--- _id: '18177' abstract: - lang: eng text: Partially Specified Boolean Networks (PSBNs) represent a family of Boolean models resulting from possible interpretations of unknown update logics. Hybrid extension of CTL (HCTL) has the power to express complex dynamical phenomena, such as oscillations or stability. We present BNClassifier to classify Boolean Networks corresponding to a given PSBN according to criteria specified in HCTL. The implementation of the tool is fully symbolic (based on BDDs). The results are visualised using the machine-learning-based technology of decision trees. acknowledgement: The work has been supported by the Czech Science Foundation grant No. GA22-10845S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. alternative_title: - LNBI article_processing_charge: No author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Luboš full_name: Brim, Luboš last_name: Brim - first_name: Ondřej full_name: Huvar, Ondřej last_name: Huvar - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: David full_name: Šafránek, David last_name: Šafránek citation: ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. BNClassifier: Classifying boolean models by dynamic properties. In: Computational Methods in Systems Biology. Vol 14971. Springer Nature; 2024:19-26. doi:10.1007/978-3-031-71671-3_2' apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2024). BNClassifier: Classifying boolean models by dynamic properties. In Computational Methods in Systems Biology (Vol. 14971, pp. 19–26). Springer Nature. https://doi.org/10.1007/978-3-031-71671-3_2' chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” In Computational Methods in Systems Biology, 14971:19–26. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-71671-3_2.' ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “BNClassifier: Classifying boolean models by dynamic properties,” in Computational Methods in Systems Biology, 2024, vol. 14971, pp. 19–26.' ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2024. BNClassifier: Classifying boolean models by dynamic properties. Computational Methods in Systems Biology. , LNBI, vol. 14971, 19–26.' mla: 'Beneš, Nikola, et al. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” Computational Methods in Systems Biology, vol. 14971, Springer Nature, 2024, pp. 19–26, doi:10.1007/978-3-031-71671-3_2.' short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, in:, Computational Methods in Systems Biology, Springer Nature, 2024, pp. 19–26. date_created: 2024-10-06T22:01:12Z date_published: 2024-09-19T00:00:00Z date_updated: 2025-09-08T09:54:27Z day: '19' department: - _id: ToHe doi: 10.1007/978-3-031-71671-3_2 ec_funded: 1 external_id: isi: - '001333144400002' intvolume: ' 14971' isi: 1 language: - iso: eng month: '09' oa_version: None page: 19-26 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Computational Methods in Systems Biology publication_identifier: eissn: - 1611-3349 isbn: - '9783031716706' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'BNClassifier: Classifying boolean models by dynamic properties' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 14971 year: '2024' ... --- _id: '18187' abstract: - lang: eng text: Quasicrystals are ordered but not periodic, which makes them fascinating objects at the interface between order and disorder. Experiments with ultracold atoms zoom in on this interface by driving a quasicrystal and exploring its fractal properties. article_processing_charge: No article_type: letter_note author: - first_name: Julian full_name: Leonard, Julian id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577 last_name: Leonard orcid: 0000-0003-3696-6870 citation: ama: Leonard J. A kicked quasicrystal. Nature Physics. 2024;20(3):351-352. doi:10.1038/s41567-023-02357-0 apa: Leonard, J. (2024). A kicked quasicrystal. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02357-0 chicago: Leonard, Julian. “A Kicked Quasicrystal.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02357-0. ieee: J. Leonard, “A kicked quasicrystal,” Nature Physics, vol. 20, no. 3. Springer Nature, pp. 351–352, 2024. ista: Leonard J. 2024. A kicked quasicrystal. Nature Physics. 20(3), 351–352. mla: Leonard, Julian. “A Kicked Quasicrystal.” Nature Physics, vol. 20, no. 3, Springer Nature, 2024, pp. 351–52, doi:10.1038/s41567-023-02357-0. short: J. Leonard, Nature Physics 20 (2024) 351–352. date_created: 2024-10-07T11:45:17Z date_published: 2024-01-19T00:00:00Z date_updated: 2024-10-14T07:54:20Z day: '19' doi: 10.1038/s41567-023-02357-0 extern: '1' intvolume: ' 20' issue: '3' language: - iso: eng month: '01' oa_version: None page: 351-352 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: A kicked quasicrystal type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2024' ... --- _id: '18188' abstract: - lang: eng text: New generations of ultracold-atom experiments are continually raising the demand for efficient solutions to optimal control problems. Here, we apply Bayesian optimization to improve a state-preparation protocol recently implemented in an ultracold-atom system to realize a two-particle fractional quantum Hall state. Compared to manual ramp design, we demonstrate the superior performance of our optimization approach in a numerical simulation – resulting in a protocol that is 10x faster at the same fidelity, even when taking into account experimentally realistic levels of disorder in the system. We extensively analyze and discuss questions of robustness and the relationship between numerical simulation and experimental realization, and how to make the best use of the surrogate model trained during optimization. We find that numerical simulation can be expected to substantially reduce the number of experiments that need to be performed with even the most basic transfer learning techniques. The proposed protocol and workflow will pave the way toward the realization of more complex many-body quantum states in experiments. article_number: '1388' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Tizian full_name: Blatz, Tizian last_name: Blatz - first_name: Joyce full_name: Kwan, Joyce last_name: Kwan - first_name: Julian full_name: Leonard, Julian id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577 last_name: Leonard - first_name: Annabelle full_name: Bohrdt, Annabelle last_name: Bohrdt citation: ama: Blatz T, Kwan J, Leonard J, Bohrdt A. Bayesian optimization for robust state preparation in quantum many-body systems. Quantum. 2024;8. doi:10.22331/q-2024-06-27-1388 apa: Blatz, T., Kwan, J., Leonard, J., & Bohrdt, A. (2024). Bayesian optimization for robust state preparation in quantum many-body systems. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/q-2024-06-27-1388 chicago: Blatz, Tizian, Joyce Kwan, Julian Leonard, and Annabelle Bohrdt. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024. https://doi.org/10.22331/q-2024-06-27-1388. ieee: T. Blatz, J. Kwan, J. Leonard, and A. Bohrdt, “Bayesian optimization for robust state preparation in quantum many-body systems,” Quantum, vol. 8. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024. ista: Blatz T, Kwan J, Leonard J, Bohrdt A. 2024. Bayesian optimization for robust state preparation in quantum many-body systems. Quantum. 8, 1388. mla: Blatz, Tizian, et al. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” Quantum, vol. 8, 1388, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024, doi:10.22331/q-2024-06-27-1388. short: T. Blatz, J. Kwan, J. Leonard, A. Bohrdt, Quantum 8 (2024). date_created: 2024-10-07T11:45:56Z date_published: 2024-06-27T00:00:00Z date_updated: 2024-10-08T11:15:55Z day: '27' doi: 10.22331/q-2024-06-27-1388 extern: '1' external_id: arxiv: - '2312.09253' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.22331/q-2024-06-27-1388 month: '06' oa: 1 oa_version: Published Version publication: Quantum publication_identifier: issn: - 2521-327X publication_status: published publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften quality_controlled: '1' scopus_import: '1' status: public title: Bayesian optimization for robust state preparation in quantum many-body systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2024' ... --- _id: '18202' abstract: - lang: eng text: "We report on adiabatic state preparation in the one-dimensional quantum Ising\r\nmodel using ultracold bosons in a tilted optical lattice. We prepare many-body\r\nground states of controllable system sizes and observe enhanced fluctuations\r\naround the transition between paramagnetic and antiferromagnetic states,\r\nmarking the precursor of quantum critical behavior. Furthermore, we find\r\nevidence for superpositions of domain walls and study their effect on the\r\nmany-body ground state by measuring the populations of each spin configuration\r\nacross the transition. These results shed new light on the effect of boundary\r\nconditions in finite-size quantum systems." article_number: '2404.07481' article_processing_charge: No arxiv: 1 author: - first_name: Sooshin full_name: Kim, Sooshin last_name: Kim - first_name: Alexander full_name: Lukin, Alexander last_name: Lukin - first_name: Matthew full_name: Rispoli, Matthew last_name: Rispoli - first_name: M. Eric full_name: Tai, M. Eric last_name: Tai - first_name: Adam M. full_name: Kaufman, Adam M. last_name: Kaufman - first_name: Perrin full_name: Segura, Perrin last_name: Segura - first_name: Yanfei full_name: Li, Yanfei last_name: Li - first_name: Joyce full_name: Kwan, Joyce last_name: Kwan - first_name: Julian full_name: Leonard, Julian id: b75b3f45-7995-11ef-9bfd-9a9cd02c3577 last_name: Leonard - first_name: Brice Bakkali-Hassani full_name: Brice Bakkali-Hassani, Brice Bakkali-Hassani last_name: Brice Bakkali-Hassani - first_name: Markus full_name: Greiner, Markus last_name: Greiner citation: ama: Kim S, Lukin A, Rispoli M, et al. Adiabatic state preparation in a quantum Ising spin chain. arXiv. doi:10.48550/arXiv.2404.07481 apa: Kim, S., Lukin, A., Rispoli, M., Tai, M. E., Kaufman, A. M., Segura, P., … Greiner, M. (n.d.). Adiabatic state preparation in a quantum Ising spin chain. arXiv. https://doi.org/10.48550/arXiv.2404.07481 chicago: Kim, Sooshin, Alexander Lukin, Matthew Rispoli, M. Eric Tai, Adam M. Kaufman, Perrin Segura, Yanfei Li, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2404.07481. ieee: S. Kim et al., “Adiabatic state preparation in a quantum Ising spin chain,” arXiv. . ista: Kim S, Lukin A, Rispoli M, Tai ME, Kaufman AM, Segura P, Li Y, Kwan J, Leonard J, Brice Bakkali-Hassani BB-H, Greiner M. Adiabatic state preparation in a quantum Ising spin chain. arXiv, 2404.07481. mla: Kim, Sooshin, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” ArXiv, 2404.07481, doi:10.48550/arXiv.2404.07481. short: S. Kim, A. Lukin, M. Rispoli, M.E. Tai, A.M. Kaufman, P. Segura, Y. Li, J. Kwan, J. Leonard, B.B.-H. Brice Bakkali-Hassani, M. Greiner, ArXiv (n.d.). date_created: 2024-10-08T11:25:52Z date_published: 2024-04-11T00:00:00Z date_updated: 2024-10-08T11:28:26Z day: '11' doi: 10.48550/arXiv.2404.07481 extern: '1' external_id: arxiv: - '2404.07481' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2404.07481 month: '04' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Adiabatic state preparation in a quantum Ising spin chain type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '18203' abstract: - lang: eng text: Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function. article_number: '783' article_processing_charge: No article_type: original author: - first_name: Aviv A. full_name: Rosenberg, Aviv A. last_name: Rosenberg - first_name: Ailie full_name: Marx, Ailie last_name: Marx - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Rosenberg AA, Marx A, Bronstein AM. A dataset of alternately located segments in protein crystal structures. Scientific Data. 2024;11. doi:10.1038/s41597-024-03595-4 apa: Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2024). A dataset of alternately located segments in protein crystal structures. Scientific Data. Springer Nature. https://doi.org/10.1038/s41597-024-03595-4 chicago: Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” Scientific Data. Springer Nature, 2024. https://doi.org/10.1038/s41597-024-03595-4. ieee: A. A. Rosenberg, A. Marx, and A. M. Bronstein, “A dataset of alternately located segments in protein crystal structures,” Scientific Data, vol. 11. Springer Nature, 2024. ista: Rosenberg AA, Marx A, Bronstein AM. 2024. A dataset of alternately located segments in protein crystal structures. Scientific Data. 11, 783. mla: Rosenberg, Aviv A., et al. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” Scientific Data, vol. 11, 783, Springer Nature, 2024, doi:10.1038/s41597-024-03595-4. short: A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Data 11 (2024). date_created: 2024-10-08T11:50:30Z date_published: 2024-07-17T00:00:00Z date_updated: 2024-10-09T10:08:08Z day: '17' doi: 10.1038/s41597-024-03595-4 extern: '1' external_id: pmid: - '39019896' has_accepted_license: '1' intvolume: ' 11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41597-024-03595-4 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Data publication_identifier: issn: - 2052-4463 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A dataset of alternately located segments in protein crystal structures 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: 11 year: '2024' ... --- _id: '18204' abstract: - lang: eng text: 'Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems.' article_number: '141' article_processing_charge: Yes article_type: original author: - first_name: Yonatan full_name: Elul, Yonatan last_name: Elul - first_name: Eyal full_name: Rozenberg, Eyal last_name: Rozenberg - first_name: Amit full_name: Boyarski, Amit last_name: Boyarski - first_name: Yael full_name: Yaniv, Yael last_name: Yaniv - first_name: Assaf full_name: Schuster, Assaf last_name: Schuster - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. Data-driven modeling of interrelated dynamical systems. Communications Physics. 2024;7. doi:10.1038/s42005-024-01626-5 apa: Elul, Y., Rozenberg, E., Boyarski, A., Yaniv, Y., Schuster, A., & Bronstein, A. M. (2024). Data-driven modeling of interrelated dynamical systems. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-024-01626-5 chicago: Elul, Yonatan, Eyal Rozenberg, Amit Boyarski, Yael Yaniv, Assaf Schuster, and Alex M. Bronstein. “Data-Driven Modeling of Interrelated Dynamical Systems.” Communications Physics. Springer Nature, 2024. https://doi.org/10.1038/s42005-024-01626-5. ieee: Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, and A. M. Bronstein, “Data-driven modeling of interrelated dynamical systems,” Communications Physics, vol. 7. Springer Nature, 2024. ista: Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. 2024. Data-driven modeling of interrelated dynamical systems. Communications Physics. 7, 141. mla: Elul, Yonatan, et al. “Data-Driven Modeling of Interrelated Dynamical Systems.” Communications Physics, vol. 7, 141, Springer Nature, 2024, doi:10.1038/s42005-024-01626-5. short: Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, A.M. Bronstein, Communications Physics 7 (2024). date_created: 2024-10-08T12:45:35Z date_published: 2024-05-01T00:00:00Z date_updated: 2024-10-09T10:12:11Z day: '01' doi: 10.1038/s42005-024-01626-5 extern: '1' intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s42005-024-01626-5 month: '05' oa: 1 oa_version: Published Version publication: Communications Physics publication_identifier: issn: - 2399-3650 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Data-driven modeling of interrelated dynamical systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2024' ... --- _id: '18205' abstract: - lang: eng text: We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Omri full_name: Wengrowicz, Omri last_name: Wengrowicz - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: Oren full_name: Cohen, Oren last_name: Cohen citation: ama: Wengrowicz O, Bronstein AM, Cohen O. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 2024;32(6):8791-8803. doi:10.1364/oe.515445 apa: Wengrowicz, O., Bronstein, A. M., & Cohen, O. (2024). Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. Optica Publishing Group. https://doi.org/10.1364/oe.515445 chicago: Wengrowicz, Omri, Alex M. Bronstein, and Oren Cohen. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” Optics Express. Optica Publishing Group, 2024. https://doi.org/10.1364/oe.515445. ieee: O. Wengrowicz, A. M. Bronstein, and O. Cohen, “Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography,” Optics Express, vol. 32, no. 6. Optica Publishing Group, pp. 8791–8803, 2024. ista: Wengrowicz O, Bronstein AM, Cohen O. 2024. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 32(6), 8791–8803. mla: Wengrowicz, Omri, et al. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” Optics Express, vol. 32, no. 6, Optica Publishing Group, 2024, pp. 8791–803, doi:10.1364/oe.515445. short: O. Wengrowicz, A.M. Bronstein, O. Cohen, Optics Express 32 (2024) 8791–8803. date_created: 2024-10-08T12:46:01Z date_published: 2024-03-11T00:00:00Z date_updated: 2024-10-09T10:26:44Z day: '11' doi: 10.1364/oe.515445 extern: '1' external_id: pmid: - '38571128' intvolume: ' 32' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1364/OE.515445 month: '03' oa: 1 oa_version: Published Version page: 8791-8803 pmid: 1 publication: Optics Express publication_identifier: issn: - 1094-4087 publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2024' ... --- _id: '18206' abstract: - lang: eng text: In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting. alternative_title: - LNCS article_processing_charge: No author: - first_name: Gilad full_name: Rave, Gilad last_name: Rave - first_name: Daniel E. full_name: Fordham, Daniel E. last_name: Fordham - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: David H. full_name: Silver, David H. last_name: Silver citation: ama: 'Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In: First International Conference on Artificial Intelligence in Healthcare. Vol 14976. Springer Nature; 2024:160-171. doi:10.1007/978-3-031-67285-9_12' apa: 'Rave, G., Fordham, D. E., Bronstein, A. M., & Silver, D. H. (2024). Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In First International Conference on Artificial Intelligence in Healthcare (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-031-67285-9_12' chicago: 'Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” In First International Conference on Artificial Intelligence in Healthcare, 14976:160–71. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-67285-9_12.' ieee: 'G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications,” in First International Conference on Artificial Intelligence in Healthcare, Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.' ista: 'Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. First International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial Intelligence in Healthcare, LNCS, vol. 14976, 160–171.' mla: 'Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” First International Conference on Artificial Intelligence in Healthcare, vol. 14976, Springer Nature, 2024, pp. 160–71, doi:10.1007/978-3-031-67285-9_12.' short: G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp. 160–171. conference: end_date: 2024-09-06 location: Swansea, United Kingdom name: 'AIiH: Artificial Intelligence in Healthcare' start_date: 2024-09-04 date_created: 2024-10-08T12:46:23Z date_published: 2024-08-15T00:00:00Z date_updated: 2024-10-09T10:33:39Z day: '15' doi: 10.1007/978-3-031-67285-9_12 extern: '1' intvolume: ' 14976' language: - iso: eng month: '08' oa_version: None page: 160-171 publication: First International Conference on Artificial Intelligence in Healthcare publication_identifier: eisbn: - '9783031672859' eissn: - 1611-3349 isbn: - '9783031672842' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14976 year: '2024' ... --- _id: '18296' abstract: - lang: eng text: It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse. article_processing_charge: No author: - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 citation: ama: Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:10.15479/AT:ISTA:18296 apa: Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18296 chicago: Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18296. ieee: O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024. ista: Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18296. mla: Kim, Olena. Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18296. short: O. Kim, (2024). contributor: - contributor_type: researcher first_name: Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim - contributor_type: researcher first_name: Yuji id: 3337E116-F248-11E8-B48F-1D18A9856A87 last_name: Okamoto orcid: 0000-0003-0408-6094 - contributor_type: researcher first_name: Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - contributor_type: researcher first_name: 'Nils ' last_name: Brose - contributor_type: researcher first_name: Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - contributor_type: supervisor first_name: Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 corr_author: '1' date_created: 2024-10-11T10:12:17Z date_published: 2024-10-11T00:00:00Z date_updated: 2026-04-16T12:20:33Z day: '11' ddc: - '570' department: - _id: PeJo - _id: RySh - _id: EM-Fac doi: 10.15479/AT:ISTA:18296 ec_funded: 1 file: - access_level: open_access checksum: 0a977e7df54c418251b10dfd3f8a015c content_type: application/zip creator: okim date_created: 2024-10-11T10:04:19Z date_updated: 2024-10-11T10:04:19Z file_id: '18297' file_name: Kim_et_al_2024_PlosBio_Source_data.zip file_size: 164382 relation: main_file success: 1 - access_level: open_access checksum: 5b9343d6b2035ac3185e390fad4d3830 content_type: text/plain creator: okim date_created: 2024-10-11T10:04:23Z date_updated: 2024-10-11T10:04:23Z file_id: '18298' file_name: info.txt file_size: 654 relation: main_file success: 1 file_date_updated: 2024-10-11T10:04:23Z has_accepted_license: '1' keyword: - Hippocampal mossy fiber synapses - short-term potentiation - long-term potentiation - presynaptic plasticity - electron microscopy - freeze-fracture replica labeling - paired recordings - forskolin - cyclic adenosine monophosphate (cAMP) - protein kinase A (PKA) - neuromodulation - synaptic vesicle pools - presynaptic Ca2+ channels - Munc13 - docking - priming - active zone month: '10' oa: 1 oa_version: Submitted Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse publisher: Institute of Science and Technology Austria related_material: record: - id: '18603' relation: used_in_publication status: public status: public title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2024' ... --- OA_place: publisher _id: '18301' abstract: - lang: eng text: Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh. alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Arian full_name: Etemadihaghighi, Arian id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f last_name: Etemadihaghighi citation: ama: Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:10.15479/at:ista:18301 apa: Etemadi, A. (2024). Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18301 chicago: Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18301. ieee: A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024. ista: Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria. mla: Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18301. short: A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-11T19:52:20Z date_published: 2024-10-15T00:00:00Z date_updated: 2026-04-07T13:02:36Z day: '15' ddc: - '000' degree_awarded: MS department: - _id: GradSch - _id: ChWo doi: 10.15479/at:ista:18301 file: - access_level: open_access checksum: 80fb7923e229ad9d39253d7c8a8083d0 content_type: application/pdf creator: aetemadi date_created: 2024-10-24T14:34:42Z date_updated: 2024-10-24T14:34:42Z file_id: '18469' file_name: thesis-arian-etemadi.pdf file_size: 8914218 relation: main_file success: 1 - access_level: closed checksum: 1c02586ed7d441d5ec441867650568d1 content_type: application/x-zip-compressed creator: aetemadi date_created: 2024-10-24T14:34:54Z date_updated: 2024-10-24T14:34:54Z file_id: '18470' file_name: thesis-arian-etemadi-latex-source.zip file_size: 9802650 relation: source_file file_date_updated: 2024-10-24T14:34:54Z has_accepted_license: '1' keyword: - surface tracking - non-manifold - hole-filling - topology change - multi-material - solid-modeling language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa: 1 oa_version: Published Version page: '39' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17219' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_embargo: 6 months OA_place: publisher OA_type: hybrid _id: '18305' abstract: - lang: eng text: Motor circuits represent the main output of the central nervous system and produce dynamic behaviors ranging from relatively simple rhythmic activities like swimming in fish and breathing in mammals to highly sophisticated dexterous movements in humans. Despite decades of research, the development and function of motor circuits remain poorly understood. Breakthroughs in the field recently provided new tools and tractable model systems that set the stage to discover the molecular mechanisms and circuit logic underlying motor control. Here, we describe recent advances from both vertebrate (mouse, frog) and invertebrate (nematode, fruit fly) systems on cellular and molecular mechanisms that enable motor circuits to develop and function and highlight conserved and divergent mechanisms necessary for motor circuit development. acknowledgement: Work in the authors’ labs is funded by the Helmholtz Association (N.Z.), National Institute of Neurological Disorders and Stroke (NINDS) R01NS116365 (P.K.), NINDS R01NS123439 and National Science Foundation IOS-2048080 (R.C.), NINDS R01NS114510 (P.P.), Natural Sciences and Engineering Research Council of Canada RGPIN-2021-03154 (K.M.) and Horizon Europe European Research Council Starting Grant Number 101041551 (L.B.S.). P.P. is the Weidenthal Family Designated Professor in Career Development. article_number: e1238242024 article_processing_charge: No article_type: original author: - first_name: Paschalis full_name: Kratsios, Paschalis last_name: Kratsios - first_name: Niccolò full_name: Zampieri, Niccolò last_name: Zampieri - first_name: Robert full_name: Carrillo, Robert last_name: Carrillo - first_name: Kota full_name: Mizumoto, Kota last_name: Mizumoto - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: Polyxeni full_name: Philippidou, Polyxeni last_name: Philippidou citation: ama: Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. 2024;44(40). doi:10.1523/JNEUROSCI.1238-24.2024 apa: Kratsios, P., Zampieri, N., Carrillo, R., Mizumoto, K., Sweeney, L. B., & Philippidou, P. (2024). Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1238-24.2024 chicago: Kratsios, Paschalis, Niccolò Zampieri, Robert Carrillo, Kota Mizumoto, Lora B. Sweeney, and Polyxeni Philippidou. “Molecular and Cellular Mechanisms of Motor Circuit Development.” The Journal of Neuroscience. Society for Neuroscience, 2024. https://doi.org/10.1523/JNEUROSCI.1238-24.2024. ieee: P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L. B. Sweeney, and P. Philippidou, “Molecular and cellular mechanisms of motor circuit development,” The Journal of Neuroscience, vol. 44, no. 40. Society for Neuroscience, 2024. ista: Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P. 2024. Molecular and cellular mechanisms of motor circuit development. The Journal of Neuroscience. 44(40), e1238242024. mla: Kratsios, Paschalis, et al. “Molecular and Cellular Mechanisms of Motor Circuit Development.” The Journal of Neuroscience, vol. 44, no. 40, e1238242024, Society for Neuroscience, 2024, doi:10.1523/JNEUROSCI.1238-24.2024. short: P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L.B. Sweeney, P. Philippidou, The Journal of Neuroscience 44 (2024). date_created: 2024-10-13T22:01:49Z date_published: 2024-10-02T00:00:00Z date_updated: 2026-01-05T14:01:26Z day: '02' ddc: - '570' department: - _id: LoSw doi: 10.1523/JNEUROSCI.1238-24.2024 external_id: isi: - '001335212200016' pmid: - '39358025' has_accepted_license: '1' intvolume: ' 44' isi: 1 issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1523/JNEUROSCI.1238-24.2024 month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits publication: The Journal of Neuroscience publication_identifier: eissn: - 1529-2401 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Molecular and cellular mechanisms of motor circuit development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18306' abstract: - lang: eng text: Neutral sodium (Na i) is an alkali metal with a favorable absorption cross section such that tenuous gases are easily illuminated at select transiting exoplanet systems. We examine both the time-averaged and time-series alkali spectral flux individually, over 4 nights at a hot Saturn system on a ∼2.8 day orbit about a Sun-like star WASP-49 A. Very Large Telescope/ESPRESSO observations are analyzed, providing new constraints. We recover the previously confirmed residual sodium flux uniquely when averaged, whereas night-to-night Na i varies by more than an order of magnitude. On HARPS/3.6 m Epoch II, we report a Doppler redshift at vΓ,NaD = + 9.7 ± 1.6 km s−1 with respect to the planet's rest frame. Upon examining the lightcurves, we confirm night-to-night variability, on the order of ∼1%–4% in NaD, rarely coinciding with exoplanet transit, not readily explained by stellar activity, starspots, tellurics, or the interstellar medium. Coincident with the ∼+10 km s−1 Doppler redshift, we detect a transient sodium absorption event dFNaD/F⋆ = 3.6% ± 1% at a relative difference of ΔFNaD(t) ∼ 4.4% ± 1%, lasting ΔtNaD ≳ 40 minutes. Since exoplanetary alkali signatures are blueshifted due to the natural vector of radiation pressure, estimated here at roughly ∼−5.7 km s−1, the radial velocity is rather at +15.4 km s−1, far larger than any known exoplanet system. Given that the redshift magnitude vΓ is in between the Roche limit and dynamically stable satellite orbits, the transient sodium may be a putative indication of a natural satellite orbiting WASP-49 A b. acknowledgement: The research described in this Letter was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics Space Administration, © 2024. California Institute of Technology. Government sponsorship acknowledged. A.V.O. and J.V.S. thank M. Lendl for constraints and discussions on the mass of WASP-49 A b. S.G.S acknowledges the support from FCT through Investigador FCT contract nr. CEECIND/00826/2018 and POPH/FSE (EC). article_number: L53 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Apurva V. full_name: Oza, Apurva V. last_name: Oza - first_name: Julia V. full_name: Seidel, Julia V. last_name: Seidel - first_name: H. Jens full_name: Hoeijmakers, H. Jens last_name: Hoeijmakers - first_name: Athira full_name: Unni, Athira last_name: Unni - first_name: Aurora Y. full_name: Kesseli, Aurora Y. last_name: Kesseli - first_name: Carl A. full_name: Schmidt, Carl A. last_name: Schmidt - first_name: Thirupathi full_name: Sivarani, Thirupathi last_name: Sivarani - first_name: Aaron full_name: Bello-Arufe, Aaron last_name: Bello-Arufe - first_name: Andrea full_name: Gebek, Andrea last_name: Gebek - first_name: Moritz full_name: Meyer Zu Westram, Moritz last_name: Meyer Zu Westram - first_name: Sérgio G. full_name: Sousa, Sérgio G. last_name: Sousa - first_name: Rosaly M.C. full_name: Lopes, Rosaly M.C. last_name: Lopes - first_name: Renyu full_name: Hu, Renyu last_name: Hu - first_name: Katherine full_name: De Kleer, Katherine last_name: De Kleer - first_name: Chloe full_name: Fisher, Chloe last_name: Fisher - first_name: Sébastien full_name: Charnoz, Sébastien last_name: Charnoz - first_name: Ashley D. full_name: Baker, Ashley D. last_name: Baker - first_name: Samuel P. full_name: Halverson, Samuel P. last_name: Halverson - first_name: Nick M. full_name: Schneider, Nick M. last_name: Schneider - first_name: Angelica full_name: Psaridi, Angelica last_name: Psaridi - first_name: Aurélien full_name: Wyttenbach, Aurélien last_name: Wyttenbach - first_name: Santiago full_name: Torres Rodriguez, Santiago id: a8df4360-4328-11ee-8f1a-e502d0c83fc2 last_name: Torres Rodriguez orcid: 0000-0002-3150-8988 - first_name: Ishita full_name: Bhatnagar, Ishita last_name: Bhatnagar - first_name: Robert E. full_name: Johnson, Robert E. last_name: Johnson citation: ama: Oza AV, Seidel JV, Hoeijmakers HJ, et al. Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. 2024;973(2). doi:10.3847/2041-8213/ad6b29 apa: Oza, A. V., Seidel, J. V., Hoeijmakers, H. J., Unni, A., Kesseli, A. Y., Schmidt, C. A., … Johnson, R. E. (2024). Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad6b29 chicago: Oza, Apurva V., Julia V. Seidel, H. Jens Hoeijmakers, Athira Unni, Aurora Y. Kesseli, Carl A. Schmidt, Thirupathi Sivarani, et al. “Redshifted Sodium Transient near Exoplanet Transit.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad6b29. ieee: A. V. Oza et al., “Redshifted sodium transient near exoplanet transit,” Astrophysical Journal Letters, vol. 973, no. 2. IOP Publishing, 2024. ista: Oza AV, Seidel JV, Hoeijmakers HJ, Unni A, Kesseli AY, Schmidt CA, Sivarani T, Bello-Arufe A, Gebek A, Meyer Zu Westram M, Sousa SG, Lopes RMC, Hu R, De Kleer K, Fisher C, Charnoz S, Baker AD, Halverson SP, Schneider NM, Psaridi A, Wyttenbach A, Torres Rodriguez S, Bhatnagar I, Johnson RE. 2024. Redshifted sodium transient near exoplanet transit. Astrophysical Journal Letters. 973(2), L53. mla: Oza, Apurva V., et al. “Redshifted Sodium Transient near Exoplanet Transit.” Astrophysical Journal Letters, vol. 973, no. 2, L53, IOP Publishing, 2024, doi:10.3847/2041-8213/ad6b29. short: A.V. Oza, J.V. Seidel, H.J. Hoeijmakers, A. Unni, A.Y. Kesseli, C.A. Schmidt, T. Sivarani, A. Bello-Arufe, A. Gebek, M. Meyer Zu Westram, S.G. Sousa, R.M.C. Lopes, R. Hu, K. De Kleer, C. Fisher, S. Charnoz, A.D. Baker, S.P. Halverson, N.M. Schneider, A. Psaridi, A. Wyttenbach, S. Torres Rodriguez, I. Bhatnagar, R.E. Johnson, Astrophysical Journal Letters 973 (2024). date_created: 2024-10-13T22:01:49Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-09-08T14:18:18Z day: '01' ddc: - '520' department: - _id: LiBu doi: 10.3847/2041-8213/ad6b29 external_id: arxiv: - '2409.19844' isi: - '001322169500001' file: - access_level: open_access checksum: 23eea2a6a0519694a84998957ad7b7fb content_type: application/pdf creator: dernst date_created: 2024-10-21T11:05:11Z date_updated: 2024-10-21T11:05:11Z file_id: '18456' file_name: 2024_AstrophysicalJourn_Oza.pdf file_size: 1249747 relation: main_file success: 1 file_date_updated: 2024-10-21T11:05:11Z has_accepted_license: '1' intvolume: ' 973' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Astrophysical Journal Letters publication_identifier: eissn: - 2041-8213 issn: - 2041-8205 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Redshifted sodium transient near exoplanet transit 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: 973 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18308' abstract: - lang: eng text: We study in this paper the problem of maintaining a solution to k-median and k-means clustering in a fully dynamic setting. To do so, we present an algorithm to efficiently maintain a coreset, a compressed version of the dataset, that allows easy computation of a clustering solution at query time. Our coreset algorithm has near-optimal update time of Õ(k) in general metric spaces, which reduces to Õ(d) in the Euclidean space ℝ^d. The query time is O(k²) in general metrics, and O(kd) in ℝ^d. To maintain a constant-factor approximation for k-median and k-means clustering in Euclidean space, this directly leads to an algorithm with update time Õ(d), and query time Õ(kd + k²). To maintain a O(polylog k)-approximation, the query time is reduced to Õ(kd). acknowledgement: "Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct 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\nDavid Saulpic: Work partially done while at ISTA. Received funding from the European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413. This work was partially funded by the grant ANR-19-CE48-0016 from the French National Research Agency (ANR)." alternative_title: - LIPIcs article_number: '100' article_processing_charge: Yes arxiv: 1 author: - first_name: Max Dupré full_name: La Tour, Max Dupré last_name: La Tour - 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: David full_name: Saulpic, David id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964 last_name: Saulpic citation: ama: 'La Tour MD, Henzinger M, Saulpic D. Fully dynamic k-means coreset in near-optimal update time. In: 32nd Annual European Symposium on Algorithms. Vol 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ESA.2024.100' apa: 'La Tour, M. D., Henzinger, M., & Saulpic, D. (2024). Fully dynamic k-means coreset in near-optimal update time. In 32nd Annual European Symposium on Algorithms (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2024.100' chicago: La Tour, Max Dupré, Monika Henzinger, and David Saulpic. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” In 32nd Annual European Symposium on Algorithms, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ESA.2024.100. ieee: M. D. La Tour, M. Henzinger, and D. Saulpic, “Fully dynamic k-means coreset in near-optimal update time,” in 32nd Annual European Symposium on Algorithms, London, United Kingdom, 2024, vol. 308. ista: 'La Tour MD, Henzinger M, Saulpic D. 2024. Fully dynamic k-means coreset in near-optimal update time. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 100.' mla: La Tour, Max Dupré, et al. “Fully Dynamic K-Means Coreset in near-Optimal Update Time.” 32nd Annual European Symposium on Algorithms, vol. 308, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ESA.2024.100. short: M.D. La Tour, M. Henzinger, D. Saulpic, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. conference: end_date: 2024-09-04 location: London, United Kingdom name: 'ESA: European Symposium on Algorithms' start_date: 2024-09-02 corr_author: '1' date_created: 2024-10-13T22:01:50Z date_published: 2024-09-23T00:00:00Z date_updated: 2025-12-02T13:49:11Z day: '23' ddc: - '000' department: - _id: MoHe doi: 10.4230/LIPIcs.ESA.2024.100 ec_funded: 1 external_id: arxiv: - '2406.19926' isi: - '001545622400100' file: - access_level: open_access checksum: 8e8c0b13049f11bb0133dfac22e32718 content_type: application/pdf creator: dernst date_created: 2024-10-21T09:41:48Z date_updated: 2024-10-21T09:41:48Z file_id: '18454' file_name: 2024_LIPICs_DuprelaTour.pdf file_size: 873561 relation: main_file success: 1 file_date_updated: 2024-10-21T09:41:48Z has_accepted_license: '1' intvolume: ' 308' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version 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 - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: 32nd Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959773386' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Fully dynamic k-means coreset in near-optimal update time 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 308 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18309' abstract: - lang: eng text: 'The problem of designing connectivity oracles supporting vertex failures is one of the basic data structures problems for undirected graphs. It is already well understood: previous works [Duan-Pettie STOC''10; Long-Saranurak FOCS''22] achieve query time linear in the number of failed vertices, and it is conditionally optimal as long as we require preprocessing time polynomial in the size of the graph and update time polynomial in the number of failed vertices. We revisit this problem in the paradigm of algorithms with predictions: we ask if the query time can be improved if the set of failed vertices can be predicted beforehand up to a small number of errors. More specifically, we design a data structure that, given a graph G = (V,E) and a set of vertices predicted to fail D̂ ⊆ V of size d = |D̂|, preprocesses it in time Õ(d|E|) and then can receive an update given as the symmetric difference between the predicted and the actual set of failed vertices D̂△D = (D̂ ⧵ D) ∪ (D ⧵ D̂) of size η = |D̂△D|, process it in time Õ(η⁴), and after that answer connectivity queries in G ⧵ D in time O(η). Viewed from another perspective, our data structure provides an improvement over the state of the art for the fully dynamic subgraph connectivity problem in the sensitivity setting [Henzinger-Neumann ESA''16]. We argue that the preprocessing time and query time of our data structure are conditionally optimal under standard fine-grained complexity assumptions.' acknowledgement: "Part of this work was done when Evangelos Kosinas was at University of Ioannina and Adam Polak was at Max Planck Institute of Informatics.\r\n" alternative_title: - LIPIcs article_number: '72' article_processing_charge: Yes arxiv: 1 author: - first_name: Bingbing full_name: Hu, Bingbing last_name: Hu - first_name: Evangelos full_name: Kosinas, Evangelos id: 4c7f9625-dbbc-11ee-9d86-bdcc2db5a949 last_name: Kosinas - first_name: Adam full_name: Polak, Adam last_name: Polak citation: ama: 'Hu B, Kosinas E, Polak A. Connectivity oracles for predictable vertex failures. In: 32nd Annual European Symposium on Algorithms. Vol 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ESA.2024.72' apa: 'Hu, B., Kosinas, E., & Polak, A. (2024). Connectivity oracles for predictable vertex failures. In 32nd Annual European Symposium on Algorithms (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2024.72' chicago: Hu, Bingbing, Evangelos Kosinas, and Adam Polak. “Connectivity Oracles for Predictable Vertex Failures.” In 32nd Annual European Symposium on Algorithms, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ESA.2024.72. ieee: B. Hu, E. Kosinas, and A. Polak, “Connectivity oracles for predictable vertex failures,” in 32nd Annual European Symposium on Algorithms, London, United Kingdom, 2024, vol. 308. ista: 'Hu B, Kosinas E, Polak A. 2024. Connectivity oracles for predictable vertex failures. 32nd Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 308, 72.' mla: Hu, Bingbing, et al. “Connectivity Oracles for Predictable Vertex Failures.” 32nd Annual European Symposium on Algorithms, vol. 308, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ESA.2024.72. short: B. Hu, E. Kosinas, A. Polak, in:, 32nd Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. conference: end_date: 2024-09-04 location: London, United Kingdom name: 'ESA: European Symposium on Algorithms' start_date: 2024-09-02 corr_author: '1' date_created: 2024-10-13T22:01:50Z date_published: 2024-09-01T00:00:00Z date_updated: 2025-12-02T13:49:52Z day: '01' ddc: - '000' department: - _id: MoHe doi: 10.4230/LIPIcs.ESA.2024.72 external_id: arxiv: - '2312.08489' isi: - '001545622400072' file: - access_level: open_access checksum: ab1f2f9161549a8763eda15db40e022c content_type: application/pdf creator: dernst date_created: 2024-10-21T10:03:48Z date_updated: 2024-10-21T10:03:48Z file_id: '18455' file_name: 2024_LIPICs_Hu.pdf file_size: 853914 relation: main_file success: 1 file_date_updated: 2024-10-21T10:03:48Z has_accepted_license: '1' intvolume: ' 308' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: 32nd Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959773386' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Connectivity oracles for predictable vertex failures 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 308 year: '2024' ... --- OA_type: closed access _id: '18310' article_processing_charge: No article_type: original author: - first_name: Maria full_name: Kitsara, Maria last_name: Kitsara - first_name: Merima full_name: Smajlhodžić-Deljo, Merima last_name: Smajlhodžić-Deljo - first_name: Lejla full_name: Gurbeta Pokvic, Lejla last_name: Gurbeta Pokvic - first_name: Bettina full_name: Bert, Bettina last_name: Bert - first_name: Nataliia full_name: Bubalo, Nataliia last_name: Bubalo - first_name: Sevilay full_name: Erden, Sevilay last_name: Erden - first_name: Nuno Henrique full_name: Franco, Nuno Henrique last_name: Franco - first_name: Giuseppe full_name: Chirico, Giuseppe last_name: Chirico - first_name: Jonathan full_name: Gómez Raja, Jonathan last_name: Gómez Raja - first_name: Fernando full_name: Gonzalez-Uarquin, Fernando last_name: Gonzalez-Uarquin - first_name: Annemarie full_name: Lang, Annemarie last_name: Lang - first_name: Nicole full_name: Linklater, Nicole last_name: Linklater - first_name: Sandra full_name: Mojsova, Sandra last_name: Mojsova - first_name: I. Anna S. full_name: Olsson, I. Anna S. last_name: Olsson - first_name: Ioanna full_name: Sandvig, Ioanna last_name: Sandvig - first_name: Alexandra full_name: Schaffert, Alexandra last_name: Schaffert - first_name: Marthe full_name: Schmit, Marthe last_name: Schmit - first_name: Sophie full_name: Schober, Sophie id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8 last_name: Schober - first_name: Bogdan full_name: Sevastre, Bogdan last_name: Sevastre - first_name: Doris full_name: Wilflingseder, Doris last_name: Wilflingseder - first_name: Arti full_name: Ahluwalia, Arti last_name: Ahluwalia - first_name: Winfried full_name: Neuhaus, Winfried last_name: Neuhaus citation: ama: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. 2024;52(6):326-333. doi:10.1177/02611929241286024 apa: Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N., Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. SAGE Publications. https://doi.org/10.1177/02611929241286024 chicago: Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” Alternatives to Laboratory Animals. SAGE Publications, 2024. https://doi.org/10.1177/02611929241286024. ieee: M. Kitsara et al., “Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE),” Alternatives to Laboratory Animals, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024. ista: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N, Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B, Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory Animals. 52(6), 326–333. mla: Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).” Alternatives to Laboratory Animals, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:10.1177/02611929241286024. short: M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo, S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang, N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit, S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives to Laboratory Animals 52 (2024) 326–333. date_created: 2024-10-13T22:01:51Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T09:56:39Z day: '01' department: - _id: PreCl doi: 10.1177/02611929241286024 external_id: isi: - '001348633700007' pmid: - '39333027' intvolume: ' 52' isi: 1 issue: '6' language: - iso: eng month: '11' oa_version: None page: 326-333 pmid: 1 publication: Alternatives to Laboratory Animals publication_identifier: eissn: - 2632-3559 issn: - 0261-1929 publication_status: published publisher: SAGE Publications quality_controlled: '1' scopus_import: '1' status: public title: Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 52 year: '2024' ... --- OA_type: closed access _id: '18311' abstract: - lang: eng text: Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. Cell Research. 2024;34:761-762. doi:10.1038/s41422-024-01035-x' apa: 'Hörmayer, L., & Friml, J. (2024). Feeling the danger: Local wound signaling in plants. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-024-01035-x' chicago: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research. Springer Nature, 2024. https://doi.org/10.1038/s41422-024-01035-x.' ieee: 'L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” Cell Research, vol. 34. Springer Nature, pp. 761–762, 2024.' ista: 'Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.' mla: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research, vol. 34, Springer Nature, 2024, pp. 761–62, doi:10.1038/s41422-024-01035-x.' short: L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762. corr_author: '1' date_created: 2024-10-13T22:01:51Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T09:57:18Z day: '01' department: - _id: JiFr doi: 10.1038/s41422-024-01035-x external_id: isi: - '001326684200001' pmid: - '39354142' intvolume: ' 34' isi: 1 language: - iso: eng month: '11' oa_version: None page: 761-762 pmid: 1 publication: Cell Research publication_identifier: eissn: - 1748-7838 issn: - 1001-0602 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Feeling the danger: Local wound signaling in plants' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2024' ... --- OA_place: publisher OA_type: free access _id: '18443' abstract: - lang: eng text: "In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maria A full_name: Sisak, Maria A id: 44A03D04-AEA4-11E9-B225-EA2DE6697425 last_name: Sisak citation: ama: Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:10.15479/at:ista:18443 apa: Sisak, M. A. (2024). T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18443 chicago: Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18443. ieee: M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024. ista: Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria. mla: Sisak, Maria A. T-Dual Branes on Hyperkähler Manifolds. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18443. short: M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-19T12:00:37Z date_published: 2024-10-24T00:00:00Z date_updated: 2026-04-07T12:42:44Z day: '24' ddc: - '516' degree_awarded: PhD department: - _id: GradSch - _id: TaHa doi: 10.15479/at:ista:18443 file: - access_level: open_access checksum: 8c4893e726aaa4b3efb82758da9b6851 content_type: application/pdf creator: msisak date_created: 2024-10-23T14:42:45Z date_updated: 2024-10-23T14:42:45Z file_id: '18467' file_name: MASisak_dissertation.pdf file_size: 1672547 relation: main_file success: 1 - access_level: closed checksum: 1831b072e861a1e5481024ca9d02b036 content_type: application/x-zip-compressed creator: msisak date_created: 2024-10-23T14:43:56Z date_updated: 2024-10-24T08:09:13Z file_id: '18468' file_name: MASisak_source.zip file_size: 617913 relation: source_file file_date_updated: 2024-10-24T08:09:13Z has_accepted_license: '1' keyword: - hyperkaehler geometry - branes - mirror symmetry - T-duality language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '178' project: - _id: 6286e8c4-2b32-11ec-9570-f5297902f67f grant_number: '26069' name: Branes on hyperkähler manifolds publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel orcid: 0000-0002-9582-2634 title: T-dual branes on hyperkähler manifolds 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository OA_type: green _id: '22065' abstract: - lang: eng text: The Benjamin–Ono equation is shown to be well-posed, both on the line and on the circle, in the Sobolev spaces H^s for s > -1/2. The proof rests on a new gauge transformation and benefits from our introduction of a modified Lax pair representation of the full hierarchy. As we will show, these developments yield important additional dividends beyond well-posedness, including (i) the unification of the diverse approaches to polynomial conservation laws; (ii) a generalization of Gérard’s explicit formula to the full hierarchy; and (iii) new virial-type identities covering all equations in the hierarchy. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Thierry full_name: Laurens, Thierry last_name: Laurens - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: Killip R, Laurens T, Vişan M. Sharp well-posedness for the Benjamin–Ono equation. Inventiones mathematicae. 2024;236(3):999-1054. doi:10.1007/s00222-024-01250-8 apa: Killip, R., Laurens, T., & Vişan, M. (2024). Sharp well-posedness for the Benjamin–Ono equation. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-024-01250-8 chicago: Killip, Rowan, Thierry Laurens, and Monica Vişan. “Sharp Well-Posedness for the Benjamin–Ono Equation.” Inventiones Mathematicae. Springer Nature, 2024. https://doi.org/10.1007/s00222-024-01250-8. ieee: R. Killip, T. Laurens, and M. Vişan, “Sharp well-posedness for the Benjamin–Ono equation,” Inventiones mathematicae, vol. 236, no. 3. Springer Nature, pp. 999–1054, 2024. ista: Killip R, Laurens T, Vişan M. 2024. Sharp well-posedness for the Benjamin–Ono equation. Inventiones mathematicae. 236(3), 999–1054. mla: Killip, Rowan, et al. “Sharp Well-Posedness for the Benjamin–Ono Equation.” Inventiones Mathematicae, vol. 236, no. 3, Springer Nature, 2024, pp. 999–1054, doi:10.1007/s00222-024-01250-8. short: R. Killip, T. Laurens, M. Vişan, Inventiones Mathematicae 236 (2024) 999–1054. das_tickbox: '1' date_created: 2026-06-19T08:13:06Z date_published: 2024-06-01T00:00:00Z date_updated: 2026-06-30T07:11:40Z day: '01' doi: 10.1007/s00222-024-01250-8 extern: '1' external_id: arxiv: - '2304.00124' intvolume: ' 236' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.00124 month: '06' oa: 1 oa_version: Preprint page: 999-1054 publication: Inventiones mathematicae publication_identifier: eissn: - 1432-1297 issn: - 0020-9910 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Sharp well-posedness for the Benjamin–Ono equation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 236 year: '2024' ... --- OA_place: repository OA_type: green _id: '22062' abstract: - lang: eng text: We prove that the derivative nonlinear Schrödinger equation in one space dimension is globally well-posed on the line in L^2 (R), which is the scaling-critical space for this equation. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Benjamin full_name: Harrop-Griffiths, Benjamin last_name: Harrop-Griffiths - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Maria full_name: Ntekoume, Maria last_name: Ntekoume - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: Harrop-Griffiths B, Killip R, Ntekoume M, Vişan M. Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R). Journal of the European Mathematical Society. 2024;28(2):843-924. doi:10.4171/jems/1490 apa: Harrop-Griffiths, B., Killip, R., Ntekoume, M., & Vişan, M. (2024). Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R). Journal of the European Mathematical Society. EMS Press. https://doi.org/10.4171/jems/1490 chicago: Harrop-Griffiths, Benjamin, Rowan Killip, Maria Ntekoume, and Monica Vişan. “Global Well-Posedness for the Derivative Nonlinear Schrödinger Equation in L^2(R).” Journal of the European Mathematical Society. EMS Press, 2024. https://doi.org/10.4171/jems/1490. ieee: B. Harrop-Griffiths, R. Killip, M. Ntekoume, and M. Vişan, “Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R),” Journal of the European Mathematical Society, vol. 28, no. 2. EMS Press, pp. 843–924, 2024. ista: Harrop-Griffiths B, Killip R, Ntekoume M, Vişan M. 2024. Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R). Journal of the European Mathematical Society. 28(2), 843–924. mla: Harrop-Griffiths, Benjamin, et al. “Global Well-Posedness for the Derivative Nonlinear Schrödinger Equation in L^2(R).” Journal of the European Mathematical Society, vol. 28, no. 2, EMS Press, 2024, pp. 843–924, doi:10.4171/jems/1490. short: B. Harrop-Griffiths, R. Killip, M. Ntekoume, M. Vişan, Journal of the European Mathematical Society 28 (2024) 843–924. date_created: 2026-06-19T08:11:46Z date_published: 2024-06-26T00:00:00Z date_updated: 2026-06-30T07:04:07Z day: '26' doi: 10.4171/jems/1490 extern: '1' external_id: arxiv: - '2204.12548' intvolume: ' 28' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2204.12548 mathsc: - 35Q55 month: '06' oa: 1 oa_version: Preprint page: 843-924 publication: Journal of the European Mathematical Society publication_identifier: eissn: - 1435-9863 issn: - 1435-9855 publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2024' ... --- OA_place: repository OA_type: green _id: '22074' abstract: - lang: eng text: We discuss how countable subadditivity of operators can be derived from subadditivity under mild forms of continuity, and provide examples manifesting such circumstances. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Loukas full_name: Grafakos, Loukas last_name: Grafakos - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: 'Grafakos L, Vişan M. Remarks on countable subadditivity. Proceedings of the Royal Society of Edinburgh: Section A Mathematics. 2024;154(5):1504-1517. doi:10.1017/prm.2023.77' apa: 'Grafakos, L., & Vişan, M. (2024). Remarks on countable subadditivity. Proceedings of the Royal Society of Edinburgh: Section A Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2023.77' chicago: 'Grafakos, Loukas, and Monica Vişan. “Remarks on Countable Subadditivity.” Proceedings of the Royal Society of Edinburgh: Section A Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2023.77.' ieee: 'L. Grafakos and M. Vişan, “Remarks on countable subadditivity,” Proceedings of the Royal Society of Edinburgh: Section A Mathematics, vol. 154, no. 5. Cambridge University Press, pp. 1504–1517, 2024.' ista: 'Grafakos L, Vişan M. 2024. Remarks on countable subadditivity. Proceedings of the Royal Society of Edinburgh: Section A Mathematics. 154(5), 1504–1517.' mla: 'Grafakos, Loukas, and Monica Vişan. “Remarks on Countable Subadditivity.” Proceedings of the Royal Society of Edinburgh: Section A Mathematics, vol. 154, no. 5, Cambridge University Press, 2024, pp. 1504–17, doi:10.1017/prm.2023.77.' short: 'L. Grafakos, M. Vişan, Proceedings of the Royal Society of Edinburgh: Section A Mathematics 154 (2024) 1504–1517.' das_tickbox: '1' date_created: 2026-06-19T08:22:51Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-06-30T11:03:28Z day: '01' doi: 10.1017/prm.2023.77 extern: '1' external_id: arxiv: - '2304.07831' intvolume: ' 154' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.07831 month: '10' oa: 1 oa_version: Preprint page: 1504-1517 publication: 'Proceedings of the Royal Society of Edinburgh: Section A Mathematics' publication_identifier: eissn: - 1473-7124 issn: - 0308-2105 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Remarks on countable subadditivity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 154 year: '2024' ...