--- OA_place: publisher OA_type: hybrid _id: '18906' abstract: - lang: eng text: "Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective.\r\nOur extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time." acknowledgement: "Monika Henzinger: This project has received funding from the European Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke, Robin Münk: This project has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 498605858 and 470029389." article_processing_charge: Yes (in subscription journal) author: - first_name: Kathrin full_name: Hanauer, Kathrin last_name: Hanauer - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Robin full_name: Münk, Robin last_name: Münk - first_name: Harald full_name: Räcke, Harald last_name: Räcke - first_name: Maximilian full_name: Vötsch, Maximilian last_name: Vötsch citation: ama: 'Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. Expander hierarchies for normalized cuts on graphs. In: Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. ACM; 2024:1016-1027. doi:10.1145/3637528.3671978' apa: 'Hanauer, K., Henzinger, M., Münk, R., Räcke, H., & Vötsch, M. (2024). Expander hierarchies for normalized cuts on graphs. In Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 1016–1027). Barcelona, Spain: ACM. https://doi.org/10.1145/3637528.3671978' chicago: Hanauer, Kathrin, Monika Henzinger, Robin Münk, Harald Räcke, and Maximilian Vötsch. “Expander Hierarchies for Normalized Cuts on Graphs.” In Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 1016–27. ACM, 2024. https://doi.org/10.1145/3637528.3671978. ieee: K. Hanauer, M. Henzinger, R. Münk, H. Räcke, and M. Vötsch, “Expander hierarchies for normalized cuts on graphs,” in Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Barcelona, Spain, 2024, pp. 1016–1027. ista: 'Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. 2024. Expander hierarchies for normalized cuts on graphs. Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. KDD: Knowledge Discovery and Data Mining, 1016–1027.' mla: Hanauer, Kathrin, et al. “Expander Hierarchies for Normalized Cuts on Graphs.” Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, ACM, 2024, pp. 1016–27, doi:10.1145/3637528.3671978. short: K. Hanauer, M. Henzinger, R. Münk, H. Räcke, M. Vötsch, in:, Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, ACM, 2024, pp. 1016–1027. conference: end_date: 2024-08-29 location: Barcelona, Spain name: 'KDD: Knowledge Discovery and Data Mining' start_date: 2024-08-05 date_created: 2025-01-27T13:20:26Z date_published: 2024-09-01T00:00:00Z date_updated: 2025-09-09T12:04:56Z day: '01' ddc: - '000' department: - _id: MoHe doi: 10.1145/3637528.3671978 ec_funded: 1 external_id: isi: - '001324524201013' file: - access_level: open_access checksum: 1265d5cf6aa5f94157631651723c4a2b content_type: application/pdf creator: dernst date_created: 2025-01-27T13:25:23Z date_updated: 2025-01-27T13:25:23Z file_id: '18907' file_name: 2024_ACMKDD_Hanauer.pdf file_size: 1450331 relation: main_file success: 1 file_date_updated: 2025-01-27T13:25:23Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1016-1027 project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: 34def286-11ca-11ed-8bc3-da5948e1613c grant_number: Z00422 name: Efficient algorithms - _id: bda196b2-d553-11ed-ba76-8e8ee6c21103 grant_number: I05982 name: Static and Dynamic Hierarchical Graph Decompositions publication: Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining publication_identifier: isbn: - '9798400704901' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Expander hierarchies for normalized cuts on graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18908' abstract: - lang: eng text: Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species. acknowledgement: The computations and data handling were enabled by resources provided by the Swedish National Infrastructure for Computing at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank all the member of the Littorina team for the stimulating discussions about the manuscripts, James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his useful comments in the latter stage of manuscript revisions. article_processing_charge: Yes article_type: letter_note author: - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Olga full_name: Ortega-Martinez, Olga last_name: Ortega-Martinez - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Roger K full_name: Butlin, Roger K last_name: Butlin - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson citation: ama: Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters. 2024;8(4):575-586. doi:10.1093/evlett/qrae014 apa: Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R., Butlin, R. K., & Johannesson, K. (2024). Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrae014 chicago: Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez, Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” Evolution Letters. Oxford University Press, 2024. https://doi.org/10.1093/evlett/qrae014. ieee: A. Le Moan et al., “Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes,” Evolution Letters, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024. ista: Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4), 575–586. mla: Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” Evolution Letters, vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:10.1093/evlett/qrae014. short: A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K. Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586. date_created: 2025-01-27T13:30:27Z date_published: 2024-04-23T00:00:00Z date_updated: 2025-09-09T12:05:51Z day: '23' ddc: - '570' department: - _id: NiBa doi: 10.1093/evlett/qrae014 external_id: isi: - '001206532900001' pmid: - '39479507' file: - access_level: open_access checksum: 2f7780b7b6b3489755f1815f476639c6 content_type: application/pdf creator: dernst date_created: 2025-01-27T13:33:14Z date_updated: 2025-01-27T13:33:14Z file_id: '18909' file_name: 2024_EvolutionLetter_Moan.pdf file_size: 24356661 relation: main_file success: 1 file_date_updated: 2025-01-27T13:33:14Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 575-586 pmid: 1 publication: Evolution Letters publication_identifier: issn: - 2056-3744 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18910' abstract: - lang: eng text: Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies. acknowledgement: G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial Chair. He has been partially funded by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant 742637, SMALLOSTERY), by National Science Foundation–US-Israel Binational Science Foundation grant 2021700, and by an Israel Science Foundation Breakthrough grant (1924/22). P.S. acknowledges funding from the Austrian Science Fund (project “AlloSpace,” I05812) and intramural funding from the Institute of Science and Technology Austria. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Gilad full_name: Haran, Gilad last_name: Haran citation: ama: Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein motions and their relation to function. Annual Review of Biophysics. 2024;53:247-273. doi:10.1146/annurev-biophys-070323-022428 apa: Schanda, P., & Haran, G. (2024). NMR and single-molecule FRET insights into fast protein motions and their relation to function. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-070323-022428 chicago: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” Annual Review of Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-070323-022428. ieee: P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast protein motions and their relation to function,” Annual Review of Biophysics, vol. 53. Annual Reviews, pp. 247–273, 2024. ista: Schanda P, Haran G. 2024. NMR and single-molecule FRET insights into fast protein motions and their relation to function. Annual Review of Biophysics. 53, 247–273. mla: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” Annual Review of Biophysics, vol. 53, Annual Reviews, 2024, pp. 247–73, doi:10.1146/annurev-biophys-070323-022428. short: P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273. corr_author: '1' date_created: 2025-01-27T13:40:34Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-09T12:06:24Z day: '01' ddc: - '570' department: - _id: PaSc doi: 10.1146/annurev-biophys-070323-022428 external_id: isi: - '001278237500012' pmid: - '38346243' file: - access_level: open_access checksum: c90861542ae3f9147939030d5bafed3c content_type: application/pdf creator: dernst date_created: 2025-01-27T13:44:59Z date_updated: 2025-01-27T13:44:59Z file_id: '18911' file_name: 2024_AnnualReviews_Schanda.pdf file_size: 3025589 relation: main_file success: 1 file_date_updated: 2025-01-27T13:44:59Z has_accepted_license: '1' intvolume: ' 53' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 247-273 pmid: 1 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Annual Review of Biophysics publication_identifier: eissn: - 1936-1238 issn: - 1936-122X publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: NMR and single-molecule FRET insights into fast protein motions and their relation to function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 53 year: '2024' ... --- OA_type: closed access _id: '18912' abstract: - lang: eng text: This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending. acknowledgement: The authors thank the anonymous reviewers for their valuable comments and suggestions for improving the paper. This work was supported by JSPS KAKENHI Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan. This work was partially supported by Israel Science Foundation Grant number 1390/19 and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful advice on wire selection and Takeo Igarashi for his assistance in arranging the collaboration of the authors. article_number: '134' article_processing_charge: No author: - first_name: Kenji full_name: Tojo, Kenji last_name: Tojo - first_name: Ariel full_name: Shamir, Ariel last_name: Shamir - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Nobuyuki full_name: Umetani, Nobuyuki last_name: Umetani citation: ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. ACM; 2024. doi:10.1145/3641519.3657453' apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2024). Fabricable 3D wire art. In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. Denver, CO, United States: ACM. https://doi.org/10.1145/3641519.3657453' chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable 3D Wire Art.” In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. ACM, 2024. https://doi.org/10.1145/3641519.3657453.' ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,” in SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, Denver, CO, United States, 2024.' ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 134.' mla: 'Tojo, Kenji, et al. “Fabricable 3D Wire Art.” SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, 134, ACM, 2024, doi:10.1145/3641519.3657453.' short: 'K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, ACM, 2024.' conference: end_date: 2024-08-01 location: Denver, CO, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2024-07-28 corr_author: '1' date_created: 2025-01-27T13:47:35Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-09T12:06:57Z day: '01' department: - _id: BeBi doi: 10.1145/3641519.3657453 external_id: isi: - '001282218200059' isi: 1 language: - iso: eng month: '07' oa_version: None publication: 'SIGGRAPH ''24: ACM SIGGRAPH 2024 Conference Papers' publication_identifier: isbn: - '9798400705250' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Fabricable 3D wire art type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18913' abstract: - lang: eng text: "With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.\r\nBy implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols." acknowledgement: This work was mostly realized while Alberto Sonnino and Lefteris Kokoris-Kogias were employed at Meta. We gratefully acknowledge support for this project from ETH Zurich and Mysten Labs. article_processing_charge: Yes (in subscription journal) author: - first_name: Giacomo full_name: Giuliari, Giacomo last_name: Giuliari - first_name: Alberto full_name: Sonnino, Alberto last_name: Sonnino - first_name: Marc full_name: Frei, Marc last_name: Frei - first_name: Fabio full_name: Streun, Fabio last_name: Streun - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Adrian full_name: Perrig, Adrian last_name: Perrig citation: ama: 'Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. An empirical study of consensus protocols’ DoS resilience. In: Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ACM; 2024:1345-1360. doi:10.1145/3634737.3656997' apa: 'Giuliari, G., Sonnino, A., Frei, M., Streun, F., Kokoris Kogias, E., & Perrig, A. (2024). An empirical study of consensus protocols’ DoS resilience. In Proceedings of the 19th ACM Asia Conference on Computer and Communications Security (pp. 1345–1360). Singapore, Singapore: ACM. https://doi.org/10.1145/3634737.3656997' chicago: Giuliari, Giacomo, Alberto Sonnino, Marc Frei, Fabio Streun, Eleftherios Kokoris Kogias, and Adrian Perrig. “An Empirical Study of Consensus Protocols’ DoS Resilience.” In Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, 1345–60. ACM, 2024. https://doi.org/10.1145/3634737.3656997. ieee: G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, and A. Perrig, “An empirical study of consensus protocols’ DoS resilience,” in Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, Singapore, Singapore, 2024, pp. 1345–1360. ista: 'Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. 2024. An empirical study of consensus protocols’ DoS resilience. Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ASIACCS: Asia Conference on Computer and Communications Security, 1345–1360.' mla: Giuliari, Giacomo, et al. “An Empirical Study of Consensus Protocols’ DoS Resilience.” Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–60, doi:10.1145/3634737.3656997. short: G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, A. Perrig, in:, Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–1360. conference: end_date: 2024-07-05 location: Singapore, Singapore name: 'ASIACCS: Asia Conference on Computer and Communications Security' start_date: 2024-07-01 date_created: 2025-01-27T13:57:00Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-09T12:07:28Z day: '01' ddc: - '000' department: - _id: ElKo doi: 10.1145/3634737.3656997 external_id: isi: - '001283918100095' file: - access_level: open_access checksum: 1e743ddf49d35390eb56e11eb0759150 content_type: application/pdf creator: dernst date_created: 2025-01-27T14:04:12Z date_updated: 2025-01-27T14:04:12Z file_id: '18914' file_name: 2024_ACMAsiaCCS_Giuliari.pdf file_size: 951940 relation: main_file success: 1 file_date_updated: 2025-01-27T14:04:12Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1345-1360 publication: Proceedings of the 19th ACM Asia Conference on Computer and Communications Security publication_identifier: isbn: - '9798400704826' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: An empirical study of consensus protocols’ DoS resilience tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_type: closed access _id: '18919' abstract: - lang: eng text: The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling. article_processing_charge: No article_type: letter_note author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva citation: ama: Baykusheva DR. Through the slopes of a light-induced phase transition. Nature Physics. 2024;20(5):684-685. doi:10.1038/s41567-024-02401-7 apa: Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02401-7 chicago: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02401-7. ieee: D. R. Baykusheva, “Through the slopes of a light-induced phase transition,” Nature Physics, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024. ista: Baykusheva DR. 2024. Through the slopes of a light-induced phase transition. Nature Physics. 20(5), 684–685. mla: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” Nature Physics, vol. 20, no. 5, Springer Nature, 2024, pp. 684–85, doi:10.1038/s41567-024-02401-7. short: D.R. Baykusheva, Nature Physics 20 (2024) 684–685. corr_author: '1' date_created: 2025-01-27T14:29:20Z date_published: 2024-05-01T00:00:00Z date_updated: 2025-09-09T12:08:10Z day: '01' department: - _id: DeBa doi: 10.1038/s41567-024-02401-7 external_id: isi: - '001162208200002' intvolume: ' 20' isi: 1 issue: '5' language: - iso: eng month: '05' oa_version: None page: 684-685 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Through the slopes of a light-induced phase transition type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18920' abstract: - lang: eng text: The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis. acknowledgement: We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H. article_number: 'eadk1954 ' article_processing_charge: Yes article_type: original author: - first_name: Miroslav full_name: Homola, Miroslav last_name: Homola - first_name: Renate Carina full_name: Büttner, Renate Carina id: 3b7984c9-17ff-11ed-b6fe-f943c4a5b626 last_name: Büttner - first_name: Tibor full_name: Füzik, Tibor last_name: Füzik - first_name: Pavel full_name: Křepelka, Pavel last_name: Křepelka - first_name: Radka full_name: Holbová, Radka last_name: Holbová - first_name: Jiří full_name: Nováček, Jiří last_name: Nováček - first_name: Marten L. full_name: Chaillet, Marten L. last_name: Chaillet - first_name: Jakub full_name: Žák, Jakub last_name: Žák - first_name: Danyil full_name: Grybchuk, Danyil last_name: Grybchuk - first_name: Friedrich full_name: Förster, Friedrich last_name: Förster - first_name: William H. full_name: Wilson, William H. last_name: Wilson - first_name: Declan C. full_name: Schroeder, Declan C. last_name: Schroeder - first_name: Pavel full_name: Plevka, Pavel last_name: Plevka citation: ama: Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 2024;10(15). doi:10.1126/sciadv.adk1954 apa: Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954 chicago: Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954. ieee: M. Homola et al., “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10, no. 15. American Association for the Advancement of Science, 2024. ista: Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954. mla: Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954. short: M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024). date_created: 2025-01-27T14:32:34Z date_published: 2024-04-01T00:00:00Z date_updated: 2025-05-14T09:29:04Z day: '01' ddc: - '570' department: - _id: EM-Fac doi: 10.1126/sciadv.adk1954 external_id: pmid: - '38598627' file: - access_level: open_access checksum: 291dd7ceccbe6bfd8e0a9157584f88e9 content_type: application/pdf creator: dernst date_created: 2025-01-27T14:40:08Z date_updated: 2025-01-27T14:40:08Z file_id: '18921' file_name: 2024_ScienceAdv_Homola.pdf file_size: 40623405 relation: main_file success: 1 file_date_updated: 2025-01-27T14:40:08Z has_accepted_license: '1' intvolume: ' 10' issue: '15' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - relation: software url: ' https://github.com/fuzikt/tomostarpy.' scopus_import: '1' status: public title: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2024' ... --- OA_type: closed access _id: '18922' abstract: - lang: eng text: 'Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them.' acknowledgement: "Giuseppe F. Italiano was partially supported by the Italian Ministry of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n" article_processing_charge: No author: - first_name: Loukas full_name: Georgiadis, Loukas last_name: Georgiadis - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano - first_name: Evangelos full_name: Kosinas, Evangelos id: 4c7f9625-dbbc-11ee-9d86-bdcc2db5a949 last_name: Kosinas citation: ama: 'Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components of directed graphs in linear time. In: 65th Annual Symposium on Foundations of Computer Science. IEEE; 2024:62-85. doi:10.1109/focs61266.2024.00015' apa: 'Georgiadis, L., Italiano, G. F., & Kosinas, E. (2024). Computing the 3-edge-connected components of directed graphs in linear time. In 65th Annual Symposium on Foundations of Computer Science (pp. 62–85). Chicago, IL, United States: IEEE. https://doi.org/10.1109/focs61266.2024.00015' chicago: Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In 65th Annual Symposium on Foundations of Computer Science, 62–85. IEEE, 2024. https://doi.org/10.1109/focs61266.2024.00015. ieee: L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected components of directed graphs in linear time,” in 65th Annual Symposium on Foundations of Computer Science, Chicago, IL, United States, 2024, pp. 62–85. ista: 'Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected components of directed graphs in linear time. 65th Annual Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science, 62–85.' mla: Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” 65th Annual Symposium on Foundations of Computer Science, IEEE, 2024, pp. 62–85, doi:10.1109/focs61266.2024.00015. short: L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations of Computer Science, IEEE, 2024, pp. 62–85. conference: end_date: 2024-10-30 location: Chicago, IL, United States name: 'FOCS: Foundations of Computer Science' start_date: 2024-10-27 corr_author: '1' date_created: 2025-01-27T14:50:23Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-09-09T12:08:47Z day: '01' department: - _id: MoHe doi: 10.1109/focs61266.2024.00015 external_id: isi: - '001419526400005' isi: 1 language: - iso: eng month: '10' oa_version: None page: 62-85 publication: 65th Annual Symposium on Foundations of Computer Science publication_identifier: isbn: - '9798331516741' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Computing the 3-edge-connected components of directed graphs in linear time type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: other OA_type: green _id: '18925' abstract: - lang: eng text: Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature. acknowledgement: Research was supported by the Austrian Science Fund (FWF), project I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported by the European Research Council (ERC) CoG 863818 (ForM-SMArt). article_processing_charge: No author: - first_name: Esra full_name: Ceylan, Esra id: cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933 last_name: Ceylan - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 citation: ama: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In: NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE; 2024. doi:10.1109/noms59830.2024.10575579' apa: 'Ceylan, E., Chatterjee, K., Schmid, S., & Svoboda, J. (2024). Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In NOMS 2024-2024 IEEE Network Operations and Management Symposium. Seoul, Republic of Korea: IEEE. https://doi.org/10.1109/noms59830.2024.10575579' chicago: 'Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE, 2024. https://doi.org/10.1109/noms59830.2024.10575579.' ieee: 'E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting of network flows: Hardness and an FPT algorithm,” in NOMS 2024-2024 IEEE Network Operations and Management Symposium, Seoul, Republic of Korea, 2024.' ista: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations and Management Symposium. NOMS: Network Operations and Management Symposiu .' mla: 'Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024, doi:10.1109/noms59830.2024.10575579.' short: E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024. conference: end_date: 2024-05-10 location: Seoul, Republic of Korea name: 'NOMS: Network Operations and Management Symposiu ' start_date: 2024-05-06 corr_author: '1' date_created: 2025-01-27T15:06:45Z date_published: 2024-05-01T00:00:00Z date_updated: 2025-11-05T07:34:27Z day: '01' department: - _id: KrCh doi: 10.1109/noms59830.2024.10575579 ec_funded: 1 external_id: isi: - '001270140300143' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://schmiste.github.io/noms24.pdf month: '05' oa: 1 oa_version: Submitted Version project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: bd622a5c-d553-11ed-ba76-bae280ba8aff grant_number: '894907' name: Graphical Games publication: NOMS 2024-2024 IEEE Network Operations and Management Symposium publication_identifier: eissn: - 2374-9709 isbn: - '9798350327946' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Congestion-free rerouting of network flows: Hardness and an FPT algorithm' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '18926' abstract: - lang: eng text: 'We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. ' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tim full_name: Laux, Tim last_name: Laux citation: ama: 'Hensel S, Laux T. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. 2024;73(1):111-148. doi:10.1512/iumj.2024.73.9701' apa: 'Hensel, S., & Laux, T. (2024). BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. Indiana University Mathematics Journal. https://doi.org/10.1512/iumj.2024.73.9701' chicago: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana University Mathematics Journal. Indiana University Mathematics Journal, 2024. https://doi.org/10.1512/iumj.2024.73.9701.' ieee: 'S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness,” Indiana University Mathematics Journal, vol. 73, no. 1. Indiana University Mathematics Journal, pp. 111–148, 2024.' ista: 'Hensel S, Laux T. 2024. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. 73(1), 111–148.' mla: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana University Mathematics Journal, vol. 73, no. 1, Indiana University Mathematics Journal, 2024, pp. 111–48, doi:10.1512/iumj.2024.73.9701.' short: S. Hensel, T. Laux, Indiana University Mathematics Journal 73 (2024) 111–148. corr_author: '1' date_created: 2025-01-27T15:20:19Z date_published: 2024-01-01T00:00:00Z date_updated: 2025-01-27T15:23:57Z day: '01' department: - _id: JuFi doi: 10.1512/iumj.2024.73.9701 external_id: arxiv: - '2112.11150' intvolume: ' 73' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2112.11150 month: '01' oa: 1 oa_version: Preprint page: 111-148 publication: Indiana University Mathematics Journal publication_identifier: issn: - 0022-2518 publication_status: published publisher: Indiana University Mathematics Journal quality_controlled: '1' scopus_import: '1' status: public title: 'BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 73 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18928' abstract: - lang: eng text: "Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.\r\nWe investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.\r\nFurther, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.\r\nWe note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds." acknowledgement: "Henzinger, Monika: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z 422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020-2024.\r\nSaha, Barna: This project is partially supported by NSF grants 1652303, 1909046, 2112533, and HDR TRIPODS Phase II grant 2217058.\r\nWe would like to thank Andrea Lincoln for many helpful discussions and insightful comments." alternative_title: - LIPIcs article_processing_charge: Yes arxiv: 1 author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Barna full_name: Saha, Barna last_name: Saha - first_name: Martin P. full_name: Seybold, Martin P. last_name: Seybold - first_name: Christopher full_name: Ye, Christopher last_name: Ye citation: ama: 'Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with predictions for dynamic graph problems. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:62:1-62:25. doi:10.4230/LIPIcs.ITCS.2024.62' apa: 'Henzinger, M., Saha, B., Seybold, M. P., & Ye, C. (2024). On the complexity of algorithms with predictions for dynamic graph problems. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287, p. 62:1-62:25). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.62' chicago: Henzinger, Monika, Barna Saha, Martin P. Seybold, and Christopher Ye. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” In 15th Innovations in Theoretical Computer Science Conference, 287:62:1-62:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.62. ieee: M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms with predictions for dynamic graph problems,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287, p. 62:1-62:25. ista: 'Henzinger M, Saha B, Seybold MP, Ye C. 2024. On the complexity of algorithms with predictions for dynamic graph problems. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 287, 62:1-62:25.' mla: Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25, doi:10.4230/LIPIcs.ITCS.2024.62. short: M. Henzinger, B. Saha, M.P. Seybold, C. Ye, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25. conference: end_date: 2024-02-02 location: Berkeley, CA, United States name: 'ITCS: Innovations in Theoretical Computer Science' start_date: 2024-01-30 corr_author: '1' date_created: 2025-01-27T15:33:42Z date_published: 2024-01-24T00:00:00Z date_updated: 2025-09-09T12:11:33Z day: '24' ddc: - '000' department: - _id: MoHe doi: 10.4230/LIPIcs.ITCS.2024.62 ec_funded: 1 external_id: arxiv: - '2307.16771' isi: - '001300389400062' file: - access_level: open_access checksum: 15085a5b3697a408b92a4a7a27293927 content_type: application/pdf creator: dernst date_created: 2025-01-27T15:33:24Z date_updated: 2025-01-27T15:33:24Z file_id: '18929' file_name: 2024_LIPICs_HenzingerMo.pdf file_size: 1084372 relation: main_file success: 1 file_date_updated: 2025-01-27T15:33:24Z has_accepted_license: '1' intvolume: ' 287' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 62:1-62:25 project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: 34def286-11ca-11ed-8bc3-da5948e1613c grant_number: Z00422 name: Efficient algorithms - _id: bda196b2-d553-11ed-ba76-8e8ee6c21103 grant_number: I05982 name: Static and Dynamic Hierarchical Graph Decompositions - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: P33775 name: Fast Algorithms for a Reactive Network Layer publication: 15th Innovations in Theoretical Computer Science Conference publication_identifier: eissn: - 1868-8969 isbn: - '9783959773096' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: On the complexity of algorithms with predictions for dynamic graph problems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 287 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18934' abstract: - lang: eng text: The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt . acknowledgement: We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021. article_number: mr1 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Zsuzsa full_name: Sárkány, Zsuzsa last_name: Sárkány - first_name: Francisco full_name: Figueiredo, Francisco id: 8125cbe2-9661-11ed-a754-afe96018f37d last_name: Figueiredo - first_name: Sandra full_name: Macedo-Ribeiro, Sandra last_name: Macedo-Ribeiro - first_name: Pedro M. full_name: Martins, Pedro M. last_name: Martins citation: ama: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289' apa: 'Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289' chicago: 'Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” Molecular Biology of the Cell. American Society for Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.' ieee: 'Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” Molecular Biology of the Cell, vol. 35, no. 3. American Society for Cell Biology, 2024.' ista: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1.' mla: 'Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” Molecular Biology of the Cell, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.' short: Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024). date_created: 2025-01-29T07:58:40Z date_published: 2024-03-01T00:00:00Z date_updated: 2025-01-29T08:16:20Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.1091/mbc.e23-07-0289 external_id: pmid: - '38117593' file: - access_level: open_access checksum: d7deb6390f294da69321cfbe352ed611 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:12:11Z date_updated: 2025-01-29T08:12:11Z file_id: '18935' file_name: 2024_MolecularBioCell_Sarkany.pdf file_size: 1699180 relation: main_file success: 1 file_date_updated: 2025-01-29T08:12:11Z has_accepted_license: '1' intvolume: ' 35' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Biology of the Cell publication_identifier: eissn: - 1939-4586 issn: - 1059-1524 publication_status: published publisher: American Society for Cell Biology quality_controlled: '1' scopus_import: '1' status: public title: 'NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2024' ... --- OA_type: closed access _id: '18937' abstract: - lang: eng text: A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions. acknowledgement: The authors would like to acknowledge MHRD, Government of India for financial support. The author is also thankful to RRCAT, Indore for providing XPS beamline-14 of Indus II to conduct experimental work. article_number: '416018' article_processing_charge: No article_type: original author: - first_name: Sujata Kumari full_name: Ray, Sujata Kumari last_name: Ray - first_name: Anupama full_name: Pati, Anupama last_name: Pati - first_name: Payala full_name: Sahoo, Payala last_name: Sahoo - first_name: A.K. full_name: Sahoo, A.K. last_name: Sahoo - first_name: Saurabh full_name: Singh, Saurabh id: 12d625da-9cb3-11ed-9667-af09d37d3f0a last_name: Singh orcid: 0000-0003-2209-5269 - first_name: Tsunehiro full_name: Takeuchi, Tsunehiro last_name: Takeuchi - first_name: S. full_name: Dash, S. last_name: Dash citation: ama: 'Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. 2024;685. doi:10.1016/j.physb.2024.416018' apa: 'Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., & Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2024.416018' chicago: 'Ray, Sujata Kumari, Anupama Pati, Payala Sahoo, A.K. Sahoo, Saurabh Singh, Tsunehiro Takeuchi, and S. Dash. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” Physica B: Condensed Matter. Elsevier, 2024. https://doi.org/10.1016/j.physb.2024.416018.' ieee: 'S. K. Ray et al., “Tunable magnetoelectronic properties in Bi3+ substituted YCrO3,” Physica B: Condensed Matter, vol. 685. Elsevier, 2024.' ista: 'Ray SK, Pati A, Sahoo P, Sahoo AK, Singh S, Takeuchi T, Dash S. 2024. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. 685, 416018.' mla: 'Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” Physica B: Condensed Matter, vol. 685, 416018, Elsevier, 2024, doi:10.1016/j.physb.2024.416018.' short: 'S.K. Ray, A. Pati, P. Sahoo, A.K. Sahoo, S. Singh, T. Takeuchi, S. Dash, Physica B: Condensed Matter 685 (2024).' date_created: 2025-01-29T08:33:04Z date_published: 2024-07-15T00:00:00Z date_updated: 2025-01-29T08:37:14Z day: '15' department: - _id: MaIb doi: 10.1016/j.physb.2024.416018 intvolume: ' 685' language: - iso: eng month: '07' oa_version: None publication: 'Physica B: Condensed Matter' publication_identifier: issn: - 0921-4526 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Tunable magnetoelectronic properties in Bi3+ substituted YCrO3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 685 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18938' abstract: - lang: eng text: The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed. acknowledgement: We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P. article_number: e2317453121 article_processing_charge: No article_type: original author: - first_name: Benjamin L full_name: Springstein, Benjamin L id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083 last_name: Springstein orcid: 0000-0002-3461-5391 - first_name: Joao A. full_name: Paulo, Joao A. last_name: Paulo - first_name: Hankum full_name: Park, Hankum last_name: Park - first_name: Kemardo full_name: Henry, Kemardo last_name: Henry - first_name: Eleanor full_name: Fleming, Eleanor last_name: Fleming - first_name: Zoë full_name: Feder, Zoë last_name: Feder - first_name: J. Wade full_name: Harper, J. Wade last_name: Harper - first_name: Ann full_name: Hochschild, Ann last_name: Hochschild citation: ama: Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(6). doi:10.1073/pnas.2317453121 apa: Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2317453121 chicago: Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2317453121. ieee: B. L. Springstein et al., “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6. National Academy of Sciences, 2024. ista: Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121. mla: Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:10.1073/pnas.2317453121. short: B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). date_created: 2025-01-29T08:39:27Z date_published: 2024-02-06T00:00:00Z date_updated: 2025-05-14T11:02:52Z day: '06' ddc: - '570' department: - _id: MaLo doi: 10.1073/pnas.2317453121 external_id: pmid: - '38289956' file: - access_level: open_access checksum: 5bd62c7cb4287e3706a1d45d6ef61fd1 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:43:16Z date_updated: 2025-01-29T08:43:16Z file_id: '18939' file_name: 2024_PNAS_Springstein.pdf file_size: 720902 relation: main_file success: 1 file_date_updated: 2025-01-29T08:43:16Z has_accepted_license: '1' intvolume: ' 121' issue: '6' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18940' abstract: - lang: eng text: BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression. acknowledgement: This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope. article_processing_charge: Yes article_type: original author: - first_name: Paul full_name: Knabl, Paul last_name: Knabl - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Autumn P full_name: Pomreinke, Autumn P last_name: Pomreinke - first_name: Bob full_name: Zimmermann, Bob last_name: Zimmermann - first_name: Katherine W full_name: Rogers, Katherine W last_name: Rogers - first_name: Daniel full_name: Čapek, Daniel last_name: Čapek - first_name: Patrick full_name: Müller, Patrick last_name: Müller - first_name: Grigory full_name: Genikhovich, Grigory last_name: Genikhovich citation: ama: Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 2024;13. doi:10.7554/elife.80803 apa: Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.80803 chicago: Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803. ieee: P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13. mla: Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.80803. short: P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024). date_created: 2025-01-29T08:48:34Z date_published: 2024-02-07T00:00:00Z date_updated: 2025-01-29T08:56:21Z day: '07' ddc: - '570' department: - _id: CaHe doi: 10.7554/elife.80803 file: - access_level: open_access checksum: 24548a184215d3f4547bba535ccfd7b1 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:50:18Z date_updated: 2025-01-29T08:50:18Z file_id: '18941' file_name: 2024_eLife_Knabl.pdf file_size: 11855972 relation: main_file success: 1 file_date_updated: 2025-01-29T08:50:18Z has_accepted_license: '1' intvolume: ' 13' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2024' ... --- OA_place: repository OA_type: green _id: '18944' abstract: - lang: eng text: 'Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria digitata located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.' article_processing_charge: No article_type: original author: - first_name: Louise full_name: Fouqueau, Louise id: 1676e173-8143-11ed-8927-fe165216a93f last_name: Fouqueau orcid: 0000-0003-0371-9339 - first_name: L full_name: Reynes, L last_name: Reynes - first_name: F full_name: Tempera, F last_name: Tempera - first_name: T full_name: Bajjouk, T last_name: Bajjouk - first_name: A full_name: Blanfuné, A last_name: Blanfuné - first_name: C full_name: Chevalier, C last_name: Chevalier - first_name: M full_name: Laurans, M last_name: Laurans - first_name: S full_name: Mauger, S last_name: Mauger - first_name: M full_name: Sourisseau, M last_name: Sourisseau - first_name: J full_name: Assis, J last_name: Assis - first_name: L full_name: Lévêque, L last_name: Lévêque - first_name: M full_name: Valero, M last_name: Valero citation: ama: Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 2024;740:23-42. doi:10.3354/meps14640 apa: Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier, C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. Inter-Research Science Center. https://doi.org/10.3354/meps14640 chicago: Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier, M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” Marine Ecology Progress Series. Inter-Research Science Center, 2024. https://doi.org/10.3354/meps14640. ieee: L. Fouqueau et al., “Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes,” Marine Ecology Progress Series, vol. 740. Inter-Research Science Center, pp. 23–42, 2024. ista: Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 740, 23–42. mla: Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” Marine Ecology Progress Series, vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:10.3354/meps14640. short: L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier, M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine Ecology Progress Series 740 (2024) 23–42. corr_author: '1' date_created: 2025-01-29T09:09:10Z date_published: 2024-07-25T00:00:00Z date_updated: 2025-01-29T09:12:34Z day: '25' department: - _id: NiBa doi: 10.3354/meps14640 intvolume: ' 740' language: - iso: eng main_file_link: - open_access: '1' url: https://inria.hal.science/hal-04624490/ month: '07' oa: 1 oa_version: Submitted Version page: 23-42 publication: Marine Ecology Progress Series publication_identifier: eissn: - 1616-1599 issn: - 0171-8630 publication_status: published publisher: Inter-Research Science Center quality_controlled: '1' scopus_import: '1' status: public title: Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 740 year: '2024' ... --- OA_type: closed access _id: '18945' abstract: - lang: eng text: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division. acknowledgement: "R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0), Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by the Structural Genomics Consortium, a registered charity (1097737) that receives funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck & Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7), A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C. (2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00) and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis. We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We thank the staff at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24. The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang (KI) for valuable discussions and technical support." article_processing_charge: No article_type: original author: - first_name: Fernando H. full_name: de Souza Gama, Fernando H. last_name: de Souza Gama - first_name: Luiz A. full_name: Dutra, Luiz A. last_name: Dutra - first_name: Michael full_name: Hawgood, Michael last_name: Hawgood - first_name: Caio Vinícius full_name: dos Reis, Caio Vinícius last_name: dos Reis - first_name: Ricardo A. M. full_name: Serafim, Ricardo A. M. last_name: Serafim - first_name: Marcos A. full_name: Ferreira, Marcos A. last_name: Ferreira - first_name: Bruno V. M. full_name: Teodoro, Bruno V. M. last_name: Teodoro - first_name: Jéssica Emi full_name: Takarada, Jéssica Emi last_name: Takarada - first_name: André S. full_name: Santiago, André S. last_name: Santiago - first_name: Dimitrios-Ilias full_name: Balourdas, Dimitrios-Ilias last_name: Balourdas - first_name: Ann-Sofie full_name: Nilsson, Ann-Sofie last_name: Nilsson - first_name: Bruno full_name: Urien, Bruno last_name: Urien - first_name: Vitor M. full_name: Almeida, Vitor M. last_name: Almeida - first_name: Carina full_name: Gileadi, Carina last_name: Gileadi - first_name: Priscila Z. full_name: Ramos, Priscila Z. last_name: Ramos - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Stanley N. S. full_name: Vasconcelos, Stanley N. S. last_name: Vasconcelos - first_name: Micael R. full_name: Cunha, Micael R. last_name: Cunha - first_name: Susanne full_name: Mueller, Susanne last_name: Mueller - first_name: Stefan full_name: Knapp, Stefan last_name: Knapp - first_name: Katlin B. full_name: Massirer, Katlin B. last_name: Massirer - first_name: Jonathan M. full_name: Elkins, Jonathan M. last_name: Elkins - first_name: Opher full_name: Gileadi, Opher last_name: Gileadi - first_name: Alessandra full_name: Mascarello, Alessandra last_name: Mascarello - first_name: Bennie B. L. G. full_name: Lemmens, Bennie B. L. G. last_name: Lemmens - first_name: Cristiano R. W. full_name: Guimarães, Cristiano R. W. last_name: Guimarães - first_name: Hatylas full_name: Azevedo, Hatylas last_name: Azevedo - first_name: Rafael M. full_name: Couñago, Rafael M. last_name: Couñago citation: ama: de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 2024;67(11):8609-8629. doi:10.1021/acs.jmedchem.3c02250 apa: de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim, R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. American Chemical Society. https://doi.org/10.1021/acs.jmedchem.3c02250 chicago: Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry. American Chemical Society, 2024. https://doi.org/10.1021/acs.jmedchem.3c02250. ieee: F. H. de Souza Gama et al., “Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε,” Journal of Medicinal Chemistry, vol. 67, no. 11. American Chemical Society, pp. 8609–8629, 2024. ista: de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B, Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629. mla: de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry, vol. 67, no. 11, American Chemical Society, 2024, pp. 8609–29, doi:10.1021/acs.jmedchem.3c02250. short: F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim, M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas, A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo, S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins, O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M. Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629. date_created: 2025-01-29T09:14:19Z date_published: 2024-05-23T00:00:00Z date_updated: 2025-01-29T09:19:15Z day: '23' department: - _id: CaBe doi: 10.1021/acs.jmedchem.3c02250 external_id: pmid: - '38780468' intvolume: ' 67' issue: '11' language: - iso: eng month: '05' oa_version: None page: 8609-8629 pmid: 1 publication: Journal of Medicinal Chemistry publication_identifier: eissn: - 1520-4804 issn: - 0022-2623 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2024' ... --- OA_place: repository OA_type: green _id: '18948' abstract: - lang: eng text: We consider a gas of N bosons with interactions in the mean-field scaling regime. We review a recent proof of the asymptotic expansion of its spectrum and eigenstates and two applications of this result, namely the derivation of an Edgeworth expansion for fluctuations of one-body operators and the computation of the binding energy of an inhomogeneous Bose gas to any order. Finally, we collect related results for the dynamics of the weakly interacting Bose gas and for the regularized Nelson model. acknowledgement: It is our pleasure to thank Marco Falconi, Nataša Pavlović, Peter Pickl, Robert Seiringer and Avy Soffer for the collaboration on the works [11, 13, 14, 21, 33, 39]. L.B. was supported by the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111). N.L. acknowledges support from the Swiss National Science Foundation through the NCCR SwissMap and funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101024712. S.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 512258249. alternative_title: - Fundamental Theories of Physics article_processing_charge: No arxiv: 1 author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Nikolai full_name: Leopold, Nikolai last_name: Leopold - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Sören full_name: Petrat, Sören last_name: Petrat citation: ama: 'Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Bassi A, Goldstein S, Tumulka R, Zanghi N, eds. Physics and the Nature of Reality. Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:10.1007/978-3-031-45434-9_22' apa: 'Bossmann, L., Leopold, N., Mitrouskas, D. J., & Petrat, S. (2024). Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In A. Bassi, S. Goldstein, R. Tumulka, & N. Zanghi (Eds.), Physics and the Nature of Reality (Vol. 215, pp. 307–321). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-45434-9_22' chicago: 'Bossmann, Lea, Nikolai Leopold, David Johannes Mitrouskas, and Sören Petrat. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” In Physics and the Nature of Reality, edited by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21. FTPH. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-45434-9_22.' ieee: 'L. Bossmann, N. Leopold, D. J. Mitrouskas, and S. Petrat, “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications,” in Physics and the Nature of Reality, vol. 215, A. Bassi, S. Goldstein, R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321.' ista: 'Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. 2024.Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Physics and the Nature of Reality. Fundamental Theories of Physics, vol. 215, 307–321.' mla: 'Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” Physics and the Nature of Reality, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024, pp. 307–21, doi:10.1007/978-3-031-45434-9_22.' short: L. Bossmann, N. Leopold, D.J. Mitrouskas, S. Petrat, in:, A. Bassi, S. Goldstein, R. Tumulka, N. Zanghi (Eds.), Physics and the Nature of Reality, Springer Nature, Cham, 2024, pp. 307–321. date_created: 2025-01-29T10:30:08Z date_published: 2024-02-04T00:00:00Z date_updated: 2025-01-29T10:35:10Z day: '04' department: - _id: RoSe doi: 10.1007/978-3-031-45434-9_22 editor: - first_name: Angelo full_name: Bassi, Angelo last_name: Bassi - first_name: Sheldon full_name: Goldstein, Sheldon last_name: Goldstein - first_name: Roderich full_name: Tumulka, Roderich last_name: Tumulka - first_name: Nino full_name: Zanghi, Nino last_name: Zanghi external_id: arxiv: - '2304.12910' intvolume: ' 215' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.12910 month: '02' oa: 1 oa_version: Preprint page: 307-321 place: Cham publication: Physics and the Nature of Reality publication_identifier: eisbn: - '9783031454349' eissn: - 2365-6425 isbn: - '9783031454332' issn: - 0168-1222 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: FTPH status: public title: 'Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 215 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18949' abstract: - lang: eng text: 'Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.' acknowledgement: "We thank the staff of the Tvärminne Zoological Station (University of Helsinki) for their hospitality during the workshop. We are also grateful to everyone who applied to attend the workshop.\r\nFunding for the workshop was provided by the European Society for Evolutionary Biology through the Special Topic Network (STN) funding scheme." article_number: kzae001 article_processing_charge: Yes article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Asher D full_name: Cutter, Asher D last_name: Cutter - first_name: Ina full_name: Satokangas, Ina last_name: Satokangas - first_name: Brian A full_name: Lerch, Brian A last_name: Lerch - first_name: Jonathan full_name: Rolland, Jonathan last_name: Rolland - first_name: Carole M full_name: Smadja, Carole M last_name: Smadja - first_name: J Carolina full_name: Segami Marzal, J Carolina last_name: Segami Marzal - first_name: Christopher R full_name: Cooney, Christopher R last_name: Cooney - first_name: Philine G D full_name: Feulner, Philine G D last_name: Feulner - first_name: Fabricius Maia Chaves Bicalho full_name: Domingos, Fabricius Maia Chaves Bicalho last_name: Domingos - first_name: Henry L full_name: North, Henry L last_name: North - first_name: Ryo full_name: Yamaguchi, Ryo last_name: Yamaguchi - first_name: Roger K full_name: Butlin, Roger K last_name: Butlin - first_name: Jochen B W full_name: Wolf, Jochen B W last_name: Wolf - first_name: Jenn full_name: Coughlan, Jenn last_name: Coughlan - first_name: Patrick full_name: Heidbreder, Patrick last_name: Heidbreder - first_name: Rebeca full_name: Hernández-Gutiérrez, Rebeca last_name: Hernández-Gutiérrez - first_name: Karen B full_name: Barnard-Kubow, Karen B last_name: Barnard-Kubow - first_name: David full_name: Peede, David last_name: Peede - first_name: Loïs full_name: Rancilhac, Loïs last_name: Rancilhac - first_name: Rodrigo Brincalepe full_name: Salvador, Rodrigo Brincalepe last_name: Salvador - first_name: Ken A full_name: Thompson, Ken A last_name: Thompson - first_name: Elizabeth A full_name: Stacy, Elizabeth A last_name: Stacy - first_name: Leonie C full_name: Moyle, Leonie C last_name: Moyle - first_name: Martin D full_name: Garlovsky, Martin D last_name: Garlovsky - first_name: Arif full_name: Maulana, Arif last_name: Maulana - first_name: Annina full_name: Kantelinen, Annina last_name: Kantelinen - first_name: N Ivalú full_name: Cacho, N Ivalú last_name: Cacho - first_name: Hilde full_name: Schneemann, Hilde last_name: Schneemann - first_name: Marisol full_name: Domínguez, Marisol last_name: Domínguez - first_name: Erik B full_name: Dopman, Erik B last_name: Dopman - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Sina J full_name: Rometsch, Sina J last_name: Rometsch - first_name: Aaron A full_name: Comeault, Aaron A last_name: Comeault - first_name: Richard M full_name: Merrill, Richard M last_name: Merrill - first_name: Elizabeth S C full_name: Scordato, Elizabeth S C last_name: Scordato - first_name: Sonal full_name: Singhal, Sonal last_name: Singhal - first_name: Varpu full_name: Pärssinen, Varpu last_name: Pärssinen - first_name: Alycia C R full_name: Lackey, Alycia C R last_name: Lackey - first_name: Sanghamitra full_name: Kumar, Sanghamitra last_name: Kumar - first_name: Joana I full_name: Meier, Joana I last_name: Meier - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet - first_name: Jonna full_name: Kulmuni, Jonna last_name: Kulmuni citation: ama: Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 2024;3(1). doi:10.1093/evolinnean/kzae001 apa: Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja, C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzae001 chicago: Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration of Speciation Research.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2024. https://doi.org/10.1093/evolinnean/kzae001. ieee: S. Stankowski et al., “Toward the integration of speciation research,” Evolutionary Journal of the Linnean Society, vol. 3, no. 1. Oxford University Press, 2024. ista: Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB, Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V, Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society. 3(1), kzae001. mla: Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” Evolutionary Journal of the Linnean Society, vol. 3, no. 1, kzae001, Oxford University Press, 2024, doi:10.1093/evolinnean/kzae001. short: S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja, J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North, R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez, K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A. Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann, M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill, E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier, N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean Society 3 (2024). corr_author: '1' date_created: 2025-01-29T10:38:17Z date_published: 2024-02-16T00:00:00Z date_updated: 2025-01-29T10:55:54Z day: '16' ddc: - '570' department: - _id: NiBa doi: 10.1093/evolinnean/kzae001 file: - access_level: open_access checksum: db08120a92527acaef476bd93f2b87f9 content_type: application/pdf creator: dernst date_created: 2025-01-29T10:52:40Z date_updated: 2025-01-29T10:52:40Z file_id: '18950' file_name: 2024_EvolJourLinneanSoc_Stankowski.pdf file_size: 3935454 relation: main_file success: 1 file_date_updated: 2025-01-29T10:52:40Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Evolutionary Journal of the Linnean Society publication_identifier: issn: - 2752-938X publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Toward the integration of speciation research tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2024' ... --- OA_place: repository OA_type: green _id: '18955' abstract: - lang: eng text: We give a simple proof that assuming the Exponential Time Hypothesis (ETH), determining the winner of a Rabin game cannot be done in time 2o(k log k) · nO(1), where k is the number of pairs of vertex subsets involved in the winning condition and n is the vertex count of the game graph. While this result follows from the lower bounds provided by Calude et al [SIAM J. Comp. 2022], our reduction is considerably simpler and arguably provides more insight into the complexity of the problem. In fact, the analogous lower bounds discussed by Calude et al, for solving Muller games and multidimensional parity games, follow as simple corollaries of our approach. Our reduction also highlights the usefulness of a certain pivot problem — Permutation SAT — which may be of independent interest. acknowledgement: This work is a part of projects CUTACOMBS (Ma. Pilipczuk), BOBR (Mi. Pilipczuk), and VAMOS (K. S. Thejaswini) that have received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant agreements No 714704, 948057, and 101020093, respectively. Ma. Pilipczuk is also partially supported by Polish National Science Centre SONATA BIS-12 grant number 2022/46/E/ST6/00143. article_processing_charge: No arxiv: 1 author: - first_name: Antonio full_name: Casares, Antonio last_name: Casares - first_name: Marcin full_name: Pilipczuk, Marcin last_name: Pilipczuk - first_name: Michał full_name: Pilipczuk, Michał last_name: Pilipczuk - first_name: Uéverton S. full_name: Souza, Uéverton S. last_name: Souza - first_name: K. S. full_name: Thejaswini, K. S. id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753 last_name: Thejaswini citation: ama: 'Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. Simple and tight complexity lower bounds for solving Rabin games. In: 2024 Symposium on Simplicity in Algorithms. Society for Industrial and Applied Mathematics; 2024:160-167. doi:10.1137/1.9781611977936.16' apa: 'Casares, A., Pilipczuk, M., Pilipczuk, M., Souza, U. S., & Thejaswini, K. S. (2024). Simple and tight complexity lower bounds for solving Rabin games. In 2024 Symposium on Simplicity in Algorithms (pp. 160–167). Alexandria, VA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977936.16' chicago: Casares, Antonio, Marcin Pilipczuk, Michał Pilipczuk, Uéverton S. Souza, and K. S. Thejaswini. “Simple and Tight Complexity Lower Bounds for Solving Rabin Games.” In 2024 Symposium on Simplicity in Algorithms, 160–67. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977936.16. ieee: A. Casares, M. Pilipczuk, M. Pilipczuk, U. S. Souza, and K. S. Thejaswini, “Simple and tight complexity lower bounds for solving Rabin games,” in 2024 Symposium on Simplicity in Algorithms, Alexandria, VA, United States, 2024, pp. 160–167. ista: 'Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. 2024. Simple and tight complexity lower bounds for solving Rabin games. 2024 Symposium on Simplicity in Algorithms. SOSA: Symposium on Simplicity in Algorithms, 160–167.' mla: Casares, Antonio, et al. “Simple and Tight Complexity Lower Bounds for Solving Rabin Games.” 2024 Symposium on Simplicity in Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 160–67, doi:10.1137/1.9781611977936.16. short: A. Casares, M. Pilipczuk, M. Pilipczuk, U.S. Souza, K.S. Thejaswini, in:, 2024 Symposium on Simplicity in Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 160–167. conference: end_date: 2024-01-10 location: Alexandria, VA, United States name: 'SOSA: Symposium on Simplicity in Algorithms' start_date: 2024-01-08 date_created: 2025-01-29T11:55:50Z date_published: 2024-01-01T00:00:00Z date_updated: 2025-04-14T07:55:54Z day: '01' department: - _id: ToHe doi: 10.1137/1.9781611977936.16 ec_funded: 1 external_id: arxiv: - '2310.20433' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.20433 month: '01' oa: 1 oa_version: Preprint page: 160-167 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 2024 Symposium on Simplicity in Algorithms publication_identifier: isbn: - '9781611977936' publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Simple and tight complexity lower bounds for solving Rabin games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...