[{"_id":"17886","quality_controlled":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks,” Neural Networks, vol. 180. Elsevier, 2024.","mla":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks, vol. 180, 106589, Elsevier, 2024, doi:10.1016/j.neunet.2024.106589.","ista":"Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 180, 106589.","ama":"Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 2024;180. doi:10.1016/j.neunet.2024.106589","apa":"Zendrikov, D., & Paraskevov, A. (2024). The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. Elsevier. https://doi.org/10.1016/j.neunet.2024.106589","chicago":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks. Elsevier, 2024. https://doi.org/10.1016/j.neunet.2024.106589.","short":"D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024)."},"doi":"10.1016/j.neunet.2024.106589","department":[{"_id":"TiVo"}],"scopus_import":"1","volume":180,"date_updated":"2025-09-08T09:12:20Z","title":"The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks","author":[{"full_name":"Zendrikov, Dmitrii","last_name":"Zendrikov","first_name":"Dmitrii"},{"first_name":"Alexander","last_name":"Paraskevov","full_name":"Paraskevov, Alexander","id":"d05e3c56-9262-11ed-9231-be692464e5ac"}],"OA_place":"publisher","external_id":{"pmid":["39217864"],"isi":["001316474600001"]},"file_date_updated":"2025-01-13T08:26:08Z","article_type":"original","publication_identifier":{"eissn":["1879-2782"],"issn":["0893-6080"]},"acknowledgement":"A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and Tim P. Vogels for useful discussions. This work was supported by a European Research Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels).","day":"01","month":"12","corr_author":"1","ddc":["570"],"status":"public","publication":"Neural Networks","OA_type":"hybrid","language":[{"iso":"eng"}],"intvolume":" 180","date_created":"2024-09-08T22:01:10Z","has_accepted_license":"1","abstract":[{"text":"Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.","lang":"eng"}],"pmid":1,"publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"106589","date_published":"2024-12-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","year":"2024","publication_status":"published","file":[{"creator":"dernst","checksum":"6a194323234e01d4ae725f674529cdb1","file_name":"2024_NeuralNetworks_Zendrikov.pdf","date_created":"2025-01-13T08:26:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":6162281,"file_id":"18825","success":1,"date_updated":"2025-01-13T08:26:08Z"}],"isi":1,"ec_funded":1,"type":"journal_article","oa":1},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Abels, Helmut, Julian L Fischer, and Maximilian Moser. “Approximation of Classical Two-Phase Flows of Viscous Incompressible Fluids by a Navier–Stokes/Allen–Cahn System.” Archive for Rational Mechanics and Analysis. Springer Nature, 2024. https://doi.org/10.1007/s00205-024-02020-9.","short":"H. Abels, J.L. Fischer, M. Moser, Archive for Rational Mechanics and Analysis 248 (2024).","ieee":"H. Abels, J. L. Fischer, and M. Moser, “Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system,” Archive for Rational Mechanics and Analysis, vol. 248, no. 5. Springer Nature, 2024.","mla":"Abels, Helmut, et al. “Approximation of Classical Two-Phase Flows of Viscous Incompressible Fluids by a Navier–Stokes/Allen–Cahn System.” Archive for Rational Mechanics and Analysis, vol. 248, no. 5, 77, Springer Nature, 2024, doi:10.1007/s00205-024-02020-9.","apa":"Abels, H., Fischer, J. L., & Moser, M. (2024). Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-024-02020-9","ama":"Abels H, Fischer JL, Moser M. Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. 2024;248(5). doi:10.1007/s00205-024-02020-9","ista":"Abels H, Fischer JL, Moser M. 2024. Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. 248(5), 77."},"doi":"10.1007/s00205-024-02020-9","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"volume":248,"department":[{"_id":"JuFi"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","_id":"17887","external_id":{"pmid":["39239088"],"arxiv":["2311.02997"],"isi":["001305530600001"]},"arxiv":1,"file_date_updated":"2024-09-09T08:43:32Z","acknowledgement":"J. Fischer and M. Moser have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"article_type":"original","day":"03","date_updated":"2025-09-08T09:11:41Z","title":"Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system","author":[{"full_name":"Abels, Helmut","last_name":"Abels","first_name":"Helmut"},{"first_name":"Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"first_name":"Maximilian","last_name":"Moser","full_name":"Moser, Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c"}],"intvolume":" 248","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","pmid":1,"date_created":"2024-09-08T22:01:10Z","abstract":[{"lang":"eng","text":"We show convergence of the Navier-Stokes/Allen-Cahn system to a classical sharp interface model for the two-phase flow of two viscous incompressible fluids with same viscosities in a smooth bounded domain in two and three space dimensions as long as a smooth solution of the limit system exists. Moreover, we obtain error estimates with the aid of a relative entropy method. Our results hold provided that the mobility mε>0 in the Allen-Cahn equation tends to zero in a subcritical way, i.e., mε=m0εβ for some β∈(0,2) and m0>0 . The proof proceeds by showing via a relative entropy argument that the solution to the Navier-Stokes/Allen-Cahn system remains close to the solution of a perturbed version of the two-phase flow problem, augmented by an extra mean curvature flow term mεHΓt in the interface motion. In a second step, it is easy to see that the solution to the perturbed problem is close to the original two-phase flow."}],"ddc":["510"],"month":"09","status":"public","publication":"Archive for Rational Mechanics and Analysis","issue":"5","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","article_number":"77","date_published":"2024-09-03T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"success":1,"file_id":"17938","date_updated":"2024-09-09T08:43:32Z","creator":"dernst","checksum":"98493a05b84e4513b6394dfad4851ddf","file_name":"2024_ArchiveRatAnalysis_Abels.pdf","relation":"main_file","date_created":"2024-09-09T08:43:32Z","content_type":"application/pdf","access_level":"open_access","file_size":811131}],"article_processing_charge":"Yes (via OA deal)","year":"2024","publication_status":"published"},{"corr_author":"1","status":"public","ddc":["570"],"month":"09","publication":"Landscape Ecology","issue":"9","language":[{"iso":"eng"}],"intvolume":" 39","date_created":"2024-09-08T22:01:11Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.\r\nObjectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.\r\nResults: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.\r\nConclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies."}],"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"172","date_published":"2024-09-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","year":"2024","publication_status":"published","file":[{"date_updated":"2024-09-11T07:14:03Z","success":1,"file_id":"18054","access_level":"open_access","content_type":"application/pdf","file_size":1494987,"creator":"dernst","file_name":"2024_LandscapeEcology_Pocull.pdf","checksum":"2e1cbc320ec1b4447a5a8562a90bcbc3","date_created":"2024-09-11T07:14:03Z","relation":"main_file"}],"isi":1,"ec_funded":1,"type":"journal_article","oa":1,"_id":"17888","oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"citation":{"mla":"Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology, vol. 39, no. 9, 172, Springer Nature, 2024, doi:10.1007/s10980-024-01899-9.","ieee":"G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects,” Landscape Ecology, vol. 39, no. 9. Springer Nature, 2024.","apa":"Pocull Belles, G., Baskett, C., & Barton, N. H. (2024). Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. Springer Nature. https://doi.org/10.1007/s10980-024-01899-9","ista":"Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 39(9), 172.","ama":"Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 2024;39(9). doi:10.1007/s10980-024-01899-9","chicago":"Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology. Springer Nature, 2024. https://doi.org/10.1007/s10980-024-01899-9.","short":"G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s10980-024-01899-9","department":[{"_id":"NiBa"}],"scopus_import":"1","volume":39,"date_updated":"2025-09-08T09:20:11Z","title":"Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects","author":[{"id":"54359172-700c-11ef-a103-c1d91ceac6d6","full_name":"Pocull Belles, Guillem","first_name":"Guillem","last_name":"Pocull Belles"},{"full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"external_id":{"isi":["001304011900001"]},"publication_identifier":{"issn":["0921-2973"],"eissn":["1572-9761"]},"file_date_updated":"2024-09-11T07:14:03Z","acknowledgement":"For the beetle barcoding, we are very thankful to Brent Emerson’s laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection. Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers for comments that greatly improved the quality of the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). CB received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the FWF grant “Löwenmaul speciation” P 32166-B32.","article_type":"original","day":"01"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"637","date_published":"2024-08-01T00:00:00Z","article_processing_charge":"Yes","year":"2024","publication_status":"published","file":[{"success":1,"file_id":"17948","date_updated":"2024-09-09T09:01:12Z","date_created":"2024-09-09T09:01:12Z","relation":"main_file","file_name":"2024_Entropy_Edelsbrunner.pdf","checksum":"624a9e2c5b49d6c38b88b0f675467ba3","creator":"dernst","file_size":8025139,"access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","isi":1,"oa":1,"month":"08","ddc":["510"],"status":"public","publication":"Entropy","issue":"8","language":[{"iso":"eng"}],"intvolume":" 26","has_accepted_license":"1","pmid":1,"date_created":"2024-09-08T22:01:11Z","abstract":[{"lang":"eng","text":"Abstract\r\nMethods used in topological data analysis naturally capture higher-order interactions in point cloud data embedded in a metric space. This methodology was recently extended to data living in an information space, by which we mean a space measured with an information theoretical distance. One such setting is a finite collection of discrete probability distributions embedded in the probability simplex measured with the relative entropy (Kullback–Leibler divergence). More generally, one can work with a Bregman divergence parameterized by a different notion of entropy. While theoretical algorithms exist for this setup, there is a paucity of implementations for exploring and comparing geometric-topological properties of various information spaces. The interest of this work is therefore twofold. First, we propose the first robust algorithms and software for geometric and topological data analysis in information space. Perhaps surprisingly, despite working with Bregman divergences, our design reuses robust libraries for the Euclidean case. Second, using the new software, we take the first steps towards understanding the geometric-topological structure of these spaces. In particular, we compare them with the more familiar spaces equipped with the Euclidean and Fisher metrics."}],"publisher":"MDPI","date_updated":"2025-09-08T09:13:44Z","title":"Understanding higher-order interactions in information space","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ölsböck, Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","orcid":"0000-0002-4672-8297","first_name":"Katharina"},{"first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"}],"external_id":{"isi":["001305543500001"],"pmid":["39202107"]},"related_material":{"link":[{"url":"https://git.ista.ac.at/katharina.oelsboeck/wrap_2_3-public/","relation":"software"}]},"acknowledgement":"We thank Anton Nikitenko for first observing that the Wrap complex can be characterized as stated in Claim (ii) of the Wrap Complex Lemma, and Ondrej Draganov for correcting a critical mistake in one of our formulas in Section 2.","publication_identifier":{"eissn":["1099-4300"]},"file_date_updated":"2024-09-09T09:01:12Z","article_type":"original","day":"01","_id":"17891","oa_version":"Published Version","quality_controlled":"1","doi":"10.3390/e26080637","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Edelsbrunner, H., Ölsböck, K., & Wagner, H. (2024). Understanding higher-order interactions in information space. Entropy. MDPI. https://doi.org/10.3390/e26080637","ista":"Edelsbrunner H, Ölsböck K, Wagner H. 2024. Understanding higher-order interactions in information space. Entropy. 26(8), 637.","ama":"Edelsbrunner H, Ölsböck K, Wagner H. Understanding higher-order interactions in information space. Entropy. 2024;26(8). doi:10.3390/e26080637","ieee":"H. Edelsbrunner, K. Ölsböck, and H. Wagner, “Understanding higher-order interactions in information space,” Entropy, vol. 26, no. 8. MDPI, 2024.","mla":"Edelsbrunner, Herbert, et al. “Understanding Higher-Order Interactions in Information Space.” Entropy, vol. 26, no. 8, 637, MDPI, 2024, doi:10.3390/e26080637.","short":"H. Edelsbrunner, K. Ölsböck, H. Wagner, Entropy 26 (2024).","chicago":"Edelsbrunner, Herbert, Katharina Ölsböck, and Hubert Wagner. “Understanding Higher-Order Interactions in Information Space.” Entropy. MDPI, 2024. https://doi.org/10.3390/e26080637."},"scopus_import":"1","department":[{"_id":"HeEd"}],"volume":26},{"isi":1,"ec_funded":1,"type":"journal_article","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-08-01T00:00:00Z","article_number":"024404","year":"2024","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","file":[{"date_updated":"2024-09-11T05:59:36Z","file_id":"18053","success":1,"file_size":445696,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-09-11T05:59:36Z","file_name":"2024_PhysReviewE_Olmeda.pdf","checksum":"67fc2cc8eee3155e5c3b7380307d8284","creator":"dernst"}],"language":[{"iso":"eng"}],"intvolume":" 110","abstract":[{"lang":"eng","text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate."}],"pmid":1,"date_created":"2024-09-08T22:01:12Z","has_accepted_license":"1","publisher":"American Physical Society","status":"public","publication":"Physical Review E","ddc":["530"],"month":"08","corr_author":"1","issue":"2","external_id":{"isi":["001299670100004"],"pmid":["39294986"]},"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"file_date_updated":"2024-09-11T05:59:36Z","article_type":"original","acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","day":"01","date_updated":"2025-09-08T09:17:18Z","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","author":[{"full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","last_name":"Olmeda","first_name":"Fabrizio"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.","ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024.","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404.","ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404","apa":"Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404","chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404.","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024)."},"doi":"10.1103/PhysRevE.110.024404","department":[{"_id":"EdHa"}],"scopus_import":"1","volume":110,"_id":"17892","oa_version":"Published Version","quality_controlled":"1"},{"type":"journal_article","isi":1,"page":"47923-47930","date_published":"2024-09-11T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","year":"2024","article_processing_charge":"No","intvolume":" 16","language":[{"iso":"eng"}],"OA_type":"closed access","publisher":"American Chemical Society","pmid":1,"abstract":[{"text":"Broadband photodetectors that can decipher the wavelength (λ) and intensity (I) of an unknown incident light are urgently demanded. Photothermoelectric (PTE) detectors can achieve ultrabroadband photodetection surpassing the bandgap limitation; however, their practical application is severely hampered by the lack of deciphering strategy. In this work, we report a variable elimination method to decipher λ and I of the incident lights based on an integrated Ag2Se film-based PTE detector. Nanostructured Ag2Se films with controlled thickness are synthesized using an ion sputtering of Ag and a room-temperature selenization method and then assembled into a detector. Under identical illumination, Ag2Se films of different thicknesses produce varying output photothermal voltages, influenced by factors including λ. By establishing a direct relationship between the photothermal voltage and the absorption of Ag2Se films of varied thickness, we successfully eliminate variables independent of λ, thus determining λ. Subsequently, I is determined by the calibrated responsivity relationship using obtained λ. Our PTE detector achieves a broadband spectrum from 400 to 950 nm and high accuracy, with deviations as low as ∼2.63 and ∼0.53% for deciphered λ and I, respectively. This method allows for self-powered broadband decipherable photodetection without a complex device architecture or computational assistance, which could boost the research enthusiasm and promote the commercialization of PTE broadband detectors.","lang":"eng"}],"date_created":"2024-09-08T22:01:13Z","publication":"ACS Applied Materials and Interfaces","status":"public","month":"09","issue":"36","external_id":{"pmid":["39194354"],"isi":["001300770000001"]},"day":"11","article_type":"original","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"acknowledgement":"The authors appreciate the Analytical & Testing Center of Sichuan University and Ceshigo Research Service for their supports on material characterization. This study is financial supported by the fund of the State Key Laboratory of Solidification Processing in Northwestern Polytechnical University (NWPU, Grant SKLSP202315), the State Key Laboratory for Mechanical Behavior of Materials (Grant 20232509), and the International Scientific and Technological Innovation Cooperation of Sichuan Province (2024YFHZ0309).","title":"Decipher the wavelength and intensity using photothermoelectric detectors","date_updated":"2025-09-08T09:15:07Z","author":[{"first_name":"Jiamin","last_name":"Zhou","full_name":"Zhou, Jiamin"},{"last_name":"Xu","first_name":"Shengduo","full_name":"Xu, Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f"},{"last_name":"Shuai","first_name":"Yi","full_name":"Shuai, Yi"},{"full_name":"Sun, Qiang","first_name":"Qiang","last_name":"Sun"},{"full_name":"Ma, Huangshui","last_name":"Ma","first_name":"Huangshui"},{"first_name":"Chao","last_name":"Wang","full_name":"Wang, Chao"},{"first_name":"Haijuan","last_name":"Wu","full_name":"Wu, Haijuan"},{"full_name":"Tan, Shanshan","last_name":"Tan","first_name":"Shanshan"},{"first_name":"Zegao","last_name":"Wang","full_name":"Wang, Zegao"},{"first_name":"Lei","last_name":"Yang","full_name":"Yang, Lei"}],"citation":{"short":"J. Zhou, S. Xu, Y. Shuai, Q. Sun, H. Ma, C. Wang, H. Wu, S. Tan, Z. Wang, L. Yang, ACS Applied Materials and Interfaces 16 (2024) 47923–47930.","chicago":"Zhou, Jiamin, Shengduo Xu, Yi Shuai, Qiang Sun, Huangshui Ma, Chao Wang, Haijuan Wu, Shanshan Tan, Zegao Wang, and Lei Yang. “Decipher the Wavelength and Intensity Using Photothermoelectric Detectors.” ACS Applied Materials and Interfaces. American Chemical Society, 2024. https://doi.org/10.1021/acsami.4c10489.","ista":"Zhou J, Xu S, Shuai Y, Sun Q, Ma H, Wang C, Wu H, Tan S, Wang Z, Yang L. 2024. Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. 16(36), 47923–47930.","ama":"Zhou J, Xu S, Shuai Y, et al. Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. 2024;16(36):47923-47930. doi:10.1021/acsami.4c10489","apa":"Zhou, J., Xu, S., Shuai, Y., Sun, Q., Ma, H., Wang, C., … Yang, L. (2024). Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.4c10489","ieee":"J. Zhou et al., “Decipher the wavelength and intensity using photothermoelectric detectors,” ACS Applied Materials and Interfaces, vol. 16, no. 36. American Chemical Society, pp. 47923–47930, 2024.","mla":"Zhou, Jiamin, et al. “Decipher the Wavelength and Intensity Using Photothermoelectric Detectors.” ACS Applied Materials and Interfaces, vol. 16, no. 36, American Chemical Society, 2024, pp. 47923–30, doi:10.1021/acsami.4c10489."},"doi":"10.1021/acsami.4c10489","volume":16,"scopus_import":"1","department":[{"_id":"MaIb"}],"quality_controlled":"1","oa_version":"None","_id":"17896"},{"issue":"19","month":"08","status":"public","publication":"Energy and Environmental Science","publisher":"Royal Society of Chemistry","abstract":[{"text":"High-entropy materials (HEMs) offer a quasi-continuous spectrum of active sites and have generated great expectations in fields such as electrocatalysis and energy storage. Despite their potential, the complex composition and associated surface phenomena of HEMs pose challenges to their rational design and development. In this context, we have synthesized FeCoNiPdWP high entropy phosphide (HEP) nanoparticles using a low-temperature colloidal method, and explored their application as bifunctional electrocatalysts for the oxygen evolution and reduction reactions (OER/ORR). Our analysis provides a detailed understanding of the individual roles and transformations of each element during OER/ORR operation. Notably, the HEPs exhibit an exceptionally low OER overpotential of 227 mV at 10 mA cm−2, attributed to the reconstructed HEP surface into a FeCoNiPdW high entropy oxyhydroxide with high oxidation states of Fe, Co, and Ni serving as the active sites. Additionally, Pd and W play crucial roles in modulating the electronic structure to optimize the adsorption energy of oxygen intermediates. For the ORR, Pd emerges as the most active component. In the reconstructed catalyst, the strong d–d orbital coupling of especially Pd, Co, and W fine-tunes ORR electron transfer pathways, delivering an ORR half-wave potential of 0.81 V with a pure four-electron reduction mechanism. The practicality of these HEPs catalysts is showcased through the assembly of aqueous zinc–air batteries. These batteries demonstrate a superior specific capacity of 886 mA h gZn−1 and maintain excellent stability over more than 700 hours of continuous operation. Overall, this study not only elucidates the role of each element in HEMs but also establishes a foundational framework for the design and development of next-generation bifunctional oxygen catalysts, broadening the potential applications of these complex materials in advanced energy systems.","lang":"eng"}],"date_created":"2024-09-08T22:01:13Z","intvolume":" 17","language":[{"iso":"eng"}],"OA_type":"closed access","publication_status":"published","article_processing_charge":"No","year":"2024","date_published":"2024-08-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"7193-7208","type":"journal_article","isi":1,"quality_controlled":"1","oa_version":"None","_id":"17897","volume":17,"scopus_import":"1","department":[{"_id":"MaIb"}],"doi":"10.1039/d4ee01912a","citation":{"short":"R. He, S. Wang, L. Yang, S. Horta, Y. Ding, C. Di, X. Zhang, Y. Xu, M. Ibáñez, Y. Zhou, S. Mebs, H. Dau, J.N. Hausmann, W. Huo, P.W. Menezes, A. Cabot, Energy and Environmental Science 17 (2024) 7193–7208.","chicago":"He, Ren, Shiqi Wang, Linlin Yang, Sharona Horta, Yang Ding, Chong Di, Xuesong Zhang, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and Environmental Science. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ee01912a.","ista":"He R, Wang S, Yang L, Horta S, Ding Y, Di C, Zhang X, Xu Y, Ibáñez M, Zhou Y, Mebs S, Dau H, Hausmann JN, Huo W, Menezes PW, Cabot A. 2024. Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. 17(19), 7193–7208.","apa":"He, R., Wang, S., Yang, L., Horta, S., Ding, Y., Di, C., … Cabot, A. (2024). Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. Royal Society of Chemistry. https://doi.org/10.1039/d4ee01912a","ama":"He R, Wang S, Yang L, et al. Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. 2024;17(19):7193-7208. doi:10.1039/d4ee01912a","ieee":"R. He et al., “Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery,” Energy and Environmental Science, vol. 17, no. 19. Royal Society of Chemistry, pp. 7193–7208, 2024.","mla":"He, Ren, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and Environmental Science, vol. 17, no. 19, Royal Society of Chemistry, 2024, pp. 7193–208, doi:10.1039/d4ee01912a."},"author":[{"full_name":"He, Ren","last_name":"He","first_name":"Ren"},{"first_name":"Shiqi","last_name":"Wang","full_name":"Wang, Shiqi"},{"first_name":"Linlin","last_name":"Yang","full_name":"Yang, Linlin"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona"},{"full_name":"Ding, Yang","first_name":"Yang","last_name":"Ding"},{"first_name":"Chong","last_name":"Di","full_name":"Di, Chong"},{"first_name":"Xuesong","last_name":"Zhang","full_name":"Zhang, Xuesong"},{"first_name":"Ying","last_name":"Xu","full_name":"Xu, Ying"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"full_name":"Zhou, Yingtang","last_name":"Zhou","first_name":"Yingtang"},{"full_name":"Mebs, Stefan","first_name":"Stefan","last_name":"Mebs"},{"full_name":"Dau, Holger","first_name":"Holger","last_name":"Dau"},{"full_name":"Hausmann, Jan Niklas","first_name":"Jan Niklas","last_name":"Hausmann"},{"first_name":"Wenyi","last_name":"Huo","full_name":"Huo, Wenyi"},{"first_name":"Prashanth W.","last_name":"Menezes","full_name":"Menezes, Prashanth W."},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"title":"Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery","date_updated":"2025-09-08T09:15:49Z","day":"22","article_type":"original","acknowledgement":"This work was financially supported by the SyDEC at project from the Spanish MCIN/AEI/FEDER (PID2022-136883OB-C22) and Generalitat de Catalunya 2021SGR01581. J. N. H. and P. W. M. acknowledge support from the German Federal Ministry of Education and Research in the framework of the project “Catlab” (03EW0015A/B). L. Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This work was supported by the European Union Horizon 2020 research and innovation program (No. 857470) and the European Regional Development Fund via the Foundation for Polish Science International Research Agenda PLUS program (No. MAB PLUS/2018/8). The publication was created within the framework of the project of the Minister of Science and Higher Education, Poland “Support for the activities of Centres of Excellence established in Poland under Horizon 2020” under contract no. MEiN/2023/DIR/3795. H. D. and S. M. thank the German Federal Ministry of Education and Research (BMBF) for supporting the Live-XAS project (05K22KE1) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) for support under Germany's Excellence Strategy – EXC 2008/1 – 390540038 – UniSysCat. The authors thank the Helmholtz-Zentrum Berlin (HZB) for beamtime allocation at the KMC-3 synchrotron beamline of the BESSY synchrotron in Berlin-Adlershof and Dr Ivo Zizak as well as Dr Michael Haumann for technical support.","publication_identifier":{"eissn":["1754-5706"],"issn":["1754-5692"]},"external_id":{"isi":["001298924700001"]}},{"ec_funded":1,"type":"book_chapter","editor":[{"first_name":"Joachim H.R. ","last_name":"Lübke","full_name":"Lübke, Joachim H.R. "},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"}],"page":"123-137","place":"New York","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-08-27T00:00:00Z","publication_status":"published","year":"2024","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software."}],"date_created":"2024-09-10T12:32:38Z","alternative_title":["Neuromethods"],"publisher":"Springer Nature","month":"08","corr_author":"1","publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"}],"day":"27","acknowledgement":"This research was supported by the European Research Council Advanced Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","publication_identifier":{"eissn":["1940-6045"],"eisbn":["9781071640197"],"isbn":["9781071640180"],"issn":["0893-2336"]},"title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","date_updated":"2025-04-14T07:27:15Z","author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo","first_name":"Tommaso"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-1-0716-4019-7_8","citation":{"chicago":"Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.","short":"D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., Springer Nature, New York, 2024, pp. 123–137.","ieee":"D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H. R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.","mla":"Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.","ista":"Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.","apa":"Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-4019-7_8","ama":"Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR, Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8"},"scopus_import":"1","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"edition":"1","_id":"18052","quality_controlled":"1","oa_version":"None"},{"language":[{"iso":"eng"}],"citation":{"ista":"Watson J, Arroyo-Urea S, García-Nafría J. 2024.DNA Cloning. In: Handbook of Molecular Biotechnology. , 66–72.","apa":"Watson, J., Arroyo-Urea, S., & García-Nafría, J. (2024). DNA Cloning. In D. Liu (Ed.), Handbook of Molecular Biotechnology (1st ed., pp. 66–72). Boca Raton: CRC Press. https://doi.org/10.1201/9781003055211-8","ama":"Watson J, Arroyo-Urea S, García-Nafría J. DNA Cloning. In: Liu D, ed. Handbook of Molecular Biotechnology. 1st ed. Boca Raton: CRC Press; 2024:66-72. doi:10.1201/9781003055211-8","mla":"Watson, Jake, et al. “DNA Cloning.” Handbook of Molecular Biotechnology, edited by Dongyou Liu, 1st ed., CRC Press, 2024, pp. 66–72, doi:10.1201/9781003055211-8.","ieee":"J. Watson, S. Arroyo-Urea, and J. García-Nafría, “DNA Cloning,” in Handbook of Molecular Biotechnology, 1st ed., D. Liu, Ed. Boca Raton: CRC Press, 2024, pp. 66–72.","short":"J. Watson, S. Arroyo-Urea, J. García-Nafría, in:, D. Liu (Ed.), Handbook of Molecular Biotechnology, 1st ed., CRC Press, Boca Raton, 2024, pp. 66–72.","chicago":"Watson, Jake, Sandra Arroyo-Urea, and Javier García-Nafría. “DNA Cloning.” In Handbook of Molecular Biotechnology, edited by Dongyou Liu, 1st ed., 66–72. Boca Raton: CRC Press, 2024. https://doi.org/10.1201/9781003055211-8."},"doi":"10.1201/9781003055211-8","abstract":[{"text":"DNA cloning is a core technique in biomedical and biotechnological research and is used to assemble and modify DNA fragments at will. While DNA cloning has traditionally relied on restriction enzymes, recent homology-based methods offer improved protocols together with seamless and directional assembly of desired products, overcoming the main disadvantages of restriction enzyme DNA cloning. This chapter provides a historical perspective on DNA cloning, presents a detailed discussion on state-of-the-art in vitro and in vivo homology-based methodologies, covering the basics of how to perform all major plasmid modifications (sub-cloning, site-directed mutagenesis, insertions, and deletions), and gives examples of how to apply these techniques for complex DNA cloning projects.","lang":"eng"}],"date_created":"2024-09-11T10:40:36Z","department":[{"_id":"PeJo"}],"scopus_import":"1","edition":"1","publisher":"CRC Press","_id":"18058","publication":"Handbook of Molecular Biotechnology","month":"09","oa_version":"None","status":"public","quality_controlled":"1","type":"book_chapter","publication_identifier":{"eisbn":["9781003055211"]},"day":"05","page":"66-72","editor":[{"full_name":"Liu, Dongyou","last_name":"Liu","first_name":"Dongyou"}],"place":"Boca Raton","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-09-11T11:16:58Z","date_published":"2024-09-05T00:00:00Z","title":"DNA Cloning","article_processing_charge":"No","year":"2024","publication_status":"published","author":[{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823"},{"full_name":"Arroyo-Urea, Sandra","first_name":"Sandra","last_name":"Arroyo-Urea"},{"full_name":"García-Nafría, Javier","first_name":"Javier","last_name":"García-Nafría"}]},{"ddc":["570"],"month":"09","status":"public","publication":"Communications Biology","has_accepted_license":"1","pmid":1,"date_created":"2024-09-15T22:01:38Z","abstract":[{"text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 7","publication_status":"published","article_processing_charge":"Yes","year":"2024","file":[{"success":1,"file_id":"18084","date_updated":"2024-09-17T09:44:29Z","relation":"main_file","date_created":"2024-09-17T09:44:29Z","checksum":"7d66af41c90e73d1b8a375eb652a9561","creator":"dernst","file_name":"2024_CommBiology_Peng.pdf","file_size":7718758,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-04T00:00:00Z","article_number":"1085","isi":1,"type":"journal_article","oa":1,"_id":"18063","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"volume":7,"project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology. Springer Nature, 2024. https://doi.org/10.1038/s42003-024-06747-9.","short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024).","ieee":"Y. Peng et al., “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” Communications Biology, vol. 7. Springer Nature, 2024.","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology, vol. 7, 1085, Springer Nature, 2024, doi:10.1038/s42003-024-06747-9.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-024-06747-9","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.","ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 2024;7. doi:10.1038/s42003-024-06747-9"},"doi":"10.1038/s42003-024-06747-9","author":[{"full_name":"Peng, Yakun","first_name":"Yakun","last_name":"Peng"},{"full_name":"Ji, Kangkang","first_name":"Kangkang","last_name":"Ji"},{"full_name":"Mao, Yanbo","last_name":"Mao","first_name":"Yanbo"},{"first_name":"Yiqun","last_name":"Wang","full_name":"Wang, Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425"},{"last_name":"Korbei","first_name":"Barbara","full_name":"Korbei, Barbara"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"full_name":"Shen, Jinbo","last_name":"Shen","first_name":"Jinbo"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"}],"title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","date_updated":"2026-04-07T11:49:33Z","day":"04","acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","article_type":"original","file_date_updated":"2024-09-17T09:44:29Z","publication_identifier":{"eissn":["2399-3642"]},"related_material":{"record":[{"status":"public","id":"20117","relation":"dissertation_contains"}]},"external_id":{"isi":["001306499600002"],"pmid":["39232040"]}},{"corr_author":"1","publication":"Advances in Mathematics","month":"11","status":"public","ddc":["510"],"date_created":"2024-09-15T22:01:39Z","abstract":[{"lang":"eng","text":"We establish a close connection between acceleration and dynamical degree for one-frequency quasi-periodic compact cocycles, by showing that two vectors derived separately from each coincide. Based on this, we provide a dynamical classification of one-frequency quasi-periodic SO(3, R)-cocycles."}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"OA_type":"hybrid","intvolume":" 457","publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2024","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":713659,"checksum":"1c80b844a91d93cf4799f4a65873b18d","creator":"dernst","file_name":"2024_AdvancesMath_Hou.pdf","date_created":"2025-01-13T08:29:27Z","relation":"main_file","date_updated":"2025-01-13T08:29:27Z","file_id":"18826","success":1}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-11-01T00:00:00Z","article_number":"109943","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"_id":"18065","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"VaKa"}],"scopus_import":"1","volume":457,"project":[{"call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Hou, Xuanji, et al. “Dynamical Classification of Analytic One-Frequency Quasi-Periodic SO(3,R)-Cocycles.” Advances in Mathematics, vol. 457, 109943, Elsevier, 2024, doi:10.1016/j.aim.2024.109943.","ieee":"X. Hou, Y. Pan, and Q. Zhou, “Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles,” Advances in Mathematics, vol. 457. Elsevier, 2024.","ama":"Hou X, Pan Y, Zhou Q. Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. 2024;457. doi:10.1016/j.aim.2024.109943","ista":"Hou X, Pan Y, Zhou Q. 2024. Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. 457, 109943.","apa":"Hou, X., Pan, Y., & Zhou, Q. (2024). Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2024.109943","chicago":"Hou, Xuanji, Yi Pan, and Qi Zhou. “Dynamical Classification of Analytic One-Frequency Quasi-Periodic SO(3,R)-Cocycles.” Advances in Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.aim.2024.109943.","short":"X. Hou, Y. Pan, Q. Zhou, Advances in Mathematics 457 (2024)."},"doi":"10.1016/j.aim.2024.109943","author":[{"full_name":"Hou, Xuanji","last_name":"Hou","first_name":"Xuanji"},{"id":"1e21c7f7-9070-11eb-847d-8b04c7169523","full_name":"Pan, Yi","first_name":"Yi","last_name":"Pan"},{"full_name":"Zhou, Qi","last_name":"Zhou","first_name":"Qi"}],"title":"Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles","date_updated":"2025-09-08T09:44:19Z","day":"01","acknowledgement":"X. Hou is partially supported by National Natural Science Foundation of China (Grant \r\n12071083) and Funds for Distinguished Youths of Hubei Province of China (\r\n2019CFA680). Y. Pan is supported by ERC Advanced Grant (#885707). Q. Zhou is partially supported by National Key R&D Program of China (2020YFA0713300), NSFC grant (\r\n12071232) and Nankai Zhide Foundation.","article_type":"original","file_date_updated":"2025-01-13T08:29:27Z","publication_identifier":{"eissn":["1090-2082"],"issn":["0001-8708"]},"arxiv":1,"OA_place":"publisher","external_id":{"isi":["001315306500001"],"arxiv":["2311.17537"]}},{"author":[{"first_name":"Guy","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik"}],"date_updated":"2025-12-02T13:46:11Z","title":"Bidding games with charging","arxiv":1,"file_date_updated":"2024-09-17T09:35:03Z","acknowledgement":"This work was supported in part by the ERC projects ERC-2020-AdG 101020093 and CoG 863818 (ForM-SMArt) and by ISF grant no. 1679/21.","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773393"]},"day":"01","external_id":{"arxiv":["2407.06288"],"isi":["001556847400008"]},"conference":{"end_date":"2024-09-13","name":"CONCUR: Conference on Concurrency Theory","location":"Calgary, Canada","start_date":"2024-09-09"},"quality_controlled":"1","oa_version":"Published Version","_id":"18066","volume":311,"scopus_import":"1","department":[{"_id":"ToHe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Avni, Guy, et al. “Bidding Games with Charging.” 35th International Conference on Concurrency Theory, vol. 311, 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.8.","ieee":"G. Avni, E. K. Goharshady, T. A. Henzinger, and K. Mallik, “Bidding games with charging,” in 35th International Conference on Concurrency Theory, Calgary, Canada, 2024, vol. 311.","ama":"Avni G, Goharshady EK, Henzinger TA, Mallik K. Bidding games with charging. In: 35th International Conference on Concurrency Theory. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.8","ista":"Avni G, Goharshady EK, Henzinger TA, Mallik K. 2024. Bidding games with charging. 35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 8.","apa":"Avni, G., Goharshady, E. K., Henzinger, T. A., & Mallik, K. (2024). Bidding games with charging. In 35th International Conference on Concurrency Theory (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2024.8","chicago":"Avni, Guy, Ehsan Kafshdar Goharshady, Thomas A Henzinger, and Kaushik Mallik. “Bidding Games with Charging.” In 35th International Conference on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.8.","short":"G. Avni, E.K. Goharshady, T.A. Henzinger, K. Mallik, in:, 35th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"doi":"10.4230/LIPIcs.CONCUR.2024.8","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"file":[{"success":1,"file_id":"18083","date_updated":"2024-09-17T09:35:03Z","checksum":"cb6f2254b84922cd7bf224f550b73f4a","file_name":"2024_LIPICS_Avni.pdf","creator":"dernst","relation":"main_file","date_created":"2024-09-17T09:35:03Z","content_type":"application/pdf","access_level":"open_access","file_size":854430}],"year":"2024","article_processing_charge":"Yes","publication_status":"published","date_published":"2024-09-01T00:00:00Z","article_number":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"isi":1,"type":"conference","ec_funded":1,"status":"public","publication":"35th International Conference on Concurrency Theory","ddc":["000"],"corr_author":"1","month":"09","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"abstract":[{"text":"Graph games lie at the algorithmic core of many automated design problems in computer science. These are games usually played between two players on a given graph, where the players keep moving a token along the edges according to pre-determined rules (turn-based, concurrent, etc.), and the winner is decided based on the infinite path (aka play) traversed by the token from a given initial position. In bidding games, the players initially get some monetary budgets which they need to use to bid for the privilege of moving the token at each step. Each round of bidding affects the players' available budgets, which is the only form of update that the budgets experience. We introduce bidding games with charging where the players can additionally improve their budgets during the game by collecting vertex-dependent monetary rewards, aka the \"charges.\" Unlike traditional bidding games (where all charges are zero), bidding games with charging allow non-trivial recurrent behaviors. For example, a reachability objective may require multiple detours to vertices with high charges to earn additional budget. We show that, nonetheless, the central property of traditional bidding games generalizes to bidding games with charging: For each vertex there exists a threshold ratio, which is the necessary and sufficient fraction of the total budget for winning the game from that vertex. While the thresholds of traditional bidding games correspond to unique fixed points of linear systems of equations, in games with charging, these fixed points are no longer unique. This significantly complicates the proof of existence and the algorithmic computation of thresholds for infinite-duration objectives. We also provide the lower complexity bounds for computing thresholds for Rabin and Streett objectives, which are the first known lower bounds in any form of bidding games (with or without charging), and we solve the following repair problem for safety and reachability games that have unsatisfiable objectives: Can we distribute a given amount of charge to the players in a way such that the objective can be satisfied?","lang":"eng"}],"date_created":"2024-09-15T22:01:39Z","has_accepted_license":"1","intvolume":" 311","language":[{"iso":"eng"}]},{"department":[{"_id":"ToHe"}],"scopus_import":"1","volume":311,"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"doi":"10.4230/LIPIcs.CONCUR.2024.12","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Boker U, Henzinger TA, Lehtinen K, Prakash A. 2024. History-determinism vs fair simulation. 35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 12.","apa":"Boker, U., Henzinger, T. A., Lehtinen, K., & Prakash, A. (2024). History-determinism vs fair simulation. In 35th International Conference on Concurrency Theory (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2024.12","ama":"Boker U, Henzinger TA, Lehtinen K, Prakash A. History-determinism vs fair simulation. In: 35th International Conference on Concurrency Theory. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.12","mla":"Boker, Udi, et al. “History-Determinism vs Fair Simulation.” 35th International Conference on Concurrency Theory, vol. 311, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.12.","ieee":"U. Boker, T. A. Henzinger, K. Lehtinen, and A. Prakash, “History-determinism vs fair simulation,” in 35th International Conference on Concurrency Theory, Calgary, Canada, 2024, vol. 311.","short":"U. Boker, T.A. Henzinger, K. Lehtinen, A. Prakash, in:, 35th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Boker, Udi, Thomas A Henzinger, Karoliina Lehtinen, and Aditya Prakash. “History-Determinism vs Fair Simulation.” In 35th International Conference on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.12."},"_id":"18067","quality_controlled":"1","oa_version":"Published Version","file_date_updated":"2024-09-17T07:31:18Z","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773393"]},"acknowledgement":"Udi Boker: Israel Science Foundation grant 2410/22\r\nThomas A. Henzinger: ERC-2020-AdG 101020093 (VAMOS)\r\nKaroliina Lehtinen: ANR QUASY 23-CE48-0008-01\r\nAditya Prakash: Chancellors’ International Scholarship from the University of Warwick and Centre for Discrete Mathematics and Its Applications (DIMAP)","day":"01","arxiv":1,"conference":{"end_date":"2024-09-13","start_date":"2024-09-09","name":"CONCUR: Conference on Concurrency Theory","location":"Calgary, Canada"},"external_id":{"isi":["001556847400012"],"arxiv":["2407.08620"]},"author":[{"last_name":"Boker","first_name":"Udi","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Karoliina","last_name":"Lehtinen","full_name":"Lehtinen, Karoliina"},{"first_name":"Aditya","last_name":"Prakash","full_name":"Prakash, Aditya"}],"date_updated":"2025-12-02T13:44:54Z","title":"History-determinism vs fair simulation","alternative_title":["LIPIcs"],"abstract":[{"text":"An automaton 𝒜 is history-deterministic if its nondeterminism can be resolved on the fly, only using the prefix of the word read so far. This mild form of nondeterminism has attracted particular attention for its applications in synthesis problems. An automaton 𝒜 is guidable with respect to a class C of automata if it can fairly simulate every automaton in C, whose language is contained in that of 𝒜. In other words, guidable automata are those for which inclusion and simulation coincide, making them particularly interesting for model-checking. We study the connection between these two notions, and specifically the question of when they coincide. For classes of automata on which they do, deciding guidability, an otherwise challenging decision problem, reduces to deciding history-determinism, a problem that is starting to be well-understood for many classes. We provide a selection of sufficient criteria for a class of automata to guarantee the coincidence of the notions, and use them to show that the notions coincide for the most common automata classes, among which are ω-regular automata and many infinite-state automata with safety and reachability acceptance conditions, including vector addition systems with states, one-counter nets, pushdown-, Parikh-, and timed-automata. We also demonstrate that history-determinism and guidability do not always coincide, for example, for the classes of timed automata with a fixed number of clocks.","lang":"eng"}],"has_accepted_license":"1","date_created":"2024-09-15T22:01:40Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"intvolume":" 311","corr_author":"1","status":"public","month":"09","ddc":["000"],"publication":"35th International Conference on Concurrency Theory","ec_funded":1,"type":"conference","isi":1,"oa":1,"article_processing_charge":"No","year":"2024","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":766902,"creator":"dernst","file_name":"2024_LIPICS_Boker.pdf","checksum":"66db11ef8e600a434079c278050c3f09","relation":"main_file","date_created":"2024-09-17T07:31:18Z","date_updated":"2024-09-17T07:31:18Z","success":1,"file_id":"18080"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"12","date_published":"2024-09-01T00:00:00Z"},{"volume":311,"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"scopus_import":"1","doi":"10.4230/LIPIcs.CONCUR.2024.29","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 35th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” In 35th International Conference on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). Strategic dominance: A new preorder for nondeterministic processes. In 35th International Conference on Concurrency Theory (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2024. Strategic dominance: A new preorder for nondeterministic processes. 35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 29.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Strategic dominance: A new preorder for nondeterministic processes. In: 35th International Conference on Concurrency Theory. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.29","mla":"Henzinger, Thomas A., et al. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” 35th International Conference on Concurrency Theory, vol. 311, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.29.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Strategic dominance: A new preorder for nondeterministic processes,” in 35th International Conference on Concurrency Theory, Calgary, Canada, 2024, vol. 311."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","oa_version":"Published Version","_id":"18068","arxiv":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773393"]},"file_date_updated":"2024-09-17T07:48:56Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","day":"01","external_id":{"isi":["001556847400029"],"arxiv":["2407.10473"]},"conference":{"end_date":"2024-09-13","start_date":"2024-09-09","location":"Calgary, Canada","name":"CONCUR: Conference on Concurrency Theory"},"OA_place":"publisher","author":[{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"date_updated":"2025-12-02T13:45:38Z","title":"Strategic dominance: A new preorder for nondeterministic processes","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"abstract":[{"text":"We study the following refinement relation between nondeterministic state-transition models: model ℬ strategically dominates model 𝒜 iff every deterministic refinement of 𝒜 is language contained in some deterministic refinement of ℬ. While language containment is trace inclusion, and the (fair) simulation preorder coincides with tree inclusion, strategic dominance falls strictly between the two and can be characterized as \"strategy inclusion\" between 𝒜 and ℬ: every strategy that resolves the nondeterminism of 𝒜 is dominated by a strategy that resolves the nondeterminism of ℬ. Strategic dominance can be checked in 2-ExpTime by a decidable first-order Presburger logic with quantification over words and strategies, called resolver logic. We give several other applications of resolver logic, including checking the co-safety, co-liveness, and history-determinism of boolean and quantitative automata, and checking the inclusion between hyperproperties that are specified by nondeterministic boolean and quantitative automata.","lang":"eng"}],"date_created":"2024-09-15T22:01:40Z","has_accepted_license":"1","intvolume":" 311","OA_type":"gold","language":[{"iso":"eng"}],"publication":"35th International Conference on Concurrency Theory","status":"public","month":"09","corr_author":"1","ddc":["000"],"oa":1,"isi":1,"type":"conference","ec_funded":1,"file":[{"relation":"main_file","date_created":"2024-09-17T07:48:56Z","file_name":"2024_LIPICS_Henzinger.pdf","creator":"dernst","checksum":"555bd343e1fb38adeab8fc465ff4fad8","file_size":964124,"content_type":"application/pdf","access_level":"open_access","file_id":"18081","success":1,"date_updated":"2024-09-17T07:48:56Z"}],"article_processing_charge":"Yes","year":"2024","publication_status":"published","date_published":"2024-09-01T00:00:00Z","article_number":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","abstract":[{"lang":"eng","text":"We present results from the JWST First Reionization Epoch Spectroscopically Complete Observations survey on the star-forming sequence (SFS) of galaxies at 1.0 < z < 1.7, around the peak of the cosmic star formation history. Star formation rates (SFRs) are measured from the redshifted, relatively dust-insensitive Paschen-α emission line, and stellar mass measurements include the F444W (4.4 μm; rest-frame H) band. We find SFRs of galaxies with log(M*/M⊙) > 9.5 that are lower than found in many earlier studies by up to 0.6 dex, but in good agreement with recent results obtained with the Prospector fitting framework. The difference (log(SFR(Paα)-SFR(Prospector)) is −0.09 ± 0.04 dex at 1010−11M⊙. We also measure the empirical relation between Paschen-α luminosity and rest-frame H-band magnitude and find that the scatter is only 0.04 dex lower than that of the SFR–M* relation and is much lower than the systematic differences among relations in the literature due to various methods of converting observed measurements to physical properties. We additionally identify examples of sources—that, with standard cutoffs via the UVJ diagram, would be deemed quiescent—with significant (log(sSFR)> −11 yr−1), typically extended, Paschen-α emission. Our results may be indicative of the potential unification of methods used to derive the SFS with careful selection of star-forming galaxies and independent SFR and stellar mass indicators."}],"date_created":"2024-09-15T22:01:40Z","publisher":"IOP Publishing","language":[{"iso":"eng"}],"intvolume":" 972","issue":"2","status":"public","month":"09","ddc":["520"],"publication":"Astrophysical Journal","isi":1,"type":"journal_article","oa":1,"publication_status":"published","article_processing_charge":"Yes","year":"2024","file":[{"checksum":"754b58c1d79adb9670ca76fa8c20ab16","file_name":"2024_AstrophysicalJourn_Neufeld.pdf","creator":"dernst","date_created":"2024-09-17T08:23:59Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":9960685,"file_id":"18082","success":1,"date_updated":"2024-09-17T08:23:59Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-01T00:00:00Z","article_number":"156","scopus_import":"1","department":[{"_id":"JoMa"}],"volume":972,"doi":"10.3847/1538-4357/ad6158","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Neufeld C, Van Dokkum P, Asali Y, Covelo-Paz A, Leja J, Lin J, Matthee JJ, Oesch PA, Reddy NA, Shivaei I, Whitaker KE, Wuyts S, Brammer G, Marchesini D, Maseda MV, Naidu RP, Nelson EJ, Velichko A, Weibel A, Xiao M. 2024. FRESCO: The Paschen-α star-forming sequence at cosmic noon. Astrophysical Journal. 972(2), 156.","apa":"Neufeld, C., Van Dokkum, P., Asali, Y., Covelo-Paz, A., Leja, J., Lin, J., … Xiao, M. (2024). FRESCO: The Paschen-α star-forming sequence at cosmic noon. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad6158","ama":"Neufeld C, Van Dokkum P, Asali Y, et al. FRESCO: The Paschen-α star-forming sequence at cosmic noon. Astrophysical Journal. 2024;972(2). doi:10.3847/1538-4357/ad6158","mla":"Neufeld, Chloe, et al. “FRESCO: The Paschen-α Star-Forming Sequence at Cosmic Noon.” Astrophysical Journal, vol. 972, no. 2, 156, IOP Publishing, 2024, doi:10.3847/1538-4357/ad6158.","ieee":"C. Neufeld et al., “FRESCO: The Paschen-α star-forming sequence at cosmic noon,” Astrophysical Journal, vol. 972, no. 2. IOP Publishing, 2024.","short":"C. Neufeld, P. Van Dokkum, Y. Asali, A. Covelo-Paz, J. Leja, J. Lin, J.J. Matthee, P.A. Oesch, N.A. Reddy, I. Shivaei, K.E. Whitaker, S. Wuyts, G. Brammer, D. Marchesini, M.V. Maseda, R.P. Naidu, E.J. Nelson, A. Velichko, A. Weibel, M. Xiao, Astrophysical Journal 972 (2024).","chicago":"Neufeld, Chloe, Pieter Van Dokkum, Yasmeen Asali, Alba Covelo-Paz, Joel Leja, Jamie Lin, Jorryt J Matthee, et al. “FRESCO: The Paschen-α Star-Forming Sequence at Cosmic Noon.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad6158."},"_id":"18069","quality_controlled":"1","oa_version":"Published Version","day":"01","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"acknowledgement":"The authors thank the anonymous referee whose comments and suggestions improved the quality of this work.\r\nThis 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 No. 1895.\r\nSupport for this work 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.\r\nThis 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\nR.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, Inc., under NASA contract NAS 5-26555\r\nCloud-based data processing and file storage for this work is provided by the AWS Cloud Credits for Research program.\r\nThis paper made use of several publicly available software packages. We thank the respective authors for sharing their work: IPython (Pérez & Granger 2007), matplotlib (Hunter 2007), seaborn (Waskom et al. 2018), NumPy (Harris et al. 2020), SciPy (Virtanen et al. 2020), jupyter (Kluyver et al. 2016), Astropy (Astropy Collaboration et al. 2013, 2018, 2022), grizli (Brammer 2018; Brammer et al. 2022), Prospector (Leja et al. 2019, 2017; Johnson et al. 2021), FSPS (Conroy et al. 2009a, 2010; Conroy & Gunn 2010a, 2010b; Foreman-Mackey et al. 2014), dynesty (Speagle 2020), EAZY (Brammer et al. 2008), Bagpipes (Carnall et al. 2018), and SExtractor (Bertin & Arnouts 1996).","file_date_updated":"2024-09-17T08:23:59Z","article_type":"original","DOAJ_listed":"1","external_id":{"isi":["001305987600001"]},"author":[{"full_name":"Neufeld, Chloe","last_name":"Neufeld","first_name":"Chloe"},{"full_name":"Van Dokkum, Pieter","last_name":"Van Dokkum","first_name":"Pieter"},{"full_name":"Asali, Yasmeen","last_name":"Asali","first_name":"Yasmeen"},{"last_name":"Covelo-Paz","first_name":"Alba","full_name":"Covelo-Paz, Alba"},{"first_name":"Joel","last_name":"Leja","full_name":"Leja, Joel"},{"full_name":"Lin, Jamie","last_name":"Lin","first_name":"Jamie"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"last_name":"Reddy","first_name":"Naveen A.","full_name":"Reddy, Naveen A."},{"last_name":"Shivaei","first_name":"Irene","full_name":"Shivaei, Irene"},{"last_name":"Whitaker","first_name":"Katherine E.","full_name":"Whitaker, Katherine E."},{"last_name":"Wuyts","first_name":"Stijn","full_name":"Wuyts, Stijn"},{"last_name":"Brammer","first_name":"Gabriel","full_name":"Brammer, Gabriel"},{"full_name":"Marchesini, Danilo","first_name":"Danilo","last_name":"Marchesini"},{"full_name":"Maseda, Michael V.","first_name":"Michael V.","last_name":"Maseda"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"full_name":"Nelson, Erica J.","first_name":"Erica J.","last_name":"Nelson"},{"last_name":"Velichko","first_name":"Anna","full_name":"Velichko, Anna"},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"full_name":"Xiao, Mengyuan","last_name":"Xiao","first_name":"Mengyuan"}],"title":"FRESCO: The Paschen-α star-forming sequence at cosmic noon","date_updated":"2025-09-08T09:43:41Z"},{"_id":"18070","corr_author":"1","quality_controlled":"1","status":"public","oa_version":"None","month":"07","publication":"Proceedings of the 44th International Conference on Distributed Computing Systems","language":[{"iso":"eng"}],"citation":{"short":"B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the 44th International Conference on Distributed Computing Systems, IEEE, 2024, pp. 857–868.","chicago":"Chatterjee, Bapi, Vyacheslav Kungurtsev, and Dan-Adrian Alistarh. “Federated SGD with Local Asynchrony.” In Proceedings of the 44th International Conference on Distributed Computing Systems, 857–68. IEEE, 2024. https://doi.org/10.1109/ICDCS60910.2024.00084.","ama":"Chatterjee B, Kungurtsev V, Alistarh D-A. Federated SGD with local asynchrony. In: Proceedings of the 44th International Conference on Distributed Computing Systems. IEEE; 2024:857-868. doi:10.1109/ICDCS60910.2024.00084","ista":"Chatterjee B, Kungurtsev V, Alistarh D-A. 2024. Federated SGD with local asynchrony. Proceedings of the 44th International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems, 857–868.","apa":"Chatterjee, B., Kungurtsev, V., & Alistarh, D.-A. (2024). Federated SGD with local asynchrony. In Proceedings of the 44th International Conference on Distributed Computing Systems (pp. 857–868). Jersey City, NJ, United States: IEEE. https://doi.org/10.1109/ICDCS60910.2024.00084","ieee":"B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Federated SGD with local asynchrony,” in Proceedings of the 44th International Conference on Distributed Computing Systems, Jersey City, NJ, United States, 2024, pp. 857–868.","mla":"Chatterjee, Bapi, et al. “Federated SGD with Local Asynchrony.” Proceedings of the 44th International Conference on Distributed Computing Systems, IEEE, 2024, pp. 857–68, doi:10.1109/ICDCS60910.2024.00084."},"doi":"10.1109/ICDCS60910.2024.00084","scopus_import":"1","abstract":[{"lang":"eng","text":"Parallel SGD in a shared-memory setting is oft-represented by the popular Hogwild! algorithm, in which lock-free updates are asynchronously performed by multiple computing processes. Unfortunately, scaling Hogwild! to distributed workers is largely unexplored. Specifically, it is unknown if any adaptation of Hogwild! to the popular decentralized multi-GPU setting offers any competitive speedup, either empirically or theoretically. In this work, we investigate the potential of decentralizing Hogwild! by incorporating simultaneously (a) asynchronous local gradient updates on the shared memory of GPUs, and (b) non-blocking asynchronous decentralized federated averaging. A naive direct implementation shows degradation in performance, arising from scheduling overheads and concurrent write conflicts on GPUs. To mitigate these drawbacks, we investigate and propose a new method, based on careful block selection rules, which update only portions of the parameter vectors. Our experiments show that the resulting decentralized training method exhibits improved throughput and competitive accuracy for standard image classification benchmarks on the CIFAR-10, CIFAR-100, and Imagenet datasets. On the theoretical side, we prove that our method guarantees sublinear ergodic convergence rates for non-convex objectives."}],"department":[{"_id":"DaAl"}],"date_created":"2024-09-15T22:01:41Z","publisher":"IEEE","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Federated SGD with local asynchrony","date_updated":"2025-09-08T09:23:48Z","date_published":"2024-07-26T00:00:00Z","publication_status":"published","year":"2024","article_processing_charge":"No","author":[{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028"},{"full_name":"Kungurtsev, Vyacheslav","first_name":"Vyacheslav","last_name":"Kungurtsev"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"conference":{"start_date":"2024-07-23","location":"Jersey City, NJ, United States","name":"ICDCS: International Conference on Distributed Computing Systems","end_date":"2024-07-26"},"type":"conference","isi":1,"external_id":{"isi":["001304430200075"]},"day":"26","publication_identifier":{"eissn":["2575-8411"],"issn":["1063-6927"],"isbn":["9798350386059"]},"page":"857-868"},{"language":[{"iso":"eng"}],"publisher":"IEEE","date_created":"2024-09-15T22:01:41Z","abstract":[{"text":"Recent advancements on DAG-based consensus protocols allow for blockchains with improved metrics and properties, such as throughput and censorship-resistance. Variants of the Bullshark [18] consensus protocol are adopted for practical use by the Sui blockchain, for improved latency. However, the protocol is leader-based, and is strongly affected by crashed leaders that can lead to various performance issues, for example, decreased transaction throughput. In this paper, we propose HammerHead, a DAG-based consensus protocol, that is inspired by Carousel [8] and provides Leader-Utilization. Our proposal differs from Carousel, which is built for a chained consensus protocol; in HammerHead chain quality is inherited by the DAG. HammerHead needs to preserve safety and liveness, despite validators committing leader vertices asynchronously. The key idea is to update leader schedules dynamically, based on the validators' scores during the previous schedule. We implement HammerHead and show a minor improvement in performance for cases without faults. The major improvements in comparison to Bullshark appear in faulty settings. Specifically, we show a drastic, 2x-latency improvement and up to 40% increased throughput when crash faults occur (100 validators, 33 faults).","lang":"eng"}],"month":"07","status":"public","publication":"Proceedings - International Conference on Distributed Computing Systems","oa":1,"isi":1,"type":"conference","page":"1377-1387","date_published":"2024-07-26T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","article_processing_charge":"No","year":"2024","doi":"10.1109/ICDCS60910.2024.00129","citation":{"chicago":"Tsimos, Giorgos, Anastasios Kichidis, Alberto Sonnino, and Eleftherios Kokoris Kogias. “HammerHead: Leader Reputation for Dynamic Scheduling.” In Proceedings - International Conference on Distributed Computing Systems, 1377–87. IEEE, 2024. https://doi.org/10.1109/ICDCS60910.2024.00129.","short":"G. Tsimos, A. Kichidis, A. Sonnino, E. Kokoris Kogias, in:, Proceedings - International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–1387.","ieee":"G. Tsimos, A. Kichidis, A. Sonnino, and E. Kokoris Kogias, “HammerHead: Leader reputation for dynamic scheduling,” in Proceedings - International Conference on Distributed Computing Systems, Jersey City, NJ, United States, 2024, pp. 1377–1387.","mla":"Tsimos, Giorgos, et al. “HammerHead: Leader Reputation for Dynamic Scheduling.” Proceedings - International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–87, doi:10.1109/ICDCS60910.2024.00129.","apa":"Tsimos, G., Kichidis, A., Sonnino, A., & Kokoris Kogias, E. (2024). HammerHead: Leader reputation for dynamic scheduling. In Proceedings - International Conference on Distributed Computing Systems (pp. 1377–1387). Jersey City, NJ, United States: IEEE. https://doi.org/10.1109/ICDCS60910.2024.00129","ama":"Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. HammerHead: Leader reputation for dynamic scheduling. In: Proceedings - International Conference on Distributed Computing Systems. IEEE; 2024:1377-1387. doi:10.1109/ICDCS60910.2024.00129","ista":"Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. 2024. HammerHead: Leader reputation for dynamic scheduling. Proceedings - International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems, 1377–1387."},"scopus_import":"1","department":[{"_id":"ElKo"}],"quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2309.12713"}],"_id":"18071","external_id":{"arxiv":["2309.12713"],"isi":["001304430200120"]},"conference":{"end_date":"2024-07-26","name":"ICDCS: International Conference on Distributed Computing Systems","location":"Jersey City, NJ, United States","start_date":"2024-07-23"},"arxiv":1,"day":"26","acknowledgement":"This work is supported by Mysten Labs. We thank the Mysten Labs Engineering teams for valuable feedback broadly, and specifically to Laura Makdah for helping implementing the early reputation score system for validators and Dmitry Perelman for managing the overall implementation effort.","publication_identifier":{"issn":["1063-6927"],"isbn":["9798350386059"],"eissn":["2575-8411"]},"title":"HammerHead: Leader reputation for dynamic scheduling","date_updated":"2025-09-08T09:42:36Z","author":[{"full_name":"Tsimos, Giorgos","first_name":"Giorgos","last_name":"Tsimos"},{"first_name":"Anastasios","last_name":"Kichidis","full_name":"Kichidis, Anastasios"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"}]},{"intvolume":" 84","language":[{"iso":"eng"}],"publisher":"Cell Press","has_accepted_license":"1","pmid":1,"date_created":"2024-09-15T22:01:41Z","abstract":[{"text":"The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis.","lang":"eng"}],"ddc":["570"],"month":"09","status":"public","publication":"Molecular Cell","issue":"17","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"P3254-3270.E9","date_published":"2024-09-05T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"dernst","file_name":"2024_MolecularCell_HernandezArmendariz.pdf","checksum":"3f360e0287b8ec79fb2b8b02b5070360","date_created":"2024-09-16T07:38:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":11654644,"file_id":"18075","success":1,"date_updated":"2024-09-16T07:38:38Z"}],"article_processing_charge":"Yes (in subscription journal)","year":"2024","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.molcel.2024.07.022","citation":{"chicago":"Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” Molecular Cell. Cell Press, 2024. https://doi.org/10.1016/j.molcel.2024.07.022.","short":"A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner, J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9.","mla":"Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” Molecular Cell, vol. 84, no. 17, Cell Press, 2024, p. P3254–3270.E9, doi:10.1016/j.molcel.2024.07.022.","ieee":"A. Hernandez-Armendariz et al., “A liquid-like coat mediates chromosome clustering during mitotic exit,” Molecular Cell, vol. 84, no. 17. Cell Press, p. P3254–3270.E9, 2024.","ama":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. 2024;84(17):P3254-3270.E9. doi:10.1016/j.molcel.2024.07.022","apa":"Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner, A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2024.07.022","ista":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9."},"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"volume":84,"scopus_import":"1","department":[{"_id":"AnSa"}],"quality_controlled":"1","oa_version":"Published Version","_id":"18072","external_id":{"isi":["001309051100001"],"pmid":["39153474"]},"article_type":"original","acknowledgement":"We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs. This work was supported by the German Research Foundation (DFG project number 402723784) and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie Actions, COFUND grant agreement 664726).","file_date_updated":"2024-09-16T07:38:38Z","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"day":"05","date_updated":"2025-09-08T09:23:02Z","title":"A liquid-like coat mediates chromosome clustering during mitotic exit","author":[{"full_name":"Hernandez-Armendariz, Alberto","first_name":"Alberto","last_name":"Hernandez-Armendariz"},{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti","orcid":"0000-0002-9645-6576","first_name":"Valerio"},{"full_name":"Hayashi, Yuki","last_name":"Hayashi","first_name":"Yuki"},{"full_name":"Koskova, Zuzana","first_name":"Zuzana","last_name":"Koskova"},{"last_name":"Brunner","first_name":"Andreas","full_name":"Brunner, Andreas"},{"full_name":"Ellenberg, Jan","first_name":"Jan","last_name":"Ellenberg"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"first_name":"Sara","last_name":"Cuylen-Haering","full_name":"Cuylen-Haering, Sara"}]},{"author":[{"full_name":"Kettel, Paulina","first_name":"Paulina","last_name":"Kettel"},{"first_name":"Laura","last_name":"Marosits","full_name":"Marosits, Laura"},{"full_name":"Spinetti, Elena","last_name":"Spinetti","first_name":"Elena"},{"first_name":"Michael","last_name":"Rechberger","full_name":"Rechberger, Michael"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina"},{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","orcid":"0000-0001-9198-2182 ","first_name":"Philipp"},{"full_name":"Niedermoser, Isabell","first_name":"Isabell","last_name":"Niedermoser"},{"last_name":"Fischer","first_name":"Irmgard","full_name":"Fischer, Irmgard"},{"last_name":"Versteeg","first_name":"Gijs A.","full_name":"Versteeg, Gijs A."},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Covino","first_name":"Roberto","full_name":"Covino, Roberto"},{"last_name":"Karagöz","first_name":"G. Elif","full_name":"Karagöz, G. Elif"}],"date_updated":"2025-09-08T09:22:11Z","title":"Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering","file_date_updated":"2025-01-13T08:43:20Z","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"article_type":"original","acknowledgement":"We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help in the generation of stable cell lines and the statistical analyses of the data. We thank Venja Vieweger for her help with the characterization of the WLLI and D123P IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for the critical reading and editing of the manuscript. We are thankful to our colleagues Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez, Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We are grateful to Life Science Editors, especially Katrina Woolcock for her useful edits and comments on the manuscript. We acknowledge funding from Austrian Science Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B, P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center 1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project ID 450648163), and the International Max Planck Research School on Cellular Biophysics (to RC), the Center for Scientific Computing of the Goethe University and the Jülich Supercomputing Centre for computational resources and support.","day":"15","OA_place":"publisher","external_id":{"isi":["001306286100002"],"pmid":["39232130"]},"_id":"18073","oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","department":[{"_id":"MaLo"},{"_id":"JiFr"}],"volume":43,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler, I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz, EMBO Journal 43 (2024) 4668–4698.","chicago":"Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal. Embo Press, 2024. https://doi.org/10.1038/s44318-024-00207-0.","ista":"Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 43(20), 4668–4698.","ama":"Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 2024;43(20):4668-4698. doi:10.1038/s44318-024-00207-0","apa":"Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler, P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. Embo Press. https://doi.org/10.1038/s44318-024-00207-0","ieee":"P. Kettel et al., “Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering,” EMBO Journal, vol. 43, no. 20. Embo Press, pp. 4668–4698, 2024.","mla":"Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal, vol. 43, no. 20, Embo Press, 2024, pp. 4668–98, doi:10.1038/s44318-024-00207-0."},"doi":"10.1038/s44318-024-00207-0","article_processing_charge":"Yes","year":"2024","publication_status":"published","file":[{"date_updated":"2025-01-13T08:43:20Z","success":1,"file_id":"18827","content_type":"application/pdf","access_level":"open_access","file_size":10080854,"creator":"dernst","checksum":"04f4df1a561083f2846676442fc4eb3c","file_name":"2024_Embo_Kettel.pdf","relation":"main_file","date_created":"2025-01-13T08:43:20Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-15T00:00:00Z","page":"4668-4698","type":"journal_article","isi":1,"oa":1,"issue":"20","status":"public","publication":"EMBO Journal","month":"10","ddc":["570"],"pmid":1,"abstract":[{"text":"Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.","lang":"eng"}],"date_created":"2024-09-15T22:01:42Z","has_accepted_license":"1","publisher":"Embo Press","OA_type":"gold","language":[{"iso":"eng"}],"intvolume":" 43"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17202"}]},"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2024-09-19T09:20:33Z","day":"18","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","OA_place":"publisher","author":[{"last_name":"Sagi","first_name":"Oliver","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"}],"date_updated":"2026-04-16T12:20:39Z","title":"Hybrid circuits on planar Germanium","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"citation":{"chicago":"Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18076.","short":"O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology Austria, 2024.","mla":"Sagi, Oliver. Hybrid Circuits on Planar Germanium. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18076.","ieee":"O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology Austria, 2024.","ista":"Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and Technology Austria.","ama":"Sagi O. Hybrid circuits on planar Germanium. 2024. doi:10.15479/at:ista:18076","apa":"Sagi, O. (2024). Hybrid circuits on planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18076"},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"doi":"10.15479/at:ista:18076","project":[{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"}],"oa_version":"Published Version","_id":"18076","page":"111","oa":1,"type":"dissertation","ec_funded":1,"file":[{"date_updated":"2024-09-18T14:13:01Z","success":1,"file_id":"18093","content_type":"application/pdf","access_level":"open_access","file_size":86679095,"creator":"osagi","file_name":"OliverSagi_Thesis_pdfa.pdf","checksum":"d01d0e2846c2f3ac5bb14d321554a4cd","relation":"main_file","date_created":"2024-09-18T14:13:01Z"},{"date_updated":"2024-09-19T09:20:33Z","file_id":"18094","content_type":"application/x-zip-compressed","access_level":"local","file_size":172098524,"creator":"osagi","checksum":"0543f473d509ee545f4ed3a56f742f4b","file_name":"Thesis_OliverSagi.zip","relation":"source_file","date_created":"2024-09-18T14:14:02Z"}],"year":"2024","article_processing_charge":"No","publication_status":"published","date_published":"2024-09-18T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson\r\njunctions have recently emerged as building blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor from the Ge quantum well. The Josephson junction is then integrated\r\ninto an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults, combined with the recent advances in the spin qubit field, pave the way towards novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material."}],"has_accepted_license":"1","date_created":"2024-09-16T12:58:36Z","language":[{"iso":"eng"}],"supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"09","ddc":["539"],"corr_author":"1","status":"public"}]