Version","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","OA_type":"hybrid","PlanS_conform":"1","title":"Local rigidity for symplectic billiards","doi":"10.1007/s12220-025-02148-4","external_id":{"isi":["001546433200002"],"arxiv":["2501.08849"]},"project":[{"grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"issue":"10","ec_funded":1,"year":"2025","scopus_import":"1","OA_place":"publisher","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."}],"publication_status":"published","corr_author":"1","status":"public","date_published":"2025-08-07T00:00:00Z","arxiv":1,"publisher":"Springer Nature","author":[{"full_name":"Tsodikovich, Daniel","first_name":"Daniel","id":"04531810-fb3e-11ef-87f0-800a4ce333db","last_name":"Tsodikovich"}],"day":"07","article_processing_charge":"Yes (via OA deal)","file":[{"file_name":"2025_JourGeomAnalysis_Tsodikovich.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"checksum":"ed86500742b3fd93db3287558a630383","file_id":"20907","file_size":484344,"date_created":"2025-12-30T09:28:58Z","content_type":"application/pdf","date_updated":"2025-12-30T09:28:58Z"}]},{"OA_type":"hybrid","doi":"10.1007/s00236-025-00502-1","title":"Gray-box runtime enforcement of hyperproperties","PlanS_conform":"1","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).","oa_version":"Published Version","issue":"3","external_id":{"isi":["001546115300001"]},"project":[{"grant_number":"F8502","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","name":"Interface Theory for Security and Privacy"}],"status":"public","corr_author":"1","scopus_import":"1","year":"2025","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"}],"OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","day":"01","file":[{"file_name":"2025_ActaInformatica_Hsu.pdf","creator":"dernst","relation":"main_file","file_size":6505049,"file_id":"20267","checksum":"90a43350fd4a8c5cb5b1b0e1aea7970d","success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2025-09-02T05:53:47Z","date_created":"2025-09-02T05:53:47Z"}],"date_published":"2025-09-01T00:00:00Z","publisher":"Springer Nature","author":[{"last_name":"Hsu","first_name":"Tzu Han","full_name":"Hsu, Tzu Han"},{"last_name":"Oliveira Da Costa","id":"8b282559-50b0-11ef-861e-d6ace0d92e9b","full_name":"Oliveira Da Costa, Ana A","first_name":"Ana A"},{"last_name":"Wintenberg","first_name":"Andrew","full_name":"Wintenberg, Andrew"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"last_name":"Bonakdarpour","first_name":"Borzoo","full_name":"Bonakdarpour, Borzoo"}],"publication_identifier":{"issn":["0001-5903"],"eissn":["1432-0525"]},"has_accepted_license":"1","_id":"20186","department":[{"_id":"ToHe"}],"isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"30","language":[{"iso":"eng"}],"month":"09","intvolume":"        62","ddc":["000"],"publication":"Acta Informatica","citation":{"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>.","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>","short":"T.H. Hsu, A.A. Oliveira da Costa, A. Wintenberg, E. Bartocci, B. Bonakdarpour, Acta Informatica 62 (2025).","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.","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."},"type":"journal_article","quality_controlled":"1","date_updated":"2025-09-30T14:20:11Z","file_date_updated":"2025-09-02T05:53:47Z","date_created":"2025-08-17T22:01:36Z","article_type":"original","oa":1,"volume":62,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"}]