[{"publisher":"Fundació de la comunitat valenciana SCITO","doi":"10.29363/nanoge.matsusspring.2025.220","day":"03","type":"conference_abstract","title":"Solid state diffusion in metal-semiconductors core-shell nanoparticle","_id":"20054","citation":{"chicago":"Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell Nanoparticle.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">https://doi.org/10.29363/nanoge.matsusspring.2025.220</a>.","ama":"Horta S. Solid state diffusion in metal-semiconductors core-shell nanoparticle. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">10.29363/nanoge.matsusspring.2025.220</a>","ieee":"S. Horta, “Solid state diffusion in metal-semiconductors core-shell nanoparticle,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025.","ista":"Horta S. 2025. Solid state diffusion in metal-semiconductors core-shell nanoparticle. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 220.","apa":"Horta, S. (2025). Solid state diffusion in metal-semiconductors core-shell nanoparticle. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">https://doi.org/10.29363/nanoge.matsusspring.2025.220</a>","mla":"Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell Nanoparticle.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 220, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.220\">10.29363/nanoge.matsusspring.2025.220</a>.","short":"S. Horta, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025."},"year":"2025","oa_version":"None","month":"03","publication":"Proceedings of the MATSUS Spring 2025 Conference","article_processing_charge":"No","date_updated":"2025-09-23T09:04:03Z","corr_author":"1","conference":{"location":"Sevilla, Spain","start_date":"2025-03-03","end_date":"2025-03-07","name":"MATSUS: Materials for Sustainable Development Conference"},"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2025-03-03T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-21T08:22:29Z","publication_status":"published","department":[{"_id":"MaIb"}],"author":[{"last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona"}],"article_number":"220"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"publication_status":"published","date_created":"2025-07-21T08:33:20Z","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"author":[{"orcid":"0000-0002-6962-8598","last_name":"Lee","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X"},{"last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona"},{"last_name":"Rayaroth Puthiyaveettil","full_name":"Rayaroth Puthiyaveettil, Aiswarya","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","first_name":"Aiswarya"},{"first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"article_number":"173","OA_type":"closed access","date_updated":"2026-02-19T09:25:57Z","corr_author":"1","conference":{"start_date":"2025-03-03","name":"MATSUS: Materials for Sustainable Development Conference","end_date":"2025-03-07","location":"Sevilla, Spain"},"acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the Lab Support Facility (LSF).","quality_controlled":"1","abstract":[{"text":"Supercrystals represent three-dimensional orderings of colloidal nanocrystals (NCs), showcasing collective properties in photonics, phononics, and electronics applications.1,2 Recent studies have shown that such assemblies are directly produced during nanocrystal reactions.3–6 However, a fundamental understanding of in situ formed supercrystals that withstand typical NC purification processes remains underexplored, which is important for further use. Herein, we report the reaction precursor-mediated formation of stable PbTe supercrystals. Rationalizing the formation of these assemblies through small-angle x-ray scattering (SAXS) measurements, we unveil their formation mechanism. Our findings reveal that the supercrystal formation occurs in the presence of an excess of lead oleates in the crude solution. It should be noted that the formed supercrystals can be stabilized under specific conditions determined by the lead oleate cluster concentration, content of trioctylphosphine telluride (TOP-Te), NC size and the need of an annealing step at mild conditions. Furthermore, this approach allows for the continuous growth of a secondary phase within the supercrystal; for example in the case of PbTe supercrystals, a PbS shell can be grown on each PbTe NC constituent, resulting in core-shell PbTe-PbS supercrystals. Our work elucidates that reaction precursors play an important role in in situ SC formation and stabilization, implying the possibility of applying this knowledge to other NC reactions.","lang":"eng"}],"language":[{"iso":"eng"}],"date_published":"2025-03-15T00:00:00Z","status":"public","month":"03","publication":"Proceedings of the MATSUS Spring 2025 Conference","article_processing_charge":"No","doi":"10.29363/nanoge.matsusspring.2025.173","publisher":"Fundació de la comunitat valenciana SCITO","day":"15","type":"conference","title":"Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case","_id":"20055","citation":{"short":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, M. Ibáñez, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025.","apa":"Lee, S., Balazs, D., Horta, S., Rayaroth Puthiyaveettil, A., &#38; Ibáñez, M. (2025). Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>","ista":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. 2025. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 173.","mla":"Lee, Seungho, et al. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 173, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>.","ieee":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, and M. Ibáñez, “Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025.","ama":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>","chicago":"Lee, Seungho, Daniel Balazs, Sharona Horta, Aiswarya Rayaroth Puthiyaveettil, and Maria Ibáñez. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>."},"year":"2025","oa_version":"None"},{"year":"2025","issue":"4","_id":"20056","oa_version":"Preprint","title":"Discovering stochastic dynamical equations from ecological time series data","article_processing_charge":"No","pmid":1,"month":"04","date_published":"2025-04-01T00:00:00Z","abstract":[{"text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).","lang":"eng"}],"status":"public","OA_type":"green","acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","arxiv":1,"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"article_type":"original","publication_status":"published","author":[{"full_name":"Nabeel, Arshed","first_name":"Arshed","last_name":"Nabeel"},{"last_name":"Karichannavar","full_name":"Karichannavar, Ashwin","first_name":"Ashwin"},{"last_name":"Palathingal","full_name":"Palathingal, Shuaib","first_name":"Shuaib"},{"last_name":"Jhawar","full_name":"Jhawar, Jitesh","first_name":"Jitesh"},{"orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"last_name":"Raj M","full_name":"Raj M, Danny","first_name":"Danny"},{"first_name":"Vishwesha","full_name":"Guttal, Vishwesha","last_name":"Guttal"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"oa":1,"citation":{"chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117."},"volume":205,"page":"E100-E117","doi":"10.1086/734083","day":"01","publisher":"University of Chicago Press","related_material":{"record":[{"id":"20121","relation":"software","status":"public"}]},"type":"journal_article","publication":"The American Naturalist","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"intvolume":"       205","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"date_updated":"2025-09-30T14:14:43Z","OA_place":"repository","external_id":{"isi":["001433250500001"],"pmid":["40179429"],"arxiv":["2205.02645"]},"date_created":"2025-07-21T08:37:27Z","department":[{"_id":"EdHa"}]},{"publication":"Biology","DOAJ_listed":"1","citation":{"ieee":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky, “Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels,” <i>Biology</i>, vol. 14, no. 8. MDPI, 2025.","apa":"Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., &#38; Bernecky, C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. MDPI. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>","mla":"Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>, vol. 14, no. 8, 930, MDPI, 2025, doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>.","ista":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. Biology. 14(8), 930.","short":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology 14 (2025).","chicago":"Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi, and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>. MDPI, 2025. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>.","ama":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. 2025;14(8). doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>"},"volume":14,"day":"24","publisher":"MDPI","doi":"10.3390/biology14080930","type":"journal_article","file_date_updated":"2025-07-31T09:11:09Z","date_created":"2025-07-25T08:28:26Z","article_number":"930","PlanS_conform":"1","department":[{"_id":"CaBe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"intvolume":"        14","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2079-7737"]},"date_updated":"2025-09-30T14:10:07Z","has_accepted_license":"1","OA_place":"publisher","external_id":{"isi":["001557922100001"]},"article_processing_charge":"Yes","month":"07","year":"2025","issue":"8","_id":"20077","oa_version":"Published Version","title":"Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels","publication_status":"published","article_type":"original","author":[{"last_name":"Rosani","first_name":"Umberto","full_name":"Rosani, Umberto"},{"last_name":"Altan","full_name":"Altan, Nehir","first_name":"Nehir"},{"last_name":"Venier","first_name":"Paola","full_name":"Venier, Paola"},{"last_name":"Bortoletto","first_name":"Enrico","full_name":"Bortoletto, Enrico"},{"full_name":"Volpi, Nicola","first_name":"Nicola","last_name":"Volpi"},{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"}],"file":[{"success":1,"checksum":"f5e059e66803fa54249c1db029aef0f6","date_updated":"2025-07-31T09:11:09Z","file_name":"2025_Biology_Rosani.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2025-07-31T09:11:09Z","file_id":"20097","relation":"main_file","file_size":1885781}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"abstract":[{"lang":"eng","text":"Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates, where it mediates cell adhesion, immune regulation, and tissue remodeling through its interaction with specific receptors. Although HA has been detected in a few invertebrate species, the lack of fundamental components of the molecular HA pathway poses relevant objections about its functional role in these species. Mining genomic and transcriptomic data, we considered the conservation of the gene locus encoding for the extracellular link protein (XLINK) in marine mussels as well as its expression patterns. Structural and phylogenetic analyses were undertaken to evaluate possible similarities with vertebrate orthologs and to infer the origin of this gene in invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus galloprovincialis. As a result, we confirm that the mussel can produce HA (up to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These loci are conserved in Mytilidae species and show a complex evolutionary path. Mussel XLINK genes appeared to be expressed during developmental stages in three mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h post-fertilization. In conclusion, the presence of HA and an active gene with the potential to bind HA suggests that mussels have the potential to synthesize and use HA and are among the few invertebrates encoding this gene."}],"date_published":"2025-07-24T00:00:00Z","status":"public","OA_type":"gold","acknowledgement":"This research was funded by the Italian Ministry of University and Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype diversity in Mytilus galloprovincialis (HAMIGA)).","ddc":["570"]},{"arxiv":1,"OA_type":"hybrid","status":"public","date_published":"2025-07-23T00:00:00Z","scopus_import":"1","abstract":[{"text":"Let A be an abelian variety defined over a number field K, E/K be an elliptic curve, and ϕ : A → Em be an isogeny defined over K. Let P ∈ A(K) be such that ϕ(P)=(Q1,..., Qm) with RankZ(⟨Q1,...,Qm⟩)=1. We will study a divisibility sequence related to the point P and show its relation with elliptic divisibility sequences.","lang":"eng"}],"oa":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Barańczuk, Stefan","first_name":"Stefan","last_name":"Barańczuk"},{"full_name":"Naskręcki, Bartosz","first_name":"Bartosz","last_name":"Naskręcki"},{"orcid":"0000-0002-0854-0306","last_name":"Verzobio","first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo"}],"publication_status":"epub_ahead","article_type":"original","title":"Divisibility sequences related to abelian varieties isogenous to a power of an elliptic curve","oa_version":"Published Version","_id":"20078","year":"2025","month":"07","article_processing_charge":"Yes (via OA deal)","corr_author":"1","external_id":{"arxiv":["2309.09699"],"isi":["001541172400002"]},"OA_place":"publisher","date_updated":"2025-09-30T14:09:38Z","publication_identifier":{"issn":["0022-314X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       279","PlanS_conform":"1","department":[{"_id":"TiBr"}],"date_created":"2025-07-27T22:01:25Z","type":"journal_article","doi":"10.1016/j.jnt.2025.06.001","day":"23","publisher":"Elsevier","page":"170-183","volume":279,"citation":{"ama":"Barańczuk S, Naskręcki B, Verzobio M. Divisibility sequences related to abelian varieties isogenous to a power of an elliptic curve. <i>Journal of Number Theory</i>. 2025;279:170-183. doi:<a href=\"https://doi.org/10.1016/j.jnt.2025.06.001\">10.1016/j.jnt.2025.06.001</a>","chicago":"Barańczuk, Stefan, Bartosz Naskręcki, and Matteo Verzobio. “Divisibility Sequences Related to Abelian Varieties Isogenous to a Power of an Elliptic Curve.” <i>Journal of Number Theory</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jnt.2025.06.001\">https://doi.org/10.1016/j.jnt.2025.06.001</a>.","short":"S. Barańczuk, B. Naskręcki, M. Verzobio, Journal of Number Theory 279 (2025) 170–183.","apa":"Barańczuk, S., Naskręcki, B., &#38; Verzobio, M. (2025). Divisibility sequences related to abelian varieties isogenous to a power of an elliptic curve. <i>Journal of Number Theory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jnt.2025.06.001\">https://doi.org/10.1016/j.jnt.2025.06.001</a>","mla":"Barańczuk, Stefan, et al. “Divisibility Sequences Related to Abelian Varieties Isogenous to a Power of an Elliptic Curve.” <i>Journal of Number Theory</i>, vol. 279, Elsevier, 2025, pp. 170–83, doi:<a href=\"https://doi.org/10.1016/j.jnt.2025.06.001\">10.1016/j.jnt.2025.06.001</a>.","ista":"Barańczuk S, Naskręcki B, Verzobio M. 2025. Divisibility sequences related to abelian varieties isogenous to a power of an elliptic curve. Journal of Number Theory. 279, 170–183.","ieee":"S. Barańczuk, B. Naskręcki, and M. Verzobio, “Divisibility sequences related to abelian varieties isogenous to a power of an elliptic curve,” <i>Journal of Number Theory</i>, vol. 279. Elsevier, pp. 170–183, 2025."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jnt.2025.06.001"}],"publication":"Journal of Number Theory"},{"publication":"Reproductive Biomedicine Online","publisher":"Elsevier","day":"17","doi":"10.1016/j.rbmo.2025.104942","type":"journal_article","citation":{"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>.","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>","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.","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.","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).","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>.","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>"},"volume":51,"date_created":"2025-07-27T22:01:25Z","department":[{"_id":"SiHi"}],"article_number":"104942","date_updated":"2025-09-30T14:10:46Z","external_id":{"pmid":["40680553"],"isi":["001549819000002"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        51","publication_identifier":{"issn":["1472-6483"],"eissn":["1472-6491"]},"pmid":1,"month":"07","article_processing_charge":"No","title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","issue":"3","_id":"20079","year":"2025","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication_status":"published","article_type":"original","author":[{"last_name":"Yotova","first_name":"Iveta","full_name":"Yotova, Iveta"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"last_name":"Rainer","first_name":"Lisa","full_name":"Rainer, Lisa"},{"full_name":"Kaup, Leonie","first_name":"Leonie","last_name":"Kaup"},{"full_name":"Heine, Jana","first_name":"Jana","last_name":"Heine"},{"last_name":"Sandrieser","full_name":"Sandrieser, Lejla","first_name":"Lejla"},{"first_name":"René","full_name":"Wenzl, René","last_name":"Wenzl"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"}],"OA_type":"closed access","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.","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."}],"scopus_import":"1","date_published":"2025-07-17T00:00:00Z","status":"public"},{"publisher":"Frontiers Media","doi":"10.3389/fpls.2025.1612366","day":"04","type":"journal_article","ec_funded":1,"citation":{"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>.","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>","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.","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.","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>","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>.","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025)."},"DOAJ_listed":"1","volume":16,"publication":"Frontiers in Plant Science","date_updated":"2025-09-30T14:08:22Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"corr_author":"1","intvolume":"        16","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-462X"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"file_date_updated":"2025-07-31T07:28:54Z","date_created":"2025-07-27T22:01:26Z","article_number":"1612366","PlanS_conform":"1","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","year":"2025","_id":"20080","oa_version":"Published Version","pmid":1,"month":"07","article_processing_charge":"Yes","OA_type":"gold","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.","ddc":["580"],"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"}],"date_published":"2025-07-04T00:00:00Z","scopus_import":"1","status":"public","file":[{"date_updated":"2025-07-31T07:28:54Z","file_name":"2025_FrontiersPlantSc_Gallemi.pdf","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","success":1,"file_size":3665187,"relation":"main_file","file_id":"20093","access_level":"open_access","date_created":"2025-07-31T07:28:54Z","creator":"dernst","content_type":"application/pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"oa":1,"project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"article_type":"original","publication_status":"published","author":[{"orcid":"0000-0003-4675-6893","last_name":"Gallemi","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marçal"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C","first_name":"Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López"},{"last_name":"Zarevski","first_name":"Nikola","full_name":"Zarevski, Nikola","id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a"},{"last_name":"Pribyl","full_name":"Pribyl, Jan","first_name":"Jan"},{"last_name":"Skládal","full_name":"Skládal, Petr","first_name":"Petr"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}]},{"date_published":"2025-07-11T00:00:00Z","scopus_import":"1","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"}],"status":"public","OA_type":"green","arxiv":1,"publication_status":"epub_ahead","article_type":"original","author":[{"id":"9583e921-e1ad-11ec-9862-cef099626dc9","full_name":"Esposito, Amedeo Roberto","first_name":"Amedeo Roberto","last_name":"Esposito"},{"last_name":"Gastpar","first_name":"Michael","full_name":"Gastpar, Michael"},{"full_name":"Issa, Ibrahim","first_name":"Ibrahim","last_name":"Issa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"_id":"20081","year":"2025","oa_version":"Preprint","title":"Sibson α-mutual information and its variational representations","article_processing_charge":"No","month":"07","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"OA_place":"repository","date_updated":"2026-02-16T11:49:40Z","external_id":{"arxiv":["2405.08352"]},"date_created":"2025-07-27T22:01:26Z","department":[{"_id":"MaMo"}],"citation":{"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>","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>.","short":"A.R. Esposito, M. Gastpar, I. Issa, IEEE Transactions on Information Theory (2025).","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.","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>","ista":"Esposito AR, Gastpar M, Issa I. 2025. Sibson α-mutual information and its variational representations. IEEE Transactions on Information Theory.","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>."},"day":"11","doi":"10.1109/TIT.2025.3587340","publisher":"IEEE","type":"journal_article","publication":"IEEE Transactions on Information Theory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.08352"}]},{"corr_author":"1","date_updated":"2025-08-04T07:46:33Z","OA_place":"publisher","has_accepted_license":"1","publication_identifier":{"eissn":["2752-5295"]},"intvolume":"         4","language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"035005","PlanS_conform":"1","department":[{"_id":"CaMu"}],"file_date_updated":"2025-08-04T07:38:14Z","date_created":"2025-07-31T14:03:16Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"20107"}]},"ec_funded":1,"type":"journal_article","doi":"10.1088/2752-5295/adec11","day":"15","publisher":"IOP Publishing","volume":4,"citation":{"short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research: Climate 4 (2025).","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>","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.","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>.","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.","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>","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>."},"DOAJ_listed":"1","publication":"Environmental Research: Climate","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.","ddc":["550"],"OA_type":"gold","status":"public","abstract":[{"lang":"eng","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."}],"scopus_import":"1","date_published":"2025-07-15T00:00:00Z","oa":1,"file":[{"content_type":"application/pdf","creator":"dernst","date_created":"2025-08-04T07:38:14Z","access_level":"open_access","file_id":"20108","relation":"main_file","file_size":2807041,"success":1,"checksum":"ca679496767021e792b0378c48fdee8c","file_name":"2025_EnvironResearchClimate_Hwong.pdf","date_updated":"2025-08-04T07:38:14Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","full_name":"Hwong, Yi-Ling","last_name":"Hwong","orcid":"0000-0001-9281-3479"},{"last_name":"Byers","full_name":"Byers, Edward","first_name":"Edward"},{"last_name":"Werning","first_name":"Michaela","full_name":"Werning, Michaela"},{"last_name":"Quilcaille","full_name":"Quilcaille, Yann","first_name":"Yann"}],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_type":"original","publication_status":"published","title":"Sustainable development key to limiting climate change-driven wildfire damages","oa_version":"Published Version","year":"2025","_id":"20098","issue":"3","month":"07","article_processing_charge":"Yes"},{"publication_status":"published","article_type":"original","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"author":[{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson"},{"last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"file_size":27695214,"relation":"main_file","file_id":"20106","access_level":"open_access","date_created":"2025-08-04T06:53:07Z","creator":"dernst","content_type":"application/pdf","date_updated":"2025-08-04T06:53:07Z","file_name":"2025_CellReports_Watson.pdf","checksum":"556ff9760661ecd23949d75031043b1f","success":1}],"oa":1,"date_published":"2025-08-01T00:00:00Z","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."}],"scopus_import":"1","status":"public","OA_type":"gold","ddc":["570"],"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.).","article_processing_charge":"Yes","month":"08","_id":"20099","issue":"8","year":"2025","oa_version":"Published Version","title":"Cell-specific wiring routes information flow through hippocampal CA3","date_created":"2025-08-03T22:01:30Z","file_date_updated":"2025-08-04T06:53:07Z","PlanS_conform":"1","department":[{"_id":"PeJo"}],"article_number":"116080","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        44","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"OA_place":"publisher","has_accepted_license":"1","date_updated":"2025-09-30T14:12:02Z","corr_author":"1","external_id":{"isi":["001544472300002"]},"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.","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>.","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.","short":"J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (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>.","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>"},"DOAJ_listed":"1","volume":44,"day":"01","publisher":"Elsevier","doi":"10.1016/j.celrep.2025.116080","type":"journal_article","ec_funded":1},{"article_processing_charge":"Yes","month":"06","oa_version":"Published Version","_id":"20100","year":"2025","title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","author":[{"last_name":"Vedula","id":"94f2fe44-70fa-11f0-b76b-92922c09452b","full_name":"Vedula, Sanketh","first_name":"Sanketh"},{"first_name":"Alexander","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","orcid":"0000-0001-9699-8730"},{"last_name":"Marx","full_name":"Marx, Ailie","first_name":"Ailie"}],"article_type":"original","publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file":[{"checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","success":1,"file_name":"2025_CompStrucBiotechJour_Vedula.pdf","date_updated":"2025-08-04T06:25:23Z","date_created":"2025-08-04T06:25:23Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":6609770,"relation":"main_file","file_id":"20104"}],"status":"public","abstract":[{"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.","lang":"eng"}],"date_published":"2025-06-27T00:00:00Z","scopus_import":"1","ddc":["000","570"],"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_type":"gold","publication":"Computational and Structural Biotechnology Journal","volume":27,"DOAJ_listed":"1","citation":{"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>.","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>","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.","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.","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>.","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>","short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298."},"type":"journal_article","related_material":{"link":[{"relation":"software","url":"https://github.com/sankethvedula/AFChimera"}],"record":[{"id":"20103","relation":"software","status":"public"}]},"day":"27","publisher":"Elsevier","doi":"10.1016/j.csbj.2025.07.039","page":"3292-3298","department":[{"_id":"AlBr"}],"PlanS_conform":"1","file_date_updated":"2025-08-04T06:25:23Z","date_created":"2025-08-03T22:01:31Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2001-0370"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        27","external_id":{"isi":["001583543100001"]},"has_accepted_license":"1","OA_place":"publisher","date_updated":"2025-11-27T14:09:59Z"},{"publication_status":"published","article_type":"original","author":[{"last_name":"Baier","full_name":"Baier, Felix","first_name":"Felix"},{"full_name":"Reinhard, Katja","first_name":"Katja","last_name":"Reinhard"},{"last_name":"Nuttin","full_name":"Nuttin, Bram","first_name":"Bram"},{"last_name":"Sans-Dublanc","first_name":"Arnau","full_name":"Sans-Dublanc, Arnau"},{"last_name":"Liu","full_name":"Liu, Chen","first_name":"Chen"},{"first_name":"Victoria","full_name":"Tong, Victoria","last_name":"Tong"},{"full_name":"Murmann, Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie","last_name":"Murmann"},{"full_name":"Wierda, Keimpe","first_name":"Keimpe","last_name":"Wierda"},{"last_name":"Farrow","full_name":"Farrow, Karl","first_name":"Karl"},{"full_name":"Hoekstra, Hopi E.","first_name":"Hopi E.","last_name":"Hoekstra"}],"file":[{"content_type":"application/pdf","date_created":"2025-12-30T07:39:45Z","creator":"dernst","access_level":"open_access","file_id":"20884","relation":"main_file","file_size":53301589,"success":1,"checksum":"7ea846a7a49b3b2a248f6a27ab13d591","file_name":"2025_Nature_Baier.pdf","date_updated":"2025-12-30T07:39:45Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","date_published":"2025-07-23T00:00:00Z","status":"public","OA_type":"hybrid","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.","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","pmid":1,"month":"07","year":"2025","_id":"20101","oa_version":"Published Version","title":"The neural basis of species-specific defensive behaviour in Peromyscus mice","date_created":"2025-08-03T22:01:31Z","file_date_updated":"2025-12-30T07:39:45Z","department":[{"_id":"GradSch"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"intvolume":"       645","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_updated":"2026-01-05T11:38:40Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"pmid":["40702175"]},"publication":"Nature","citation":{"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>","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>.","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.","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>.","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.","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>","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."},"volume":645,"page":"439-447","publisher":"Springer Nature","doi":"10.1038/s41586-025-09241-2","day":"23","related_material":{"record":[{"id":"20883","relation":"research_data","status":"public"}]},"type":"journal_article"},{"publication":"Molecular Ecology","day":"01","publisher":"Wiley","doi":"10.1111/mec.70025","type":"journal_article","citation":{"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).","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>","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.","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","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>","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>."},"volume":34,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file_date_updated":"2025-12-30T09:25:17Z","date_created":"2025-08-03T22:01:31Z","article_number":"e70025","PlanS_conform":"1","department":[{"_id":"NiBa"}],"date_updated":"2025-12-30T09:25:45Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"isi":["001538172800001"]},"intvolume":"        34","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"11","article_processing_charge":"Yes (in subscription journal)","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","year":"2025","_id":"20102","issue":"21","oa_version":"Published Version","file":[{"success":1,"checksum":"ec01edda64cfbc6cbc8adf300f719644","date_updated":"2025-12-30T09:25:17Z","file_name":"2025_MolecEcology_Raffini.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2025-12-30T09:25:17Z","file_id":"20906","relation":"main_file","file_size":2767745}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"oa":1,"publication_status":"published","article_type":"original","author":[{"first_name":"Francesca","full_name":"Raffini, Francesca","last_name":"Raffini"},{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"first_name":"Emilio","full_name":"Rolán-Alvarez, Emilio","last_name":"Rolán-Alvarez"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"OA_type":"hybrid","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.","ddc":["570"],"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."}],"scopus_import":"1","date_published":"2025-11-01T00:00:00Z","status":"public"},{"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2025-08-04T06:18:55Z","author":[{"last_name":"Vedula","id":"94f2fe44-70fa-11f0-b76b-92922c09452b","full_name":"Vedula, Sanketh","first_name":"Sanketh"},{"first_name":"Alexander","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","last_name":"Bronstein"},{"first_name":"Ailie","full_name":"Marx, Ailie","last_name":"Marx"}],"department":[{"_id":"AlBr"}],"date_updated":"2025-11-27T14:09:58Z","has_accepted_license":"1","OA_place":"repository","ddc":["000"],"date_published":"2025-06-27T00:00:00Z","abstract":[{"lang":"eng","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)"}],"status":"public","main_file_link":[{"url":"https://doi.org/10.7910/DVN/DYEBVM","open_access":"1"}],"month":"06","article_processing_charge":"No","publisher":"Harvard Dataverse","day":"27","doi":"10.7910/DVN/DYEBVM","title":"Replication Data for: \"Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment\"","related_material":{"record":[{"id":"20100","relation":"used_for_analysis_in","status":"public"}]},"type":"research_data_reference","year":"2025","_id":"20103","citation":{"short":"S. Vedula, A.M. Bronstein, A. Marx, (2025).","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.","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>","ista":"Vedula S, Bronstein AM, Marx A. 2025. Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment’, Harvard Dataverse, <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>.","ama":"Vedula S, Bronstein AM, Marx A. Replication Data for: “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” 2025. doi:<a href=\"https://doi.org/10.7910/DVN/DYEBVM\">10.7910/DVN/DYEBVM</a>","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Replication Data for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’” Harvard Dataverse, 2025. <a href=\"https://doi.org/10.7910/DVN/DYEBVM\">https://doi.org/10.7910/DVN/DYEBVM</a>."},"oa_version":"Published Version"},{"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.15409324"}],"month":"05","year":"2025","citation":{"short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025).","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13988679\">https://doi.org/10.5281/ZENODO.13988679</a>","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13988679\">10.5281/ZENODO.13988679</a>.","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>.","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>","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>."},"_id":"20107","oa_version":"Published Version","doi":"10.5281/ZENODO.13988679","day":"21","publisher":"Zenodo","title":"Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"20098"}]},"type":"research_data_reference","ec_funded":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"date_created":"2025-08-04T07:34:39Z","author":[{"last_name":"Hwong","orcid":"0000-0001-9281-3479","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","full_name":"Hwong, Yi-Ling"},{"first_name":"Edward","full_name":"Byers, Edward","last_name":"Byers"},{"full_name":"Werning, Michaela","first_name":"Michaela","last_name":"Werning"},{"first_name":"Yann","full_name":"Quilcaille, Yann","last_name":"Quilcaille"}],"department":[{"_id":"CaMu"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"lang":"eng","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). "}],"date_published":"2025-05-21T00:00:00Z","status":"public","date_updated":"2025-08-04T07:46:33Z","OA_type":"green","OA_place":"repository","has_accepted_license":"1","ddc":["550"],"corr_author":"1"},{"year":"2025","_id":"20116","issue":"8","oa_version":"Published Version","title":"Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis","article_processing_charge":"Yes","pmid":1,"month":"07","scopus_import":"1","date_published":"2025-07-24T00:00:00Z","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."}],"status":"public","OA_type":"gold","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.","ddc":["580"],"article_type":"original","publication_status":"published","author":[{"last_name":"Xu","full_name":"Xu, Faqing","first_name":"Faqing"},{"full_name":"Yu, Yongqiang","first_name":"Yongqiang","last_name":"Yu"},{"first_name":"Bin","full_name":"Guan, Bin","id":"56aad729-cca2-11ed-a45a-9b4138991a48","last_name":"Guan"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"last_name":"Xu","first_name":"Zhihong","full_name":"Xu, Zhihong"},{"last_name":"Xue","first_name":"Hongwei","full_name":"Xue, Hongwei"}],"file":[{"file_id":"20120","relation":"main_file","file_size":24178018,"content_type":"application/pdf","access_level":"open_access","date_created":"2025-08-05T06:15:09Z","creator":"dernst","date_updated":"2025-08-05T06:15:09Z","file_name":"2025_CellReports_Xu.pdf","success":1,"checksum":"3c43e040a4a7a65ec67ae1d2bb81261a"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"citation":{"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.","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>.","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.","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>","short":"F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).","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>.","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>"},"DOAJ_listed":"1","volume":44,"doi":"10.1016/j.celrep.2025.116056","publisher":"Elsevier","day":"24","type":"journal_article","publication":"Cell Reports","intvolume":"        44","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2211-1247"]},"date_updated":"2025-09-30T14:13:45Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"isi":["001542038500001"],"pmid":["40714631"]},"file_date_updated":"2025-08-05T06:15:09Z","date_created":"2025-08-04T13:39:11Z","article_number":"116056","department":[{"_id":"JiFr"}],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"}},{"type":"journal_article","page":"5862-5877.e23","day":"16","publisher":"Elsevier","doi":"10.1016/j.cell.2025.07.002","volume":188,"citation":{"chicago":"Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>.","ama":"Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. 2025;188(21):5862-5877.e23. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>","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.","mla":"Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>, vol. 188, no. 21, Elsevier, 2025, p. 5862–5877.e23, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>.","apa":"Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>","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.","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."},"publication":"Cell","external_id":{"isi":["001603560700005"],"pmid":["40730155"]},"date_updated":"2025-12-29T14:15:58Z","OA_place":"publisher","has_accepted_license":"1","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"intvolume":"       188","language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"PlanS_conform":"1","department":[{"_id":"JaBr"}],"file_date_updated":"2025-12-29T14:15:25Z","date_created":"2025-08-07T05:00:04Z","title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","oa_version":"Published Version","year":"2025","_id":"20143","issue":"21","month":"10","pmid":1,"article_processing_charge":"Yes (in subscription journal)","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).","ddc":["570"],"OA_type":"hybrid","status":"public","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."}],"scopus_import":"1","date_published":"2025-10-16T00:00:00Z","oa":1,"file":[{"date_updated":"2025-12-29T14:15:25Z","file_name":"2025_Cell_Zhang.pdf","checksum":"b944de5fbd7455f58e1ff338ad352239","success":1,"file_size":32104588,"relation":"main_file","file_id":"20875","access_level":"open_access","creator":"dernst","date_created":"2025-12-29T14:15:25Z","content_type":"application/pdf"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Zhiying","full_name":"Zhang, Zhiying","last_name":"Zhang"},{"last_name":"Todeschini","full_name":"Todeschini, Thomas C.","first_name":"Thomas C."},{"first_name":"Yi","full_name":"Wu, Yi","last_name":"Wu"},{"last_name":"Kogay","full_name":"Kogay, Roman","first_name":"Roman"},{"first_name":"Ameena","full_name":"Naji, Ameena","last_name":"Naji"},{"first_name":"Joaquin","full_name":"Cardenas Rodriguez, Joaquin","last_name":"Cardenas Rodriguez"},{"full_name":"Mondi, Rupavidhya","first_name":"Rupavidhya","last_name":"Mondi"},{"last_name":"Kaganovich","full_name":"Kaganovich, Daniel","first_name":"Daniel"},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."},{"full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753"},{"last_name":"Teplova","full_name":"Teplova, Marianna","first_name":"Marianna"},{"last_name":"Amen","first_name":"Triana","full_name":"Amen, Triana"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"},{"last_name":"Patel","first_name":"Dinshaw J.","full_name":"Patel, Dinshaw J."},{"full_name":"Nobrega, Franklin L.","first_name":"Franklin L.","last_name":"Nobrega"}],"article_type":"original","publication_status":"published"},{"date_updated":"2025-08-11T07:20:03Z","OA_place":"publisher","OA_type":"gold","has_accepted_license":"1","ddc":["020"],"date_published":"2025-08-07T00:00:00Z","abstract":[{"text":"This criteria catalogue and the accompanying assessment questions were developed by a working group of KEMÖ (Kooperation E-Medien Österreich, the Austrian Academic Library Consortium). They are intended to support research institutions and organisations in the evaluation of Open Science Infrastructures. The 20 criteria outlined in the catalogue provide a structured basis for making informed decisions regarding the financial support of these infrastructures.\r\n\r\nThe assessment questions are intended to be completed by Open Science Infrastructures and can be shared with them accordingly.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2025-08-07T11:10:14Z","publication_status":"published","author":[{"first_name":"Paul","full_name":"Gredler, Paul","last_name":"Gredler"},{"last_name":"Kaier","full_name":"Kaier, Christian","first_name":"Christian"},{"orcid":"0000-0002-6026-4409","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick","first_name":"Patrick"},{"first_name":"Michael","full_name":"Zoyer, Michael","last_name":"Zoyer"},{"first_name":"Katharina","full_name":"Rieck, Katharina","last_name":"Rieck"},{"first_name":"Andreas","full_name":"Ferus, Andreas","last_name":"Ferus"},{"first_name":"Elisabeth","full_name":"Rosenberger, Elisabeth","last_name":"Rosenberger"},{"first_name":"Alexander","full_name":"Löffler, Alexander","last_name":"Löffler"},{"last_name":"Hofer","first_name":"Lisa","full_name":"Hofer, Lisa"},{"last_name":"Still","first_name":"Laura","full_name":"Still, Laura"}],"department":[{"_id":"E-Lib"}],"publisher":"Zenodo","doi":"10.5281/zenodo.15269364","day":"07","title":"Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures","type":"working_paper","year":"2025","_id":"20146","citation":{"ieee":"P. Gredler <i>et al.</i>, <i>Catalogue of criteria for assessing the funding eligibility of Open Science infrastructures</i>. Zenodo, 2025.","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.","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>.","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.","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>.","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>"},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.15269364","open_access":"1"}],"month":"08","article_processing_charge":"No"},{"type":"journal_article","page":"645-654","day":"01","doi":"10.1016/j.tins.2025.07.004","publisher":"Elsevier","volume":48,"citation":{"chicago":"Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.” <i>Trends in Neurosciences</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">https://doi.org/10.1016/j.tins.2025.07.004</a>.","ama":"Hetzer M, Toda T. Long-lived cellular molecules in the brain. <i>Trends in Neurosciences</i>. 2025;48(9):645-654. doi:<a href=\"https://doi.org/10.1016/j.tins.2025.07.004\">10.1016/j.tins.2025.07.004</a>","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>","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>.","ista":"Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends in Neurosciences. 48(9), 645–654.","ieee":"M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” <i>Trends in Neurosciences</i>, vol. 48, no. 9. Elsevier, pp. 645–654, 2025.","short":"M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654."},"publication":"Trends in Neurosciences","external_id":{"isi":["001568965400001"],"pmid":["40744775"]},"corr_author":"1","date_updated":"2025-12-29T13:47:58Z","has_accepted_license":"1","OA_place":"publisher","publication_identifier":{"issn":["0166-2236"],"eissn":["1878-108X"]},"intvolume":"        48","quality_controlled":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"PlanS_conform":"1","department":[{"_id":"MaHe"}],"date_created":"2025-08-10T22:01:29Z","file_date_updated":"2025-12-29T13:47:27Z","title":"Long-lived cellular molecules in the brain","oa_version":"Published Version","year":"2025","issue":"9","_id":"20154","month":"09","pmid":1,"article_processing_charge":"Yes (in subscription journal)","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.","ddc":["570"],"OA_type":"hybrid","status":"public","abstract":[{"lang":"eng","text":"In long-lived mammals, including humans, brain cell homeostasis is critical for maintaining brain function throughout life. Most neurons are generated during development and must maintain their cellular identity and plasticity to preserve brain function. Although extensive studies indicate the importance of recycling and regenerating cellular molecules to maintain cellular homeostasis, recent evidence has shown that some proteins and RNAs do not turn over for months and even years. We propose that these long-lived cellular molecules may be the basis for maintaining brain function in the long term, but also a potential convergent target of brain aging. We highlight key discoveries and challenges, and propose potential directions to unravel the mystery of brain cell longevity."}],"scopus_import":"1","date_published":"2025-09-01T00:00:00Z","oa":1,"file":[{"checksum":"90942491b499f70b0bf48b8aec2e7387","success":1,"file_name":"2025_TrendsNeurosciences_Hetzer.pdf","date_updated":"2025-12-29T13:47:27Z","creator":"dernst","date_created":"2025-12-29T13:47:27Z","access_level":"open_access","content_type":"application/pdf","file_size":327847,"relation":"main_file","file_id":"20873"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer"},{"first_name":"Tomohisa","full_name":"Toda, Tomohisa","last_name":"Toda"}],"publication_status":"published","article_type":"original"},{"OA_type":"green","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).","arxiv":1,"scopus_import":"1","date_published":"2025-08-01T00:00:00Z","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."}],"status":"public","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication_status":"published","article_type":"original","author":[{"last_name":"Brigati","first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","full_name":"Brigati, Giovanni"},{"full_name":"Stoltz, Gabriel","first_name":"Gabriel","last_name":"Stoltz"}],"title":"How to construct explicit decay rates for kinetic Fokker–Planck equations?","year":"2025","issue":"4","_id":"20155","oa_version":"Preprint","month":"08","article_processing_charge":"No","date_updated":"2025-11-05T13:51:40Z","OA_place":"repository","external_id":{"isi":["001550830900006"],"arxiv":["2302.14506"]},"corr_author":"1","intvolume":"        57","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"date_created":"2025-08-10T22:01:29Z","department":[{"_id":"JaMa"}],"page":"3587-3622","publisher":"Society for Industrial and Applied Mathematics","day":"01","doi":"10.1137/24M1700351","ec_funded":1,"type":"journal_article","citation":{"chicago":"Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates for Kinetic Fokker–Planck Equations?” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2025. <a href=\"https://doi.org/10.1137/24M1700351\">https://doi.org/10.1137/24M1700351</a>.","ama":"Brigati G, Stoltz G. How to construct explicit decay rates for kinetic Fokker–Planck equations? <i>SIAM Journal on Mathematical Analysis</i>. 2025;57(4):3587-3622. doi:<a href=\"https://doi.org/10.1137/24M1700351\">10.1137/24M1700351</a>","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.","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>","ista":"Brigati G, Stoltz G. 2025. How to construct explicit decay rates for kinetic Fokker–Planck equations? SIAM Journal on Mathematical Analysis. 57(4), 3587–3622.","short":"G. Brigati, G. Stoltz, SIAM Journal on Mathematical Analysis 57 (2025) 3587–3622."},"volume":57,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.14506","open_access":"1"}],"publication":"SIAM Journal on Mathematical Analysis"}]