[{"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matijevic","full_name":"Matijevic, Ivana","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024."},"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","date_published":"2024-02-21T00:00:00Z","doi":"10.7554/elife.68993","date_created":"2024-02-27T07:10:11Z","day":"21","publication":"eLife","has_accepted_license":"1","year":"2024","status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"type":"journal_article","article_type":"original","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)"},"_id":"15033","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2024-02-28T12:29:43Z","month":"02","intvolume":" 13","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"oa_version":"Published Version","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"volume":13,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"epub_ahead"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017."},"title":"Fungal infection alters collective nutritional intake of ant colonies","author":[{"first_name":"Eniko","last_name":"Csata","full_name":"Csata, Eniko"},{"last_name":"Perez-Escudero","full_name":"Perez-Escudero, Alfonso","first_name":"Alfonso"},{"last_name":"Laury","full_name":"Laury, Emmanuel","first_name":"Emmanuel"},{"first_name":"Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","full_name":"Leitner, Hanna","last_name":"Leitner"},{"first_name":"Gerard","full_name":"Latil, Gerard","last_name":"Latil"},{"first_name":"Juerge","full_name":"Heinze, Juerge","last_name":"Heinze"},{"last_name":"Simpson","full_name":"Simpson, Stephen","first_name":"Stephen"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"}],"external_id":{"pmid":["38307022"]},"article_processing_charge":"No","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"26","publication":"Current Biology","year":"2024","date_published":"2024-02-26T00:00:00Z","doi":"10.1016/j.cub.2024.01.017","date_created":"2023-10-31T13:30:20Z","page":"902-909.e6","_id":"14479","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-04T07:14:41Z","department":[{"_id":"SyCr"}],"oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication."}],"month":"02","intvolume":" 34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.26.564092"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"publication_status":"published","volume":34,"issue":"4"},{"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","author":[{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","last_name":"Varshney"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2401.08454"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x."},"article_number":"12","date_published":"2024-02-17T00:00:00Z","doi":"10.1007/s00601-024-01880-x","date_created":"2024-03-01T11:39:33Z","day":"17","publication":"Few-Body Systems","has_accepted_license":"1","year":"2024","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-04T07:07:10Z","ddc":["530"],"date_updated":"2024-03-04T07:08:16Z","status":"public","keyword":["Atomic and Molecular Physics","and Optics"],"article_type":"original","type":"journal_article","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)"},"_id":"15045","volume":65,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_id":"15049","file_size":436712,"date_updated":"2024-03-04T07:07:10Z","creator":"dernst","file_name":"2024_FewBodySys_Varshney.pdf","date_created":"2024-03-04T07:07:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1432-5411"]},"publication_status":"published","month":"02","intvolume":" 65","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport."}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator."}],"intvolume":" 6","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"15054","checksum":"ba2ae3e3a011f8897d3803c9366a67e2","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_PhysicalReviewResearch_Jin.pdf","date_created":"2024-03-04T07:53:08Z","creator":"dernst","file_size":4025988,"date_updated":"2024-03-04T07:53:08Z"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"issue":"1","volume":6,"_id":"15053","keyword":["General Physics and Astronomy"],"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)"},"article_type":"original","type":"journal_article","ddc":["530"],"date_updated":"2024-03-04T07:55:29Z","department":[{"_id":"MiLe"}],"file_date_updated":"2024-03-04T07:53:08Z","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Research","day":"13","year":"2024","has_accepted_license":"1","date_created":"2024-03-04T07:42:52Z","doi":"10.1103/physrevresearch.6.013158","date_published":"2024-02-13T00:00:00Z","article_number":"013158","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158."},"title":"Multipurpose platform for analog quantum simulation","external_id":{"arxiv":["2304.08433"]},"article_processing_charge":"Yes","author":[{"first_name":"Shuwei","last_name":"Jin","full_name":"Jin, Shuwei"},{"last_name":"Dai","full_name":"Dai, Kunlun","first_name":"Kunlun"},{"last_name":"Verstraten","full_name":"Verstraten, Joris","first_name":"Joris"},{"full_name":"Dixmerias, Maxime","last_name":"Dixmerias","first_name":"Maxime"},{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed"},{"first_name":"Christophe","full_name":"Salomon, Christophe","last_name":"Salomon"},{"first_name":"Bruno","full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf"},{"full_name":"de Jongh, Tim","last_name":"de Jongh","first_name":"Tim"},{"last_name":"Yefsah","full_name":"Yefsah, Tarik","first_name":"Tarik"}]},{"file":[{"file_name":"2024_Development_Schauer.pdf","date_created":"2024-03-04T07:24:43Z","file_size":14839986,"date_updated":"2024-03-04T07:24:43Z","creator":"dernst","success":1,"file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication_status":"published","issue":"4","volume":151,"related_material":{"record":[{"id":"14926","status":"public","relation":"research_data"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"02","intvolume":" 151","scopus_import":"1","ddc":["570"],"date_updated":"2024-03-04T07:28:25Z","file_date_updated":"2024-03-04T07:24:43Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"_id":"15048","status":"public","type":"journal_article","article_type":"original","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)"},"day":"01","publication":"Development","has_accepted_license":"1","year":"2024","date_published":"2024-02-01T00:00:00Z","doi":"10.1242/dev.202316","date_created":"2024-03-03T23:00:50Z","page":"1-18","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18."},"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}]},{"day":"14","publication":"Physical Review B","year":"2024","doi":"10.1103/physrevb.109.054305","date_published":"2024-02-14T00:00:00Z","date_created":"2024-03-04T07:41:23Z","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","quality_controlled":"1","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/physrevb.109.054305.","ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305.","ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 2024;109(5). doi:10.1103/physrevb.109.054305","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024)."},"title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","author":[{"last_name":"Cheng","full_name":"Cheng, Ruihuan","first_name":"Ruihuan"},{"first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","last_name":"Zeng","full_name":"Zeng, Zezhu"},{"first_name":"Chen","full_name":"Wang, Chen","last_name":"Wang"},{"first_name":"Niuchang","last_name":"Ouyang","full_name":"Ouyang, Niuchang"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"article_processing_charge":"No","article_number":"054305","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","volume":109,"issue":"5","ec_funded":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}],"month":"02","intvolume":" 109","scopus_import":"1","date_updated":"2024-03-04T07:48:55Z","department":[{"_id":"BiCh"}],"_id":"15052","status":"public","type":"journal_article","article_type":"original"},{"date_created":"2024-02-02T14:42:26Z","license":"https://opensource.org/licenses/MIT","date_published":"2024-02-02T00:00:00Z","doi":"10.15479/AT:ISTA:14926","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15048"}]},"file":[{"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"df7f358ae19a176cf710c0a802ce31b1","file_id":"14927","success":1,"date_updated":"2024-02-02T14:40:31Z","file_size":736,"creator":"rhauschild","date_created":"2024-02-02T14:40:31Z","file_name":"README.md"},{"success":1,"checksum":"10194cc11619eccd8f4b24472e465b7f","file_id":"14928","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Supplementary_file_1.zip","date_created":"2024-02-02T14:40:31Z","creator":"rhauschild","file_size":3543,"date_updated":"2024-02-02T14:40:31Z"}],"day":"02","year":"2024","has_accepted_license":"1","month":"02","oa":1,"publisher":"ISTA","title":"Matlab script for analysis of clone dispersal","department":[{"_id":"Bio"}],"file_date_updated":"2024-02-02T14:40:31Z","author":[{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926.","mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","short":"R. Hauschild, (2024).","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926"},"date_updated":"2024-03-04T07:28:25Z","status":"public","tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"type":"software","_id":"14926"},{"status":"public","type":"journal_article","article_type":"original","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)"},"_id":"15047","file_date_updated":"2024-03-04T07:34:00Z","department":[{"_id":"CaMu"}],"ddc":["550"],"date_updated":"2024-03-05T09:26:47Z","month":"02","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling."}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","relation":"press_release","description":"News on ISTA Website"}]},"volume":10,"issue":"8","ec_funded":1,"file":[{"checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_id":"15051","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-04T07:34:00Z","file_name":"2024_ScienceAdv_Bao.pdf","date_updated":"2024-03-04T07:34:00Z","file_size":800926,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"article_number":"eadj6801","title":"Intensification of daily tropical precipitation extremes from more organized convection","author":[{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","full_name":"Bao, Jiawei","last_name":"Bao"},{"first_name":"Bjorn","last_name":"Stevens","full_name":"Stevens, Bjorn"},{"full_name":"Kluft, Lukas","last_name":"Kluft","first_name":"Lukas"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"}],"article_processing_charge":"Yes","external_id":{"pmid":["38394192"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801."},"quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","doi":"10.1126/sciadv.adj6801","date_published":"2024-02-23T00:00:00Z","date_created":"2024-03-03T23:00:50Z","day":"23","publication":"Science Advances","has_accepted_license":"1","year":"2024"},{"status":"public","article_type":"original","type":"journal_article","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)"},"_id":"12875","department":[{"_id":"SiHi"},{"_id":"RySh"}],"file_date_updated":"2024-02-06T13:56:15Z","ddc":["570"],"date_updated":"2024-03-05T09:43:02Z","month":"01","intvolume":" 112","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"volume":112,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","relation":"press_release","description":"News on ISTA Website"}]},"issue":"2","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","creator":"dernst","file_size":5942467,"date_updated":"2024-02-06T13:56:15Z","file_name":"2024_Neuron_Cheung.pdf","date_created":"2024-02-06T13:56:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","project":[{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"title":"Multipotent progenitors instruct ontogeny of the superior colliculus","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"full_name":"Krausgruber, Thomas","last_name":"Krausgruber","first_name":"Thomas"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","first_name":"Martin","full_name":"Schrammel, Martin","last_name":"Schrammel"},{"id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","first_name":"Natalie Y","last_name":"Özgen","full_name":"Özgen, Natalie Y"},{"last_name":"Ivec","full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"external_id":{"pmid":["38096816"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","doi":"10.1016/j.neuron.2023.11.009","date_published":"2024-01-17T00:00:00Z","date_created":"2023-04-27T09:41:48Z","page":"230-246.e11","day":"17","publication":"Neuron","has_accepted_license":"1","year":"2024"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024).","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6."},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38316877"]},"author":[{"last_name":"Datler","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hansen","full_name":"Hansen, Jesse","first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Thader","full_name":"Thader, Andreas"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bauer, Lukas W","last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"publication":"Nature Structural & Molecular Biology","day":"05","year":"2024","has_accepted_license":"1","date_created":"2024-02-12T09:59:45Z","doi":"10.1038/s41594-023-01201-6","date_published":"2024-02-05T00:00:00Z","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","ddc":["570"],"date_updated":"2024-03-05T09:27:47Z","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"_id":"14979","keyword":["Molecular Biology","Structural Biology"],"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)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website"}]},"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"month":"02","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}]},{"related_material":{"link":[{"url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","relation":"press_release","description":"News on ISTA Website"}]},"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41567-023-02302-1"}],"scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_updated":"2024-03-05T09:33:38Z","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)"},"article_type":"original","type":"journal_article","_id":"14846","date_created":"2024-01-21T23:00:57Z","doi":"10.1038/s41567-023-02302-1","date_published":"2024-01-09T00:00:00Z","publication":"Nature Physics","day":"09","year":"2024","has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346"},{"first_name":"Rushikesh","full_name":"Shinde, Rushikesh","last_name":"Shinde"},{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison","last_name":"Bolger-Munro","orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison"},{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Gregory"},{"last_name":"Steccari","full_name":"Steccari, Irene","first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"last_name":"Labrousse Arias","full_name":"Labrousse Arias, David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David"},{"last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Callan-Jones, Andrew","last_name":"Callan-Jones","first_name":"Andrew"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024.","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1."},"project":[{"name":"Control of embryonic cleavage pattern","grant_number":"I03601","_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"quality_controlled":"1","publisher":"American Association for the Advancement of Science","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","date_created":"2024-01-14T23:00:56Z","date_published":"2024-01-05T00:00:00Z","doi":"10.1126/science.adi2982","page":"114-119","publication":"Science","day":"05","year":"2024","title":"The genetic basis of a recent transition to live-bearing in marine snails","article_processing_charge":"No","external_id":{"pmid":["38175895"]},"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka"},{"first_name":"Martin D.","full_name":"Garlovsky, Martin D.","last_name":"Garlovsky"},{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","last_name":"Shipilina"},{"last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando"},{"full_name":"Lifchitz, Hila","last_name":"Lifchitz","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119."},"intvolume":" 383","month":"01","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"volume":383,"issue":"6678","related_material":{"record":[{"id":"14812","status":"public","relation":"research_data"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","description":"News on ISTA Website"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"status":"public","article_type":"original","type":"journal_article","_id":"14796","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2024-03-05T09:35:25Z"},{"file_date_updated":"2024-02-23T14:20:16Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"ddc":["576","519"],"date_updated":"2024-03-06T14:22:52Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"],"status":"public","type":"dissertation","_id":"15020","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7553"},{"relation":"part_of_dissertation","id":"12081","status":"public"},{"relation":"part_of_dissertation","id":"7606","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"hledik thesis pdfa 2b.pdf","date_created":"2024-02-23T13:50:53Z","file_size":7102089,"date_updated":"2024-02-23T13:50:53Z","creator":"mhledik"},{"file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","file_size":14014790,"date_updated":"2024-02-23T14:20:16Z","creator":"mhledik"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"title":"Genetic information and biological optimization","article_processing_charge":"No","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020"},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"date_created":"2024-02-23T14:02:04Z","doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","page":"158","day":"23","year":"2024","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"volume":34,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1879-0445"]},"publication_status":"published","month":"01","intvolume":" 34","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"department":[{"_id":"EvBe"}],"date_updated":"2024-03-12T12:19:12Z","status":"public","type":"other_academic_publication","_id":"14842","date_published":"2024-01-08T00:00:00Z","doi":"10.1016/j.cub.2023.11.039","date_created":"2024-01-21T23:00:56Z","page":"R3-R5","day":"08","publication":"Current Biology","year":"2024","quality_controlled":"1","publisher":"Elsevier","oa":1,"title":"Eva Benkova","author":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.","ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p."}},{"volume":121,"issue":"8","related_material":{"record":[{"id":"13173","status":"public","relation":"research_data"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","relation":"press_release"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"file_size":13648221,"date_updated":"2024-03-12T13:42:42Z","creator":"dernst","file_name":"2024_PNAS_Koppensteiner.pdf","date_created":"2024-03-12T13:42:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"b25b2a057c266ff317a48b0d54d6fc8a","file_id":"15110"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","month":"02","intvolume":" 121","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"department":[{"_id":"RySh"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T13:42:42Z","ddc":["570"],"date_updated":"2024-03-12T13:44:18Z","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"15084","date_published":"2024-02-20T00:00:00Z","doi":"10.1073/pnas.2301449121","date_created":"2024-03-05T09:23:55Z","day":"20","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","year":"2024","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","author":[{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"},{"last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","full_name":"Önal, Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal"},{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Le Monnier","full_name":"Le Monnier, Elodie","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2","first_name":"Utsa","last_name":"Roy","full_name":"Roy, Utsa"},{"first_name":"Yukihiro","full_name":"Nakamura, Yukihiro","last_name":"Nakamura"},{"first_name":"Tetsushi","last_name":"Sadakata","full_name":"Sadakata, Tetsushi"},{"full_name":"Sanbo, Makoto","last_name":"Sanbo","first_name":"Makoto"},{"last_name":"Hirabayashi","full_name":"Hirabayashi, Masumi","first_name":"Masumi"},{"last_name":"Rhee","full_name":"Rhee, JeongSeop","first_name":"JeongSeop"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"external_id":{"pmid":["38346189"]},"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121"},"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"e2301449121"},{"date_updated":"2024-03-12T13:29:25Z","ddc":["000"],"file_date_updated":"2024-03-12T13:12:22Z","department":[{"_id":"KrCh"}],"_id":"15083","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"checksum":"068520e3efd4d008bb9177e8aedb7d22","file_id":"15109","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-03-12T13:12:22Z","file_name":"2024_PNAS_Huebner.pdf","creator":"dernst","date_updated":"2024-03-12T13:12:22Z","file_size":2203220}],"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website"}],"record":[{"relation":"research_data","status":"public","id":"15108"}]},"volume":121,"issue":"10","ec_funded":1,"abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"oa_version":"Published Version","pmid":1,"month":"03","intvolume":" 121","citation":{"ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024).","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","full_name":"Hübner, Valentin","last_name":"Hübner"},{"full_name":"Staab, Manuel","last_name":"Staab","first_name":"Manuel"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38408249"]},"title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","article_number":"e2315558121","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2024","day":"05","publication":"Proceedings of the National Academy of Sciences","date_published":"2024-03-05T00:00:00Z","doi":"10.1073/pnas.2315558121","date_created":"2024-03-05T09:18:49Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1},{"year":"2024","has_accepted_license":"1","day":"09","date_created":"2024-03-12T13:02:58Z","doi":"10.5281/ZENODO.10639167","date_published":"2024-02-09T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"15083","status":"public"}]},"abstract":[{"lang":"eng","text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://10.5281/zenodo.10639167","open_access":"1"}],"publisher":"Zenodo","month":"02","citation":{"chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","short":"V. Hübner, M. Kleshnina, (2024).","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167"},"date_updated":"2024-03-12T13:29:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"article_processing_charge":"No","author":[{"full_name":"Hübner, Valentin","last_name":"Hübner","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"}],"department":[{"_id":"KrCh"}],"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","_id":"15108","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)"},"type":"research_data_reference","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584."},"title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Schmidt","full_name":"Schmidt, Hauke","first_name":"Hauke"},{"first_name":"Sebastian","full_name":"Rast, Sebastian","last_name":"Rast"},{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","full_name":"Bao, Jiawei","last_name":"Bao"},{"last_name":"Cassim","full_name":"Cassim, Amrit","first_name":"Amrit"},{"full_name":"Fang, Shih Wei","last_name":"Fang","first_name":"Shih Wei"},{"first_name":"Diego","full_name":"Jimenez-De La Cuesta, Diego","last_name":"Jimenez-De La Cuesta"},{"last_name":"Keil","full_name":"Keil, Paul","first_name":"Paul"},{"first_name":"Lukas","last_name":"Kluft","full_name":"Kluft, Lukas"},{"full_name":"Kroll, Clarissa","last_name":"Kroll","first_name":"Clarissa"},{"full_name":"Lang, Theresa","last_name":"Lang","first_name":"Theresa"},{"last_name":"Niemeier","full_name":"Niemeier, Ulrike","first_name":"Ulrike"},{"first_name":"Andrea","last_name":"Schneidereit","full_name":"Schneidereit, Andrea"},{"last_name":"Williams","full_name":"Williams, Andrew I.L.","first_name":"Andrew I.L."},{"full_name":"Stevens, Bjorn","last_name":"Stevens","first_name":"Bjorn"}],"acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","oa":1,"quality_controlled":"1","publisher":"European Geosciences Union","publication":"Geoscientific Model Development","day":"22","year":"2024","has_accepted_license":"1","date_created":"2024-03-10T23:00:53Z","date_published":"2024-02-22T00:00:00Z","doi":"10.5194/gmd-17-1563-2024","page":"1563-1584","_id":"15097","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)"},"type":"journal_article","article_type":"original","ddc":["550"],"date_updated":"2024-03-13T09:01:20Z","file_date_updated":"2024-03-13T08:59:21Z","department":[{"_id":"CaMu"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study."}],"intvolume":" 17","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"15111","checksum":"270d2340402729b0532f7072ea914cae","creator":"dernst","file_size":13364601,"date_updated":"2024-03-13T08:59:21Z","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","date_created":"2024-03-13T08:59:21Z"}],"publication_status":"published","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"issue":"4","volume":17},{"year":"2024","has_accepted_license":"1","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","day":"26","date_created":"2023-01-16T11:45:22Z","doi":"10.1017/prm.2024.7","date_published":"2024-02-26T00:00:00Z","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","citation":{"chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7","apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2203.02015"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Naskręcki, Bartosz","last_name":"Naskręcki","first_name":"Bartosz"},{"last_name":"Verzobio","orcid":"0000-0002-0854-0306","full_name":"Verzobio, Matteo","first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb"}],"title":"Common valuations of division polynomials","article_number":"2203.02015","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1017/prm.2024.7","open_access":"1"}],"scopus_import":"1","month":"02","date_updated":"2024-03-13T11:55:21Z","ddc":["510"],"department":[{"_id":"TiBr"}],"_id":"12311","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)"},"type":"journal_article","article_type":"original","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"status":"public"},{"publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"abstract":[{"text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tig.2024.01.002"}],"month":"02","date_updated":"2024-03-13T12:08:57Z","ddc":["570"],"department":[{"_id":"NiBa"}],"_id":"15099","article_type":"review","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2024","day":"22","publication":"Trends in Genetics","doi":"10.1016/j.tig.2024.01.002","date_published":"2024-02-22T00:00:00Z","date_created":"2024-03-10T23:00:54Z","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","quality_controlled":"1","publisher":"Cell Press","oa":1,"citation":{"apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"external_id":{"pmid":["38395682"]},"article_processing_charge":"Yes (in subscription journal)","title":"Diverse pathways to speciation revealed by marine snails"},{"date_updated":"2024-03-13T12:20:23Z","department":[{"_id":"JuFi"}],"_id":"15098","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"publication_status":"epub_ahead","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.","lang":"eng"}],"month":"02","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0.","ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024."},"title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti"},{"full_name":"Luongo, Eliseo","last_name":"Luongo","first_name":"Eliseo"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2306.11081"]},"project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"day":"27","publication":"Mathematische Annalen","year":"2024","date_published":"2024-02-27T00:00:00Z","doi":"10.1007/s00208-024-02812-0","date_created":"2024-03-10T23:00:54Z","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"date_updated":"2024-03-14T13:14:18Z","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"_id":"14843","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"publication_status":"inpress","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","relation":"press_release"}],"record":[{"status":"public","id":"15101","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"month":"01","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002."},"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","author":[{"first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, JingJing","last_name":"Chen"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"last_name":"Arai","full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"article_processing_charge":"No","external_id":{"pmid":["38215739"]},"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"day":"11","publication":"Neuron","year":"2024","date_published":"2024-01-11T00:00:00Z","doi":"10.1016/j.neuron.2023.12.002","date_created":"2024-01-21T23:00:56Z","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and 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), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","publisher":"Elsevier","quality_controlled":"1"},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"15104","checksum":"db4947474ffa271e66c254b6fe876a55","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-03-11T14:10:58Z","file_name":"Thesis_Jingjing CHEN.docx","creator":"jchen","date_updated":"2024-03-12T07:12:17Z","file_size":11271363},{"relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","embargo":"2024-04-01","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_id":"15105","creator":"jchen","file_size":16627311,"date_updated":"2024-03-11T14:11:06Z","file_name":"Thesis_Jingjing CHEN_merged.pdf","date_created":"2024-03-11T14:11:06Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14843"}]},"ec_funded":1,"_id":"15101","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","supervisor":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-14T13:14:19Z","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T07:12:17Z","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2024","day":"11","page":"84","doi":"10.15479/at:ista:15101","date_published":"2024-03-11T00:00:00Z","date_created":"2024-03-11T10:09:54Z","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"citation":{"ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Chen","full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse"},{"_id":"15122","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)"},"type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2024-03-19T07:24:03Z","file_date_updated":"2024-03-19T07:16:38Z","department":[{"_id":"MaSe"}],"oa_version":"Published Version","abstract":[{"text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA.","lang":"eng"}],"intvolume":" 6","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2024_PhysicalReviewResearch_Sack.pdf","date_created":"2024-03-19T07:16:38Z","file_size":2777593,"date_updated":"2024-03-19T07:16:38Z","creator":"dernst","success":1,"checksum":"274c9f1b15b3547a10a03f39e4ccc582","file_id":"15123","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"volume":6,"issue":"1","article_number":"013223","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223."},"title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","article_processing_charge":"Yes","external_id":{"arxiv":["2307.14427"]},"author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack"},{"last_name":"Egger","full_name":"Egger, Daniel J.","first_name":"Daniel J."}],"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Research","day":"01","year":"2024","has_accepted_license":"1","date_created":"2024-03-17T23:00:59Z","date_published":"2024-03-01T00:00:00Z","doi":"10.1103/PhysRevResearch.6.013223"},{"acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","publisher":"Springer Nature","quality_controlled":"1","day":"04","publication":"Nature Microbiology","year":"2024","date_published":"2024-03-04T00:00:00Z","doi":"10.1038/s41564-024-01600-5","date_created":"2024-03-17T23:00:58Z","page":"698-711","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.","ieee":"P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711.","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5."},"title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","author":[{"first_name":"Phillip","full_name":"Nußbaum, Phillip","last_name":"Nußbaum"},{"full_name":"Kureisaite-Ciziene, Danguole","last_name":"Kureisaite-Ciziene","first_name":"Danguole"},{"first_name":"Dom","full_name":"Bellini, Dom","last_name":"Bellini"},{"full_name":"Van Der Does, Chris","last_name":"Van Der Does","first_name":"Chris"},{"first_name":"Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160","last_name":"Kojic","full_name":"Kojic, Marko"},{"first_name":"Najwa","last_name":"Taib","full_name":"Taib, Najwa"},{"last_name":"Yeates","full_name":"Yeates, Anna","first_name":"Anna"},{"first_name":"Maxime","full_name":"Tourte, Maxime","last_name":"Tourte"},{"first_name":"Simonetta","last_name":"Gribaldo","full_name":"Gribaldo, Simonetta"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Löwe, Jan","last_name":"Löwe","first_name":"Jan"},{"full_name":"Albers, Sonja Verena","last_name":"Albers","first_name":"Sonja Verena"}],"article_processing_charge":"No","external_id":{"pmid":["38443575"]},"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"month":"03","intvolume":" 9","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2058-5276"]},"publication_status":"published","volume":9,"issue":"3","_id":"15118","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-19T07:30:53Z","department":[{"_id":"MaLo"}]},{"author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"article_processing_charge":"No","external_id":{"arxiv":["2106.01274"]},"title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","citation":{"mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333.","ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333","chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"413-430","doi":"10.1214/22-AIHP1333","date_published":"2024-02-01T00:00:00Z","date_created":"2024-03-17T23:00:58Z","year":"2024","day":"01","publication":"Annales de l'institut Henri Poincare Probability and Statistics","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","department":[{"_id":"JuFi"}],"date_updated":"2024-03-19T08:14:17Z","type":"journal_article","article_type":"original","status":"public","_id":"15119","volume":60,"issue":"1","publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"month":"02","intvolume":" 60","abstract":[{"text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness.","lang":"eng"}],"oa_version":"Preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121."},"title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","author":[{"last_name":"Habig","full_name":"Habig, Michael","first_name":"Michael"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Judith","full_name":"Müller, Judith","last_name":"Müller"},{"last_name":"Stukenbrock","full_name":"Stukenbrock, Eva H.","first_name":"Eva H."},{"id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","full_name":"Leitner, Hanna","last_name":"Leitner"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38442176"]},"article_number":"e2316284121","project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"day":"12","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","year":"2024","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2316284121","date_created":"2023-10-31T13:30:00Z","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2024-03-19T09:07:20Z","file_date_updated":"2024-03-19T09:02:57Z","department":[{"_id":"SyCr"}],"_id":"14478","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","creator":"dernst","file_name":"2024_PNAS_Habig.pdf","date_created":"2024-03-19T09:02:57Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15124","checksum":"f5e871db617b682edc71fcd08670dc81"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","volume":121,"issue":"11","ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"month":"03","intvolume":" 121","scopus_import":"1"},{"date_created":"2021-09-27T10:48:23Z","doi":"10.1007/s10107-024-02064-5","date_published":"2024-03-07T00:00:00Z","publication":"Mathematical Programming","day":"07","year":"2024","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","title":"Generalized minimum 0-extension problem and discrete convexity","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2109.10203"]},"author":[{"orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5."},"article_number":"2109.10203","language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-27T10:54:51Z","file_name":"Generalized-0-Ext.pdf","creator":"mdvorak","date_updated":"2021-09-27T10:54:51Z","file_size":603672,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","file_id":"10046","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"month":"03","scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2021-09-27T10:54:51Z","ddc":["004"],"date_updated":"2024-03-19T08:20:31Z","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"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)"},"article_type":"original","type":"journal_article","_id":"10045"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","date_created":"2024-03-17T23:00:58Z","doi":"10.1007/s10107-024-02066-3","date_published":"2024-03-06T00:00:00Z","year":"2024","publication":"Mathematical Programming","day":"06","project":[{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"external_id":{"arxiv":["2301.09217"]},"article_processing_charge":"No","author":[{"full_name":"Zheng, Da Wei","last_name":"Zheng","first_name":"Da Wei"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","citation":{"ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).","apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3.","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"scopus_import":"1","month":"03","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"status":"public","id":"13236","relation":"earlier_version"}]},"publication_status":"epub_ahead","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"15121","department":[{"_id":"MoHe"}],"date_updated":"2024-03-19T08:32:32Z"},{"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","date_created":"2024-03-17T23:00:57Z","doi":"10.1016/j.ces.2024.119959","date_published":"2024-03-04T00:00:00Z","publication":"Chemical Engineering Science","day":"04","year":"2024","article_number":"119959","title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","article_processing_charge":"No","author":[{"last_name":"Yao","full_name":"Yao, Zihao","first_name":"Zihao"},{"full_name":"Liu, Xu","last_name":"Liu","first_name":"Xu"},{"first_name":"Rhys","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys","last_name":"Bunting"},{"last_name":"Wang","full_name":"Wang, Jianguo","first_name":"Jianguo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.","ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.","ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959","apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).","ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024."},"intvolume":" 291","month":"03","scopus_import":"1","oa_version":"None","abstract":[{"text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.","lang":"eng"}],"volume":291,"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0009-2509"]},"status":"public","type":"journal_article","article_type":"original","_id":"15114","department":[{"_id":"MaIb"}],"date_updated":"2024-03-19T08:47:42Z"},{"department":[{"_id":"AnSa"}],"file_date_updated":"2024-03-19T10:22:42Z","ddc":["550"],"date_updated":"2024-03-19T11:41:32Z","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)"},"type":"journal_article","article_type":"original","_id":"15116","volume":121,"related_material":{"record":[{"relation":"research_data","id":"15126","status":"public"}]},"issue":"11","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","file_name":"2024_PNAS_Giubertoni.pdf","date_created":"2024-03-19T10:22:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","file_id":"15125"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"intvolume":" 121","month":"03","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly."}],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38451946"]},"author":[{"first_name":"Giulia","full_name":"Giubertoni, Giulia","last_name":"Giubertoni"},{"full_name":"Feng, Liru","last_name":"Feng","first_name":"Liru"},{"last_name":"Klein","full_name":"Klein, Kevin","first_name":"Kevin"},{"last_name":"Giannetti","full_name":"Giannetti, Guido","first_name":"Guido"},{"first_name":"Luco","full_name":"Rutten, Luco","last_name":"Rutten"},{"full_name":"Choi, Yeji","last_name":"Choi","first_name":"Yeji"},{"full_name":"Van Der Net, Anouk","last_name":"Van Der Net","first_name":"Anouk"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"first_name":"Dimitra","last_name":"Micha","full_name":"Micha, Dimitra"},{"last_name":"Hunger","full_name":"Hunger, Johannes","first_name":"Johannes"},{"last_name":"Deblais","full_name":"Deblais, Antoine","first_name":"Antoine"},{"full_name":"Bonn, Daniel","last_name":"Bonn","first_name":"Daniel"},{"first_name":"Nico","last_name":"Sommerdijk","full_name":"Sommerdijk, Nico"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Ilie","full_name":"Ilie, Ioana M.","first_name":"Ioana M."},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"last_name":"Woutersen","full_name":"Woutersen, Sander","first_name":"Sander"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121."},"article_number":"e2313162121","date_created":"2024-03-17T23:00:57Z","date_published":"2024-03-12T00:00:00Z","doi":"10.1073/pnas.2313162121","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"12","year":"2024","has_accepted_license":"1","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress."},{"citation":{"ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["38452088"]},"author":[{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"}],"year":"2024","publication":"Science","day":"08","page":"eadg6757","date_created":"2024-03-17T23:00:57Z","doi":"10.1126/science.adg6757","date_published":"2024-03-08T00:00:00Z","acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","publisher":"AAAS","quality_controlled":"1","date_updated":"2024-03-20T07:42:52Z","department":[{"_id":"PeJo"}],"_id":"15117","type":"journal_article","article_type":"review","status":"public","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6687","volume":383,"abstract":[{"text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 383","month":"03"},{"file_date_updated":"2024-03-14T14:14:35Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_updated":"2024-03-20T09:36:57Z","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"ddc":["514","500","516"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","_id":"15094","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","id":"11660","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11658","status":"public"},{"relation":"part_of_dissertation","id":"13182","status":"public"},{"relation":"part_of_dissertation","id":"15090","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"15091"},{"relation":"part_of_dissertation","id":"15093","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"15112","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","success":1,"date_updated":"2024-03-14T08:55:07Z","file_size":4106872,"creator":"scultrer","date_created":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf"},{"file_id":"15113","checksum":"bcbd213490f5a7e68855a092bbce93f1","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis (1).zip","date_created":"2024-03-14T08:56:24Z","creator":"scultrer","file_size":4746234,"date_updated":"2024-03-14T14:14:35Z"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"title":"Persistence and Morse theory for discrete geometric structures","citation":{"mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Discretization in Geometry and Dynamics"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"108","date_created":"2024-03-08T15:28:10Z","doi":"10.15479/at:ista:15094","date_published":"2024-03-08T00:00:00Z","year":"2024","has_accepted_license":"1","day":"08","oa":1,"publisher":"Institute of Science and Technology Austria"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2311.01115"}],"month":"01","abstract":[{"text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15094"}]},"publication_status":"published","publication_identifier":{"eisbn":["9781611977912"]},"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorigthms","start_date":"2024-01-07","location":"Alexandria, VA, USA","end_date":"2024-01-10"},"type":"conference","status":"public","_id":"15093","department":[{"_id":"HeEd"},{"_id":"MoHe"}],"date_updated":"2024-03-20T09:36:56Z","oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","page":"243 - 295","date_created":"2024-03-08T10:27:39Z","date_published":"2024-01-04T00:00:00Z","doi":"10.1137/1.9781611977912.11","year":"2024","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","day":"04","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"},{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"article_processing_charge":"No","external_id":{"arxiv":["2311.01115"]},"author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Ost, Lara","last_name":"Ost","first_name":"Lara"}],"editor":[{"full_name":"Woodruff, David P.","last_name":"Woodruff","first_name":"David P."}],"title":"Dynamically maintaining the persistent homology of time series","citation":{"ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"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)"},"type":"preprint","status":"public","_id":"15091","article_number":"2212.03128","article_processing_charge":"No","external_id":{"arxiv":["2212.03128"]},"author":[{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","first_name":"Ondrej","full_name":"Draganov, Ondrej","last_name":"Draganov"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"department":[{"_id":"HeEd"}],"title":"Chromatic alpha complexes","citation":{"chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv."},"date_updated":"2024-03-20T09:36:56Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"month":"02","abstract":[{"text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided.","lang":"eng"}],"oa_version":"Preprint","date_created":"2024-03-08T10:13:59Z","related_material":{"record":[{"id":"15094","status":"public","relation":"dissertation_contains"}]},"date_published":"2024-02-07T00:00:00Z","publication_status":"submitted","year":"2024","language":[{"iso":"eng"}],"publication":"arXiv","day":"07"},{"department":[{"_id":"TiVo"}],"date_updated":"2024-03-25T07:04:05Z","type":"journal_article","article_type":"original","status":"public","_id":"15171","ec_funded":1,"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41593-024-01597-4","open_access":"1"}],"month":"03","abstract":[{"lang":"eng","text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena."}],"oa_version":"Published Version","author":[{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"article_processing_charge":"Yes (via OA deal)","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","citation":{"chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience.","mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020"}],"date_published":"2024-03-20T00:00:00Z","doi":"10.1038/s41593-024-01597-4","date_created":"2024-03-24T23:01:00Z","year":"2024","day":"20","publication":"Nature Neuroscience","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel."},{"_id":"15172","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"status":"public","type":"journal_article","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory.","chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory. IEEE, n.d. https://doi.org/10.1109/TIT.2024.3367767.","ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory. doi:10.1109/TIT.2024.3367767","apa":"Esposito, A. R., & Mondelli, M. (n.d.). Concentration without independence via information measures. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3367767","short":"A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory (n.d.).","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” IEEE Transactions on Information Theory. IEEE.","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory, IEEE, doi:10.1109/TIT.2024.3367767."},"date_updated":"2024-03-25T07:15:51Z","title":"Concentration without independence via information measures","department":[{"_id":"MaMo"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.07245"]},"author":[{"last_name":"Esposito","full_name":"Esposito, Amedeo Roberto","id":"9583e921-e1ad-11ec-9862-cef099626dc9","first_name":"Amedeo Roberto"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"oa_version":"None","abstract":[{"text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.","lang":"eng"}],"month":"02","quality_controlled":"1","scopus_import":"1","publisher":"IEEE","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","day":"20","year":"2024","publication_status":"inpress","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"date_created":"2024-03-24T23:01:00Z","doi":"10.1109/TIT.2024.3367767","date_published":"2024-02-20T00:00:00Z","related_material":{"record":[{"status":"public","id":"14922","relation":"earlier_version"}]}},{"date_created":"2024-03-24T23:00:59Z","doi":"10.3847/1538-4357/ad1e5f","date_published":"2024-03-01T00:00:00Z","publication":"Astrophysical Journal","day":"01","year":"2024","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","acknowledgement":"J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094, and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and from the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge support from Australian Research Council Laureate Fellowship FL180100060. H.A. and I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded by CEA and CNES. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. B.W. acknowledges support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. C.P. thanks Marsha and Ralph Schilling for the generous support of this research.","title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5","article_processing_charge":"Yes","external_id":{"arxiv":["2309.05714"]},"author":[{"full_name":"Greene, Jenny E.","last_name":"Greene","first_name":"Jenny E."},{"last_name":"Labbe","full_name":"Labbe, Ivo","first_name":"Ivo"},{"last_name":"Goulding","full_name":"Goulding, Andy D.","first_name":"Andy D."},{"last_name":"Furtak","full_name":"Furtak, Lukas J.","first_name":"Lukas J."},{"full_name":"Chemerynska, Iryna","last_name":"Chemerynska","first_name":"Iryna"},{"last_name":"Kokorev","full_name":"Kokorev, Vasily","first_name":"Vasily"},{"first_name":"Pratika","last_name":"Dayal","full_name":"Dayal, Pratika"},{"first_name":"Marta","last_name":"Volonteri","full_name":"Volonteri, Marta"},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"},{"last_name":"Wang","full_name":"Wang, Bingjie","first_name":"Bingjie"},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"last_name":"Burgasser","full_name":"Burgasser, Adam J.","first_name":"Adam J."},{"first_name":"Rachel","last_name":"Bezanson","full_name":"Bezanson, Rachel"},{"last_name":"Atek","full_name":"Atek, Hakim","first_name":"Hakim"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"first_name":"Sam E.","full_name":"Cutler, Sam E.","last_name":"Cutler"},{"last_name":"Feldmann","full_name":"Feldmann, Robert","first_name":"Robert"},{"first_name":"Seiji","last_name":"Fujimoto","full_name":"Fujimoto, Seiji"},{"first_name":"Karl","full_name":"Glazebrook, Karl","last_name":"Glazebrook"},{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"last_name":"Khullar","full_name":"Khullar, Gourav","first_name":"Gourav"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"first_name":"Danilo","last_name":"Marchesini","full_name":"Marchesini, Danilo"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"full_name":"Miller, Tim B.","last_name":"Miller","first_name":"Tim B."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"first_name":"Richard","full_name":"Pan, Richard","last_name":"Pan"},{"full_name":"Papovich, Casey","last_name":"Papovich","first_name":"Casey"},{"last_name":"Price","full_name":"Price, Sedona H.","first_name":"Sedona H."},{"full_name":"Van Dokkum, Pieter","last_name":"Van Dokkum","first_name":"Pieter"},{"full_name":"Weaver, John R.","last_name":"Weaver","first_name":"John R."},{"last_name":"Whitaker","full_name":"Whitaker, Katherine E.","first_name":"Katherine E."},{"full_name":"Zitrin, Adi","last_name":"Zitrin","first_name":"Adi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal, vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.","ieee":"J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical Journal, vol. 964. IOP Publishing, 2024.","short":"J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev, P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R. Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook, A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price, P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964 (2024).","apa":"Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I., Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f","chicago":"Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska, Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f.","ista":"Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE, Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39."},"article_number":"39","volume":964,"language":[{"iso":"eng"}],"file":[{"file_name":"2024_AstrophysicalJourn_Greene.pdf","date_created":"2024-03-25T08:02:43Z","file_size":2700137,"date_updated":"2024-03-25T08:02:43Z","creator":"dernst","success":1,"file_id":"15176","checksum":"389a880e176799d5c062ea7cb82d08c9","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"intvolume":" 964","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth."}],"file_date_updated":"2024-03-25T08:02:43Z","department":[{"_id":"JoMa"}],"ddc":["550"],"date_updated":"2024-03-25T08:04:13Z","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)"},"type":"journal_article","article_type":"original","_id":"15170"},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Marek Filakovský: This research was supported by Charles University (project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35), and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All data is provided in full in the results section of this paper. Jakub Opršal: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Uli Wagner: This research was supported by the Austrian Science Fund (FWF project P31312-N35).","date_created":"2024-03-24T23:00:59Z","doi":"10.4230/LIPIcs.STACS.2024.34","date_published":"2024-03-01T00:00:00Z","publication":"41st International Symposium on Theoretical Aspects of Computer Science","day":"01","year":"2024","has_accepted_license":"1","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"article_number":"34","title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","external_id":{"arxiv":["2312.12981"]},"article_processing_charge":"No","author":[{"full_name":"Filakovský, Marek","last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima","first_name":"Tamio Vesa"},{"last_name":"Opršal","full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242","first_name":"Jakub"},{"id":"0433290C-AF8F-11E9-A4C7-F729E6697425","first_name":"Gianluca","last_name":"Tasinato","full_name":"Tasinato, Gianluca"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.STACS.2024.34.","ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 289, 34.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In 41st International Symposium on Theoretical Aspects of Computer Science (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2024.34","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand, France, 2024, vol. 289."},"intvolume":" 289","month":"03","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the \"linearly ordered chromatic number\" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023)."}],"ec_funded":1,"volume":289,"language":[{"iso":"eng"}],"file":[{"date_created":"2024-03-25T07:44:30Z","file_name":"2024_LIPICs_Filakovsky.pdf","creator":"dernst","date_updated":"2024-03-25T07:44:30Z","file_size":927290,"file_id":"15175","checksum":"0524d4189fd1ed08989546511343edf3","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773119"]},"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)"},"conference":{"start_date":"2024-03-12","location":"Clermont-Ferrand, France","end_date":"2024-03-14","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"type":"conference","_id":"15168","file_date_updated":"2024-03-25T07:44:30Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2024-03-25T07:45:54Z"},{"volume":126,"publication_identifier":{"eissn":["1873-4030"],"issn":["1350-4533"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"974acbf2731e7382dcf5920ac762e551","file_id":"15177","success":1,"creator":"dernst","date_updated":"2024-03-25T08:29:52Z","file_size":10039402,"date_created":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 126","abstract":[{"lang":"eng","text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction."}],"oa_version":"Published Version","file_date_updated":"2024-03-25T08:29:52Z","department":[{"_id":"PreCl"}],"date_updated":"2024-03-25T08:31:01Z","ddc":["610"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15164","date_published":"2024-04-01T00:00:00Z","doi":"10.1016/j.medengphy.2024.104143","date_created":"2024-03-24T23:00:58Z","has_accepted_license":"1","year":"2024","day":"01","publication":"Medical Engineering and Physics","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","author":[{"first_name":"Juan D.","full_name":"Silva-Henao, Juan D.","last_name":"Silva-Henao"},{"first_name":"Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","last_name":"Schober","full_name":"Schober, Sophie"},{"last_name":"Pahr","full_name":"Pahr, Dieter H.","first_name":"Dieter H."},{"first_name":"Andreas G.","full_name":"Reisinger, Andreas G.","last_name":"Reisinger"}],"article_processing_charge":"Yes (in subscription journal)","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","citation":{"ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"104143"},{"scopus_import":"1","month":"03","intvolume":" 20","abstract":[{"lang":"eng","text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results."}],"oa_version":"Published Version","issue":"3","related_material":{"link":[{"url":"https://github.com/Neuroinflab/kCSD-python","relation":"software"}]},"volume":20,"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"15169","department":[{"_id":"TiVo"}],"date_updated":"2024-03-25T07:54:23Z","publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","doi":"10.1371/journal.pcbi.1011941","date_published":"2024-03-14T00:00:00Z","date_created":"2024-03-24T23:00:59Z","year":"2024","day":"14","publication":"PLoS Computational Biology","article_number":"e1011941","author":[{"last_name":"Chintaluri","full_name":"Chintaluri, Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","first_name":"Chaitanya"},{"first_name":"Marta","last_name":"Bejtka","full_name":"Bejtka, Marta"},{"first_name":"Wladyslaw","full_name":"Sredniawa, Wladyslaw","last_name":"Sredniawa"},{"last_name":"Czerwinski","full_name":"Czerwinski, Michal","first_name":"Michal"},{"first_name":"Jakub M.","last_name":"Dzik","full_name":"Dzik, Jakub M."},{"first_name":"Joanna","last_name":"Jedrzejewska-Szmek","full_name":"Jedrzejewska-Szmek, Joanna"},{"first_name":"Daniel K.","full_name":"Wojciki, Daniel K.","last_name":"Wojciki"}],"article_processing_charge":"Yes","title":"kCSD-python, reliable current source density estimation with quality control","citation":{"short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024).","ieee":"C. Chintaluri et al., “kCSD-python, reliable current source density estimation with quality control,” PLoS Computational Biology, vol. 20, no. 3. Public Library of Science, 2024.","apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011941","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 2024;20(3). doi:10.1371/journal.pcbi.1011941","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"033315","citation":{"mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:10.1103/PhysRevA.109.033315.","ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” Physical Review A, vol. 109, no. 3. American Physical Society, 2024.","short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","apa":"Al Hyder, R., Chevy, F., & Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.033315","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 2024;109(3). doi:10.1103/PhysRevA.109.033315","chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.033315.","ista":"Al Hyder R, Chevy F, Leyronas X. 2024. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 109(3), 033315."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2311.14536"]},"author":[{"last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed"},{"first_name":"F.","last_name":"Chevy","full_name":"Chevy, F."},{"last_name":"Leyronas","full_name":"Leyronas, X.","first_name":"X."}],"title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2024","publication":"Physical Review A","day":"19","date_created":"2024-03-24T23:00:59Z","date_published":"2024-03-19T00:00:00Z","doi":"10.1103/PhysRevA.109.033315","_id":"15167","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-25T07:36:55Z","department":[{"_id":"MiLe"}],"abstract":[{"text":"We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.14536","open_access":"1"}],"scopus_import":"1","intvolume":" 109","month":"03","publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"volume":109,"issue":"3"},{"department":[{"_id":"MaKw"}],"date_updated":"2024-03-25T08:09:43Z","type":"journal_article","article_type":"original","status":"public","_id":"15163","volume":347,"issue":"6","publication_identifier":{"issn":["0012-365X"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.11615"}],"month":"03","intvolume":" 347","abstract":[{"lang":"eng","text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs."}],"oa_version":"Preprint","author":[{"full_name":"Campbell, Rutger","last_name":"Campbell","first_name":"Rutger"},{"first_name":"Florian","last_name":"Hörsch","full_name":"Hörsch, Florian"},{"last_name":"Moore","full_name":"Moore, Benjamin","first_name":"Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.11615"]},"title":"Decompositions into two linear forests of bounded lengths","citation":{"mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962.","ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"113962","date_published":"2024-03-19T00:00:00Z","doi":"10.1016/j.disc.2024.113962","date_created":"2024-03-24T23:00:58Z","year":"2024","day":"19","publication":"Discrete Mathematics","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them."},{"quality_controlled":"1","publisher":"American Astronomical Society","oa":1,"acknowledgement":"We thank the anonymous referee for constructive comments that helped improve the manuscript. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program Nos. 1243 and 1895. The specific observations analyzed can be accessed via doi:10.17909/4xx0-zj76. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work for R.P.N. was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Support for this work for G.I. was provided by NASA through grant JWST-GO-01895 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nFacility: JWST - James Webb Space Telescope, HST - Hubble Space Telescope satellite\r\nSoftware: Python, matplotlib (Hunter 2007), numpy (Harris et al. 2020), scipy (Virtanen et al. 2020), Astropy (Astropy Collaboration et al. 2013, 2018), Imfit (Erwin 2015).","date_published":"2024-03-07T00:00:00Z","doi":"10.3847/1538-4357/ad2345","date_created":"2024-03-25T08:54:47Z","has_accepted_license":"1","year":"2024","day":"07","publication":"The Astrophysical Journal","project":[{"grant_number":"101076224","name":"Young galaxies as tracers and agents of cosmic reionization","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"article_number":"129","author":[{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"first_name":"John","full_name":"Chisholm, John","last_name":"Chisholm"},{"first_name":"Anna-Christina","last_name":"Eilers","full_name":"Eilers, Anna-Christina"},{"first_name":"Andy","full_name":"Goulding, Andy","last_name":"Goulding"},{"full_name":"Greene, Jenny","last_name":"Greene","first_name":"Jenny"},{"last_name":"Kashino","full_name":"Kashino, Daichi","first_name":"Daichi"},{"first_name":"Ivo","last_name":"Labbe","full_name":"Labbe, Ivo"},{"full_name":"Lilly, Simon J.","last_name":"Lilly","first_name":"Simon J."},{"last_name":"Mackenzie","full_name":"Mackenzie, Ruari","first_name":"Ruari"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"last_name":"Weibel","full_name":"Weibel, Andrea","first_name":"Andrea"},{"first_name":"Stijn","last_name":"Wuyts","full_name":"Wuyts, Stijn"},{"first_name":"Mengyuan","last_name":"Xiao","full_name":"Xiao, Mengyuan"},{"first_name":"Rongmon","last_name":"Bordoloi","full_name":"Bordoloi, Rongmon"},{"first_name":"Rychard","last_name":"Bouwens","full_name":"Bouwens, Rychard"},{"first_name":"Pieter","full_name":"van Dokkum, Pieter","last_name":"van Dokkum"},{"last_name":"Illingworth","full_name":"Illingworth, Garth","first_name":"Garth"},{"last_name":"Kramarenko","full_name":"Kramarenko, Ivan","first_name":"Ivan"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"first_name":"Charlotte","full_name":"Mason, Charlotte","last_name":"Mason"},{"first_name":"Romain A.","last_name":"Meyer","full_name":"Meyer, Romain A."},{"full_name":"Nelson, Erica J.","last_name":"Nelson","first_name":"Erica J."},{"first_name":"Naveen A.","full_name":"Reddy, Naveen A.","last_name":"Reddy"},{"last_name":"Shivaei","full_name":"Shivaei, Irene","first_name":"Irene"},{"first_name":"Robert A.","last_name":"Simcoe","full_name":"Simcoe, Robert A."},{"first_name":"Minghao","full_name":"Yue, Minghao","last_name":"Yue"}],"article_processing_charge":"Yes","title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","citation":{"short":"J.J. Matthee, R.P. Naidu, G. Brammer, J. Chisholm, A.-C. Eilers, A. Goulding, J. Greene, D. Kashino, I. Labbe, S.J. Lilly, R. Mackenzie, P.A. Oesch, A. Weibel, S. Wuyts, M. Xiao, R. Bordoloi, R. Bouwens, P. van Dokkum, G. Illingworth, I. Kramarenko, M.V. Maseda, C. Mason, R.A. Meyer, E.J. Nelson, N.A. Reddy, I. Shivaei, R.A. Simcoe, M. Yue, The Astrophysical Journal 963 (2024).","ieee":"J. J. Matthee et al., “Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys,” The Astrophysical Journal, vol. 963, no. 2. American Astronomical Society, 2024.","ama":"Matthee JJ, Naidu RP, Brammer G, et al. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 2024;963(2). doi:10.3847/1538-4357/ad2345","apa":"Matthee, J. J., Naidu, R. P., Brammer, G., Chisholm, J., Eilers, A.-C., Goulding, A., … Yue, M. (2024). Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2345","mla":"Matthee, Jorryt J., et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal, vol. 963, no. 2, 129, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2345.","ista":"Matthee JJ, Naidu RP, Brammer G, Chisholm J, Eilers A-C, Goulding A, Greene J, Kashino D, Labbe I, Lilly SJ, Mackenzie R, Oesch PA, Weibel A, Wuyts S, Xiao M, Bordoloi R, Bouwens R, van Dokkum P, Illingworth G, Kramarenko I, Maseda MV, Mason C, Meyer RA, Nelson EJ, Reddy NA, Shivaei I, Simcoe RA, Yue M. 2024. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 963(2), 129.","chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriel Brammer, John Chisholm, Anna-Christina Eilers, Andy Goulding, Jenny Greene, et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2345."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"03","intvolume":" 963","abstract":[{"text":"Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization.","lang":"eng"}],"oa_version":"Published Version","issue":"2","volume":963,"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication_status":"published","file":[{"date_updated":"2024-03-25T09:31:58Z","file_size":6047536,"creator":"dernst","date_created":"2024-03-25T09:31:58Z","file_name":"2024_AstrophysicalJourn_Matthee.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"dc7af4694f9f94a551417ab49fa43edf","file_id":"15184","success":1}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"15180","file_date_updated":"2024-03-25T09:31:58Z","department":[{"_id":"JoMa"}],"date_updated":"2024-03-25T09:37:27Z","ddc":["550"]},{"department":[{"_id":"FyKo"}],"file_date_updated":"2024-03-25T09:42:10Z","date_updated":"2024-03-25T09:44:53Z","ddc":["580"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15179","volume":10,"issue":"10","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"file_id":"15185","checksum":"a19c43b260ea0bbaf895a29712e3153c","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-25T09:42:10Z","file_name":"2024_ScienceAdv_Palkina.pdf","date_updated":"2024-03-25T09:42:10Z","file_size":1499302,"creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 10","abstract":[{"text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Palkina, Kseniia A.","last_name":"Palkina","first_name":"Kseniia A."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"last_name":"Perfilov","full_name":"Perfilov, Maxim M.","first_name":"Maxim M."},{"first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova"},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Garcia-Perez, Elena","last_name":"Garcia-Perez","first_name":"Elena"},{"last_name":"Vazquez-Vilar","full_name":"Vazquez-Vilar, Marta","first_name":"Marta"},{"first_name":"Marta","last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta"},{"first_name":"Victor","last_name":"Vazquez-Vilriales","full_name":"Vazquez-Vilriales, Victor"},{"last_name":"Shakhova","full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S."},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"full_name":"Belozerova, Olga A.","last_name":"Belozerova","first_name":"Olga A."},{"first_name":"Sergey I.","last_name":"Kovalchuk","full_name":"Kovalchuk, Sergey I."},{"last_name":"Alekberova","full_name":"Alekberova, Anna","first_name":"Anna"},{"full_name":"Malyshevskaia, Alena K.","last_name":"Malyshevskaia","first_name":"Alena K."},{"full_name":"Bugaeva, Evgenia N.","last_name":"Bugaeva","first_name":"Evgenia N."},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"full_name":"Balakireva, Anastasia","last_name":"Balakireva","first_name":"Anastasia"},{"full_name":"Sytov, Nikita","last_name":"Sytov","first_name":"Nikita"},{"full_name":"Bezlikhotnova, Anastasia","last_name":"Bezlikhotnova","first_name":"Anastasia"},{"last_name":"Boldyreva","full_name":"Boldyreva, Daria I.","first_name":"Daria I."},{"full_name":"Babenko, Vladislav V.","last_name":"Babenko","first_name":"Vladislav V."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Vladimir V.","full_name":"Choob, Vladimir V.","last_name":"Choob"},{"first_name":"Diego","last_name":"Orzaez","full_name":"Orzaez, Diego"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"first_name":"Karen S.","full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan"}],"article_processing_charge":"Yes","title":"A hybrid pathway for self-sustained luminescence","citation":{"mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","ieee":"K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.","ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"adk1992","date_published":"2024-03-01T00:00:00Z","doi":"10.1126/sciadv.adk1992","date_created":"2024-03-25T08:54:33Z","has_accepted_license":"1","year":"2024","day":"01","publication":"Science Advances","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund)."},{"quality_controlled":"1","publisher":"American Geophysical Union","oa":1,"acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","date_published":"2024-03-19T00:00:00Z","doi":"10.1029/2023gl106523","date_created":"2024-03-25T10:27:30Z","has_accepted_license":"1","year":"2024","day":"19","publication":"Geophysical Research Letters","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"article_number":" e2023GL106523","author":[{"last_name":"Hwong","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"article_processing_charge":"Yes (in subscription journal)","title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","citation":{"ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523.","chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 2024;51(6). doi:10.1029/2023gl106523","apa":"Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” Geophysical Research Letters, vol. 51, no. 6. American Geophysical Union, 2024.","mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union, 2024, doi:10.1029/2023gl106523."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","intvolume":" 51","abstract":[{"lang":"eng","text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain."}],"oa_version":"Published Version","volume":51,"issue":"6","ec_funded":1,"publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"publication_status":"published","file":[{"date_created":"2024-03-25T11:28:25Z","file_name":"2024_GeophysResLetters_Hwong.pdf","date_updated":"2024-03-25T11:28:25Z","file_size":1280108,"creator":"dernst","file_id":"15187","checksum":"eacb011091a503b9e7b748fef639ba4c","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["General Earth and Planetary Sciences","Geophysics"],"_id":"15186","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-25T11:28:25Z","date_updated":"2024-03-25T11:32:06Z","ddc":["550"]},{"abstract":[{"text":"We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 6","publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"file_id":"15183","checksum":"4e0e58d1f58386fb016284c84db2a300","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-25T09:24:55Z","file_name":"2024_PhysicalReviewResearch_Becker.pdf","date_updated":"2024-03-25T09:24:55Z","file_size":2207067,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","volume":6,"ec_funded":1,"_id":"15181","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-03-25T09:27:37Z","ddc":["530"],"file_date_updated":"2024-03-25T09:24:55Z","department":[{"_id":"MiLe"}],"acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"has_accepted_license":"1","year":"2024","day":"01","publication":"Physical Review Research","doi":"10.1103/physrevresearch.6.013257","date_published":"2024-03-01T00:00:00Z","date_created":"2024-03-25T08:57:07Z","article_number":"013257","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"citation":{"ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).","apa":"Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257","ama":"Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013257","mla":"Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no. 1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.","ista":"Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 6(1), 013257.","chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"A.","full_name":"Becker, A.","last_name":"Becker"},{"id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios","last_name":"Koutentakis","full_name":"Koutentakis, Georgios"},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."}],"article_processing_charge":"Yes","external_id":{"arxiv":["2310.17995"]},"title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions"},{"acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"13","publication":"Advanced Energy Materials","year":"2024","doi":"10.1002/aenm.202400408","date_published":"2024-03-13T00:00:00Z","date_created":"2024-03-25T08:57:40Z","article_number":"2400408","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408.","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408"},"title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"last_name":"Milillo","full_name":"Milillo, Francesco","first_name":"Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","last_name":"Calcabrini","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877"},{"full_name":"Fiedler, Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","first_name":"Christine"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","last_name":"Horta","full_name":"Horta, Sharona"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"full_name":"Strumolo, Marissa J.","last_name":"Strumolo","first_name":"Marissa J."},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"first_name":"Michael","last_name":"Tkadletz","full_name":"Tkadletz, Michael"},{"first_name":"Richard L.","last_name":"Brutchey","full_name":"Brutchey, Richard L."},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"month":"03","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1614-6840"],"issn":["1614-6832"]},"publication_status":"epub_ahead","_id":"15182","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-03-25T09:21:05Z","department":[{"_id":"MaIb"},{"_id":"LifeSc"}]},{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"15165","department":[{"_id":"CaMu"}],"file_date_updated":"2024-03-25T08:36:00Z","ddc":["550"],"date_updated":"2024-03-25T10:00:57Z","intvolume":" 51","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India.","lang":"eng"}],"ec_funded":1,"issue":"5","volume":51,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"243bd966aca968ec7d9e474af8639f8d","file_id":"15178","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2024_GeophysResLetters_Goswami.pdf","date_created":"2024-03-25T08:36:00Z","file_size":2887134,"date_updated":"2024-03-25T08:36:00Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"project":[{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"article_number":"e2023GL106569","title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","article_processing_charge":"Yes","author":[{"last_name":"Goswami","full_name":"Goswami, Bidyut B","orcid":"0000-0001-8602-3083","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:10.1029/2023GL106569.","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.","chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569.","ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569."},"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"The author gratefully acknowledges ISTA for supporting this research through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement No. 805041).","date_created":"2024-03-24T23:00:58Z","doi":"10.1029/2023GL106569","date_published":"2024-03-16T00:00:00Z","publication":"Geophysical Research Letters","day":"16","year":"2024","has_accepted_license":"1"},{"status":"public","article_type":"letter_note","type":"journal_article","_id":"15166","department":[{"_id":"MaIb"}],"date_updated":"2024-03-25T10:31:20Z","intvolume":" 383","month":"03","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Reducing defects boosts room-temperature performance of a thermoelectric device"}],"issue":"6688","volume":383,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"title":"Electron highways are cooler","article_processing_charge":"No","author":[{"id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","first_name":"Navita","last_name":"Navita","full_name":"Navita, Navita"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Jakhar, N., & Ibáñez, M. (2024). Electron highways are cooler. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.ado4077","ama":"Jakhar N, Ibáñez M. Electron highways are cooler. Science. 2024;383(6688):1184. doi:10.1126/science.ado4077","ieee":"N. Jakhar and M. Ibáñez, “Electron highways are cooler,” Science, vol. 383, no. 6688. American Association for the Advancement of Science, p. 1184, 2024.","short":"N. Jakhar, M. Ibáñez, Science 383 (2024) 1184.","mla":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science, vol. 383, no. 6688, American Association for the Advancement of Science, 2024, p. 1184, doi:10.1126/science.ado4077.","ista":"Jakhar N, Ibáñez M. 2024. Electron highways are cooler. Science. 383(6688), 1184.","chicago":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.ado4077."},"quality_controlled":"1","publisher":"American Association for the Advancement of Science","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","date_created":"2024-03-24T23:00:58Z","doi":"10.1126/science.ado4077","date_published":"2024-03-14T00:00:00Z","page":"1184","publication":"Science","day":"14","year":"2024"}]