--- _id: '14241' abstract: - lang: eng text: We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects. acknowledgement: "The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n" article_number: '20' 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. Stealth shaper: Reflectivity optimization as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591542' apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591542' chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.' ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings, Los Angeles, CA, United States, 2023.' ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20.' mla: 'Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542.' short: K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023. conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-08-27T22:01:17Z date_published: 2023-07-23T00:00:00Z date_updated: 2023-09-05T07:22:03Z day: '23' department: - _id: BeBi doi: 10.1145/3588432.3591542 external_id: arxiv: - '2305.05944' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.05944 month: '07' oa: 1 oa_version: Preprint publication: SIGGRAPH 2023 Conference Proceedings publication_identifier: isbn: - '9798400701597' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Stealth shaper: Reflectivity optimization as surface stylization' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12562' abstract: - lang: eng text: Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons. acknowledgement: The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University. article_processing_charge: No article_type: original author: - first_name: David R. full_name: Ladle, David R. last_name: Ladle - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022 apa: Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022 chicago: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022. ieee: D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023. ista: Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512. mla: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022. short: D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512. date_created: 2023-02-15T14:46:14Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-09-05T12:13:34Z day: '01' department: - _id: SiHi doi: 10.1152/jn.00172.2022 external_id: isi: - '000957721600001' pmid: - '36695533' intvolume: ' 129' isi: 1 issue: '3' keyword: - Physiology - General Neuroscience language: - iso: eng month: '03' oa_version: None page: 501-512 pmid: 1 publication: Journal of Neurophysiology publication_identifier: eissn: - 1522-1598 issn: - 0022-3077 publication_status: published publisher: American Physiological Society quality_controlled: '1' status: public title: Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 129 year: '2023' ... --- _id: '13310' abstract: - lang: eng text: Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation. acknowledgement: 'This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.' alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Mahyar full_name: Karimi, Mahyar id: f1dedef5-2f78-11ee-989a-c4c97bccf506 last_name: Karimi orcid: 0009-0005-0820-1696 - first_name: Konstantin full_name: Kueffner, Konstantin id: 8121a2d0-dc85-11ea-9058-af578f3b4515 last_name: Kueffner orcid: 0000-0001-8974-2542 - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 citation: ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17' apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17' chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17. ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382. ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.' mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17. short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2023-07-25T18:32:40Z date_published: 2023-07-18T00:00:00Z date_updated: 2023-09-05T15:14:00Z day: '18' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1007/978-3-031-37703-7_17 ec_funded: 1 external_id: arxiv: - '2305.15979' file: - access_level: open_access checksum: ccaf94bf7d658ba012c016e11869b54c content_type: application/pdf creator: dernst date_created: 2023-07-31T08:11:20Z date_updated: 2023-07-31T08:11:20Z file_id: '13327' file_name: 2023_LNCS_CAV_HenzingerT.pdf file_size: 647760 relation: main_file success: 1 file_date_updated: 2023-07-31T08:11:20Z has_accepted_license: '1' intvolume: ' 13965' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version page: 358–382 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Computer Aided Verification publication_identifier: eisbn: - '9783031377037' eissn: - 1611-3349 isbn: - '9783031377020' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Monitoring algorithmic fairness 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13965 year: '2023' ... --- _id: '12205' abstract: - lang: eng text: "Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC." acknowledgement: "E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL." article_processing_charge: No article_type: original author: - first_name: Jacek full_name: Glajzer, Jacek last_name: Glajzer - first_name: Dan Cacsire full_name: Castillo-Tong, Dan Cacsire last_name: Castillo-Tong - first_name: Rolf full_name: Richter, Rolf last_name: Richter - first_name: Ignace full_name: Vergote, Ignace last_name: Vergote - first_name: Hagen full_name: Kulbe, Hagen last_name: Kulbe - first_name: Adriaan full_name: Vanderstichele, Adriaan last_name: Vanderstichele - first_name: Ilary full_name: Ruscito, Ilary last_name: Ruscito - first_name: Fabian full_name: Trillsch, Fabian last_name: Trillsch - first_name: Alexander full_name: Mustea, Alexander last_name: Mustea - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Charlie full_name: Gourley, Charlie last_name: Gourley - first_name: Hani full_name: Gabra, Hani last_name: Gabra - first_name: Eliane T. full_name: Taube, Eliane T. last_name: Taube - first_name: Oliver full_name: Dorigo, Oliver last_name: Dorigo - first_name: David full_name: Horst, David last_name: Horst - first_name: Carlotta full_name: Keunecke, Carlotta last_name: Keunecke - first_name: Joanna full_name: Baum, Joanna last_name: Baum - first_name: Timothy full_name: Angelotti, Timothy last_name: Angelotti - first_name: Jalid full_name: Sehouli, Jalid last_name: Sehouli - first_name: Elena Ioana full_name: Braicu, Elena Ioana last_name: Braicu citation: ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3' apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3' chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.' ieee: 'J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.' ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.' mla: 'Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.' short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45. date_created: 2023-01-16T09:44:36Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-09-05T15:18:37Z day: '01' ddc: - '610' department: - _id: JoDa doi: 10.1245/s10434-022-12459-3 external_id: isi: - '000852125500006' file: - access_level: open_access checksum: 36a1200e1011f4b2155a8041d0308f34 content_type: application/pdf creator: dernst date_created: 2023-02-02T13:01:20Z date_updated: 2023-02-02T13:01:20Z file_id: '12490' file_name: 2023_AnnalsSurgicalOncology_Glajzer.pdf file_size: 365865 relation: main_file success: 1 file_date_updated: 2023-02-02T13:01:20Z has_accepted_license: '1' intvolume: ' 30' isi: 1 keyword: - Oncology - Surgery language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 35-45 publication: Annals of Surgical Oncology publication_identifier: eissn: - 1534-4681 issn: - 1068-9265 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12115' relation: other status: public scopus_import: '1' status: public title: 'Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2023' ... --- _id: '12115' acknowledgement: This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu). article_processing_charge: No article_type: original author: - first_name: Jacek full_name: Glajzer, Jacek last_name: Glajzer - first_name: Dan Cacsire full_name: Castillo-Tong, Dan Cacsire last_name: Castillo-Tong - first_name: Rolf full_name: Richter, Rolf last_name: Richter - first_name: Ignace full_name: Vergote, Ignace last_name: Vergote - first_name: Hagen full_name: Kulbe, Hagen last_name: Kulbe - first_name: Adriaan full_name: Vanderstichele, Adriaan last_name: Vanderstichele - first_name: Ilary full_name: Ruscito, Ilary last_name: Ruscito - first_name: Fabian full_name: Trillsch, Fabian last_name: Trillsch - first_name: Alexander full_name: Mustea, Alexander last_name: Mustea - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Charlie full_name: Gourley, Charlie last_name: Gourley - first_name: Hani full_name: Gabra, Hani last_name: Gabra - first_name: Eliane T. full_name: Taube, Eliane T. last_name: Taube - first_name: Oliver full_name: Dorigo, Oliver last_name: Dorigo - first_name: David full_name: Horst, David last_name: Horst - first_name: Carlotta full_name: Keunecke, Carlotta last_name: Keunecke - first_name: Joanna full_name: Baum, Joanna last_name: Baum - first_name: Timothy full_name: Angelotti, Timothy last_name: Angelotti - first_name: Jalid full_name: Sehouli, Jalid last_name: Sehouli - first_name: Elena Ioana full_name: Braicu, Elena Ioana last_name: Braicu citation: ama: 'Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z' apa: 'Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z' chicago: 'Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.' ieee: 'J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.' ista: 'Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.' mla: 'Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z.' short: J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47. date_created: 2023-01-12T11:56:22Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-09-05T15:18:36Z day: '01' department: - _id: JoDa doi: 10.1245/s10434-022-12681-z external_id: isi: - '000879151800001' intvolume: ' 30' isi: 1 keyword: - Oncology - Surgery language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1245/s10434-022-12681-z month: '01' oa: 1 oa_version: Published Version page: 46-47 publication: Annals of Surgical Oncology publication_identifier: eissn: - 1534-4681 issn: - 1068-9265 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12205' relation: other status: public scopus_import: '1' status: public title: 'ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2023' ... --- _id: '14253' abstract: - lang: eng text: Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell. acknowledgement: We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.). article_number: '5231' article_processing_charge: Yes article_type: original author: - first_name: Nicholas C. full_name: Vierra, Nicholas C. last_name: Vierra - first_name: Luisa full_name: Ribeiro-Silva, Luisa last_name: Ribeiro-Silva - first_name: Michael full_name: Kirmiz, Michael last_name: Kirmiz - first_name: Deborah full_name: Van Der List, Deborah last_name: Van Der List - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 - first_name: Olivia A. full_name: Mack, Olivia A. last_name: Mack - first_name: James full_name: Carroll, James last_name: Carroll - first_name: Elodie full_name: Le Monnier, Elodie id: 3B59276A-F248-11E8-B48F-1D18A9856A87 last_name: Le Monnier - first_name: Sue A. full_name: Aicher, Sue A. last_name: Aicher - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: James S. full_name: Trimmer, James S. last_name: Trimmer citation: ama: Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 2023;14. doi:10.1038/s41467-023-40930-6 apa: Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40930-6 chicago: Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6. ieee: N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231. mla: Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231, Springer Nature, 2023, doi:10.1038/s41467-023-40930-6. short: N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023). date_created: 2023-09-03T22:01:14Z date_published: 2023-08-26T00:00:00Z date_updated: 2023-09-06T06:53:32Z day: '26' ddc: - '570' department: - _id: RySh doi: 10.1038/s41467-023-40930-6 external_id: pmid: - '37633939' file: - access_level: open_access checksum: 6ab8aab4e957f626a09a1c73db3388fb content_type: application/pdf creator: dernst date_created: 2023-09-06T06:50:07Z date_updated: 2023-09-06T06:50:07Z file_id: '14270' file_name: 2023_NatureComm_Vierra.pdf file_size: 9412549 relation: main_file success: 1 file_date_updated: 2023-09-06T06:50:07Z has_accepted_license: '1' intvolume: ' 14' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling 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: 14 year: '2023' ... --- _id: '14259' abstract: - lang: eng text: "We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning." acknowledgement: This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro). alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Maximilian full_name: Prokop, Maximilian last_name: Prokop - first_name: Sabine full_name: Rieder, Sabine last_name: Rieder citation: ama: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20' apa: 'Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20' chicago: Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th International Conference on Computer Aided Verification , 13964:390–414. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20. ieee: J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414. ista: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.' mla: Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20. short: J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2023-09-03T22:01:16Z date_published: 2023-07-17T00:00:00Z date_updated: 2023-09-06T08:27:33Z day: '17' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-031-37706-8_20 file: - access_level: open_access checksum: ed66278b61bb869e1baba3d9b9081271 content_type: application/pdf creator: dernst date_created: 2023-09-06T08:25:50Z date_updated: 2023-09-06T08:25:50Z file_id: '14276' file_name: 2023_LNCS_CAV_Kretinsky.pdf file_size: 428354 relation: main_file success: 1 file_date_updated: 2023-09-06T08:25:50Z has_accepted_license: '1' intvolume: ' 13964' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 390-414 publication: '35th International Conference on Computer Aided Verification ' publication_identifier: eissn: - 1611-3349 isbn: - '9783031377051' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Guessing winning policies in LTL synthesis by semantic learning 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: 13964 year: '2023' ... --- _id: '14105' abstract: - lang: eng text: "Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks:\r\nobject detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. " article_processing_charge: No author: - first_name: Samarth full_name: Sinha, Samarth last_name: Sinha - first_name: Peter full_name: Gehler, Peter last_name: Gehler - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Bernt full_name: Schiele, Bernt last_name: Schiele citation: ama: 'Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under distribution shift. In: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/wacv56688.2023.00278' apa: 'Sinha, S., Gehler, P., Locatello, F., & Schiele, B. (2023). TeST: Test-time Self-Training under distribution shift. In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Waikoloa, HI, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/wacv56688.2023.00278' chicago: 'Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele. “TeST: Test-Time Self-Training under Distribution Shift.” In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/wacv56688.2023.00278.' ieee: 'S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training under distribution shift,” in 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Waikoloa, HI, United States, 2023.' ista: 'Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision.' mla: 'Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.” 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/wacv56688.2023.00278.' short: S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023. conference: end_date: 2023-01-07 location: Waikoloa, HI, United States name: 'WACV: Winter Conference on Applications of Computer Vision' start_date: 2023-01-02 date_created: 2023-08-21T12:11:38Z date_published: 2023-02-06T00:00:00Z date_updated: 2023-09-06T10:26:56Z day: '06' department: - _id: FrLo doi: 10.1109/wacv56688.2023.00278 extern: '1' external_id: arxiv: - '2209.11459' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2209.11459 month: '02' oa: 1 oa_version: Preprint publication: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision publication_identifier: eissn: - 2642-9381 isbn: - '9781665493475' publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: 'TeST: Test-time Self-Training under distribution shift' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14256' abstract: - lang: eng text: "Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries." acknowledgement: The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions. article_number: L9 article_processing_charge: Yes (in subscription journal) article_type: letter_note author: - first_name: S. full_name: Mathis, S. last_name: Mathis - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 citation: ama: 'Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 2023;676. doi:10.1051/0004-6361/202346832' apa: 'Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832' chicago: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.' ieee: 'S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” Astronomy and Astrophysics, vol. 676. EDP Sciences, 2023.' ista: 'Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9.' mla: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.' short: S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023). date_created: 2023-09-03T22:01:15Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-09-06T11:05:58Z day: '01' ddc: - '520' department: - _id: LiBu doi: 10.1051/0004-6361/202346832 external_id: arxiv: - '2306.11587' isi: - '001046037700007' file: - access_level: open_access checksum: 7b30d26fb2b7bcb5b5be1414950615f9 content_type: application/pdf creator: dernst date_created: 2023-09-06T07:13:19Z date_updated: 2023-09-06T07:13:19Z file_id: '14271' file_name: 2023_AstronomyAstrophysics_Mathis.pdf file_size: 458120 relation: main_file success: 1 file_date_updated: 2023-09-06T07:13:19Z has_accepted_license: '1' intvolume: ' 676' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Astronomy and Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 676 year: '2023' ... --- _id: '14261' abstract: - lang: eng text: In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing. acknowledgement: Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jakob full_name: Gamper, Jakob last_name: Gamper - first_name: Florian full_name: Kluibenschedl, Florian id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9 last_name: Kluibenschedl - first_name: Alexander K.H. full_name: Weiss, Alexander K.H. last_name: Weiss - first_name: Thomas S. full_name: Hofer, Thomas S. last_name: Hofer citation: ama: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707 apa: Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707 chicago: Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707. ieee: J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023. ista: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403. mla: Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707. short: J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403. date_created: 2023-09-03T22:01:16Z date_published: 2023-08-11T00:00:00Z date_updated: 2023-09-06T11:04:31Z day: '11' ddc: - '530' - '540' department: - _id: GradSch doi: 10.1021/acs.jpclett.3c01707 external_id: isi: - '001048165800001' pmid: - '37566743' file: - access_level: open_access checksum: 637454e2b3a357498d8d622d241c4bf6 content_type: application/pdf creator: dernst date_created: 2023-09-06T07:32:39Z date_updated: 2023-09-06T07:32:39Z file_id: '14272' file_name: 2023_JourPhysChemistry_Gamper.pdf file_size: 4986859 relation: main_file success: 1 file_date_updated: 2023-09-06T07:32:39Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '33' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 7395-7403 pmid: 1 publication: Journal of Physical Chemistry Letters publication_identifier: eissn: - 1948-7185 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum 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: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2023' ... --- _id: '14208' abstract: - lang: eng text: This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory. alternative_title: - PMLR article_processing_charge: No author: - first_name: Zhenyu full_name: Zhu, Zhenyu last_name: Zhu - first_name: Fanghui full_name: Liu, Fanghui last_name: Liu - first_name: Grigorios G full_name: Chrysos, Grigorios G last_name: Chrysos - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Volkan full_name: Cevher, Volkan last_name: Cevher citation: ama: 'Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. Benign overfitting in deep neural networks under lazy training. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:43105-43128.' apa: 'Zhu, Z., Liu, F., Chrysos, G. G., Locatello, F., & Cevher, V. (2023). Benign overfitting in deep neural networks under lazy training. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 43105–43128). Honolulu, Hawaii, United States: ML Research Press.' chicago: Zhu, Zhenyu, Fanghui Liu, Grigorios G Chrysos, Francesco Locatello, and Volkan Cevher. “Benign Overfitting in Deep Neural Networks under Lazy Training.” In Proceedings of the 40th International Conference on Machine Learning, 202:43105–28. ML Research Press, 2023. ieee: Z. Zhu, F. Liu, G. G. Chrysos, F. Locatello, and V. Cevher, “Benign overfitting in deep neural networks under lazy training,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, United States, 2023, vol. 202, pp. 43105–43128. ista: Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. 2023. Benign overfitting in deep neural networks under lazy training. Proceedings of the 40th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 202, 43105–43128. mla: Zhu, Zhenyu, et al. “Benign Overfitting in Deep Neural Networks under Lazy Training.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 43105–28. short: Z. Zhu, F. Liu, G.G. Chrysos, F. Locatello, V. Cevher, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 43105–43128. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, United States name: International Conference on Machine Learning start_date: 2023-07-23 date_created: 2023-08-22T14:18:18Z date_published: 2023-05-30T00:00:00Z date_updated: 2023-09-13T08:46:46Z day: '30' department: - _id: FrLo extern: '1' external_id: arxiv: - '2305.19377' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.19377 month: '05' oa: 1 oa_version: Preprint page: 43105-43128 publication: Proceedings of the 40th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Benign overfitting in deep neural networks under lazy training type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14209' abstract: - lang: eng text: Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks. article_number: '2304.10253' article_processing_charge: No author: - first_name: Max F. full_name: Burg, Max F. last_name: Burg - first_name: Florian full_name: Wenzel, Florian last_name: Wenzel - first_name: Dominik full_name: Zietlow, Dominik last_name: Zietlow - first_name: Max full_name: Horn, Max last_name: Horn - first_name: Osama full_name: Makansi, Osama last_name: Makansi - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Chris full_name: Russell, Chris last_name: Russell citation: ama: Burg MF, Wenzel F, Zietlow D, et al. A data augmentation perspective on diffusion models and retrieval. arXiv. doi:10.48550/arXiv.2304.10253 apa: Burg, M. F., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., & Russell, C. (n.d.). A data augmentation perspective on diffusion models and retrieval. arXiv. https://doi.org/10.48550/arXiv.2304.10253 chicago: Burg, Max F., Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco Locatello, and Chris Russell. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.10253. ieee: M. F. Burg et al., “A data augmentation perspective on diffusion models and retrieval,” arXiv. . ista: Burg MF, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. A data augmentation perspective on diffusion models and retrieval. arXiv, 2304.10253. mla: Burg, Max F., et al. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, 2304.10253, doi:10.48550/arXiv.2304.10253. short: M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, ArXiv (n.d.). date_created: 2023-08-22T14:18:43Z date_published: 2023-04-20T00:00:00Z date_updated: 2023-09-13T08:51:56Z day: '20' department: - _id: FrLo doi: 10.48550/arXiv.2304.10253 extern: '1' external_id: arxiv: - '2304.10253' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.10253 month: '04' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: A data augmentation perspective on diffusion models and retrieval type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14211' abstract: - lang: eng text: 'Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data.' article_processing_charge: No author: - first_name: Francesco full_name: Montagna, Francesco last_name: Montagna - first_name: Nicoletta full_name: Noceti, Nicoletta last_name: Noceti - first_name: Lorenzo full_name: Rosasco, Lorenzo last_name: Rosasco - first_name: Kun full_name: Zhang, Kun last_name: Zhang - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Causal discovery with score matching on additive models with arbitrary noise. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.' apa: Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Causal discovery with score matching on additive models with arbitrary noise. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany. chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” In 2nd Conference on Causal Learning and Reasoning, 2023. ieee: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Causal discovery with score matching on additive models with arbitrary noise,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023. ista: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Causal discovery with score matching on additive models with arbitrary noise. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.' mla: Montagna, Francesco, et al. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” 2nd Conference on Causal Learning and Reasoning, 2023. short: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023. conference: end_date: 2023-04-14 location: Tübingen, Germany name: 'CLeaR: Conference on Causal Learning and Reasoning' start_date: 2023-04-11 date_created: 2023-08-22T14:19:21Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-09-13T09:00:31Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2304.03265' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2304.03265 month: '04' oa: 1 oa_version: Preprint publication: 2nd Conference on Causal Learning and Reasoning publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Causal discovery with score matching on additive models with arbitrary noise type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14212' abstract: - lang: eng text: This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar. article_processing_charge: No author: - first_name: Francesco full_name: Montagna, Francesco last_name: Montagna - first_name: Nicoletta full_name: Noceti, Nicoletta last_name: Noceti - first_name: Lorenzo full_name: Rosasco, Lorenzo last_name: Rosasco - first_name: Kun full_name: Zhang, Kun last_name: Zhang - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Scalable causal discovery with score matching. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.' apa: Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Scalable causal discovery with score matching. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany. chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Scalable Causal Discovery with Score Matching.” In 2nd Conference on Causal Learning and Reasoning, 2023. ieee: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Scalable causal discovery with score matching,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023. ista: 'Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Scalable causal discovery with score matching. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.' mla: Montagna, Francesco, et al. “Scalable Causal Discovery with Score Matching.” 2nd Conference on Causal Learning and Reasoning, 2023. short: F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023. conference: end_date: 2023-04-14 location: Tübingen, Germany name: 'CLeaR: Conference on Causal Learning and Reasoning' start_date: 2023-04-11 date_created: 2023-08-22T14:19:40Z date_published: 2023-04-01T00:00:00Z date_updated: 2023-09-13T09:03:24Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2304.03382' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2304.03382 month: '04' oa: 1 oa_version: Preprint publication: 2nd Conference on Causal Learning and Reasoning publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Scalable causal discovery with score matching type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14214' abstract: - lang: eng text: 'Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work.' article_processing_charge: No author: - first_name: Yuejiang full_name: Liu, Yuejiang last_name: Liu - first_name: Alexandre full_name: Alahi, Alexandre last_name: Alahi - first_name: Chris full_name: Russell, Chris last_name: Russell - first_name: Max full_name: Horn, Max last_name: Horn - first_name: Dominik full_name: Zietlow, Dominik last_name: Zietlow - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Liu Y, Alahi A, Russell C, et al. Causal triplet: An open challenge for intervention-centric causal representation learning. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.' apa: 'Liu, Y., Alahi, A., Russell, C., Horn, M., Zietlow, D., Schölkopf, B., & Locatello, F. (2023). Causal triplet: An open challenge for intervention-centric causal representation learning. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.' chicago: 'Liu, Yuejiang, Alexandre Alahi, Chris Russell, Max Horn, Dominik Zietlow, Bernhard Schölkopf, and Francesco Locatello. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” In 2nd Conference on Causal Learning and Reasoning, 2023.' ieee: 'Y. Liu et al., “Causal triplet: An open challenge for intervention-centric causal representation learning,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.' ista: 'Liu Y, Alahi A, Russell C, Horn M, Zietlow D, Schölkopf B, Locatello F. 2023. Causal triplet: An open challenge for intervention-centric causal representation learning. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.' mla: 'Liu, Yuejiang, et al. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” 2nd Conference on Causal Learning and Reasoning, 2023.' short: Y. Liu, A. Alahi, C. Russell, M. Horn, D. Zietlow, B. Schölkopf, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023. conference: end_date: 2023-04-14 location: Tübingen, Germany name: 'CLeaR: Conference on Causal Learning and Reasoning' start_date: 2023-04-11 date_created: 2023-08-22T14:20:18Z date_published: 2023-04-12T00:00:00Z date_updated: 2023-09-13T09:23:08Z day: '12' department: - _id: FrLo extern: '1' external_id: arxiv: - '2301.05169' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.05169 month: '04' oa: 1 oa_version: Preprint publication: 2nd Conference on Causal Learning and Reasoning publication_status: published quality_controlled: '1' status: public title: 'Causal triplet: An open challenge for intervention-centric causal representation learning' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14217' abstract: - lang: eng text: 'Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).' article_processing_charge: No author: - first_name: Luca full_name: Moschella, Luca last_name: Moschella - first_name: Valentino full_name: Maiorca, Valentino last_name: Maiorca - first_name: Marco full_name: Fumero, Marco last_name: Fumero - first_name: Antonio full_name: Norelli, Antonio last_name: Norelli - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Emanuele full_name: Rodolà, Emanuele last_name: Rodolà citation: ama: 'Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. Relative representations enable zero-shot latent space communication. In: The 11th International Conference on Learning Representations. ; 2023.' apa: Moschella, L., Maiorca, V., Fumero, M., Norelli, A., Locatello, F., & Rodolà, E. (2023). Relative representations enable zero-shot latent space communication. In The 11th International Conference on Learning Representations. Kigali, Rwanda. chicago: Moschella, Luca, Valentino Maiorca, Marco Fumero, Antonio Norelli, Francesco Locatello, and Emanuele Rodolà. “Relative Representations Enable Zero-Shot Latent Space Communication.” In The 11th International Conference on Learning Representations, 2023. ieee: L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, and E. Rodolà, “Relative representations enable zero-shot latent space communication,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023. ista: Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. 2023. Relative representations enable zero-shot latent space communication. The 11th International Conference on Learning Representations. International Conference on Machine Learning Representations. mla: Moschella, Luca, et al. “Relative Representations Enable Zero-Shot Latent Space Communication.” The 11th International Conference on Learning Representations, 2023. short: L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, E. Rodolà, in:, The 11th International Conference on Learning Representations, 2023. conference: end_date: 2023-05-05 location: Kigali, Rwanda name: International Conference on Machine Learning Representations start_date: 2023-05-01 date_created: 2023-08-22T14:22:20Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-09-13T09:44:26Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2209.15430' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2209.15430 month: '05' oa: 1 oa_version: Preprint publication: The 11th International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: Relative representations enable zero-shot latent space communication type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14222' abstract: - lang: eng text: Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional "dead leaves" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set. article_number: '2110.06562' article_processing_charge: No author: - first_name: Matthias full_name: Tangemann, Matthias last_name: Tangemann - first_name: Steffen full_name: Schneider, Steffen last_name: Schneider - first_name: Julius von full_name: Kügelgen, Julius von last_name: Kügelgen - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Peter full_name: Gehler, Peter last_name: Gehler - first_name: Thomas full_name: Brox, Thomas last_name: Brox - first_name: Matthias full_name: Kümmerer, Matthias last_name: Kümmerer - first_name: Matthias full_name: Bethge, Matthias last_name: Bethge - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: 'Tangemann M, Schneider S, Kügelgen J von, et al. Unsupervised object learning via common fate. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.' apa: Tangemann, M., Schneider, S., Kügelgen, J. von, Locatello, F., Gehler, P., Brox, T., … Schölkopf, B. (2023). Unsupervised object learning via common fate. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany. chicago: Tangemann, Matthias, Steffen Schneider, Julius von Kügelgen, Francesco Locatello, Peter Gehler, Thomas Brox, Matthias Kümmerer, Matthias Bethge, and Bernhard Schölkopf. “Unsupervised Object Learning via Common Fate.” In 2nd Conference on Causal Learning and Reasoning, 2023. ieee: M. Tangemann et al., “Unsupervised object learning via common fate,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023. ista: 'Tangemann M, Schneider S, Kügelgen J von, Locatello F, Gehler P, Brox T, Kümmerer M, Bethge M, Schölkopf B. 2023. Unsupervised object learning via common fate. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning, 2110.06562.' mla: Tangemann, Matthias, et al. “Unsupervised Object Learning via Common Fate.” 2nd Conference on Causal Learning and Reasoning, 2110.06562, 2023. short: M. Tangemann, S. Schneider, J. von Kügelgen, F. Locatello, P. Gehler, T. Brox, M. Kümmerer, M. Bethge, B. Schölkopf, in:, 2nd Conference on Causal Learning and Reasoning, 2023. conference: end_date: 2023-04-14 location: Tübingen, Germany name: 'CLeaR: Conference on Causal Learning and Reasoning' start_date: 2023-04-11 date_created: 2023-08-22T14:23:54Z date_published: 2023-04-15T00:00:00Z date_updated: 2023-09-13T11:31:14Z day: '15' department: - _id: FrLo extern: '1' external_id: arxiv: - '2110.06562' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2110.06562 month: '04' oa: 1 oa_version: Preprint publication: 2nd Conference on Causal Learning and Reasoning publication_status: published quality_controlled: '1' status: public title: Unsupervised object learning via common fate type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14218' abstract: - lang: eng text: Humans naturally decompose their environment into entities at the appropriate level of abstraction to act in the world. Allowing machine learning algorithms to derive this decomposition in an unsupervised way has become an important line of research. However, current methods are restricted to simulated data or require additional information in the form of motion or depth in order to successfully discover objects. In this work, we overcome this limitation by showing that reconstructing features from models trained in a self-supervised manner is a sufficient training signal for object-centric representations to arise in a fully unsupervised way. Our approach, DINOSAUR, significantly out-performs existing image-based object-centric learning models on simulated data and is the first unsupervised object-centric model that scales to real-world datasets such as COCO and PASCAL VOC. DINOSAUR is conceptually simple and shows competitive performance compared to more involved pipelines from the computer vision literature. article_processing_charge: No author: - first_name: Maximilian full_name: Seitzer, Maximilian last_name: Seitzer - first_name: Max full_name: Horn, Max last_name: Horn - first_name: Andrii full_name: Zadaianchuk, Andrii last_name: Zadaianchuk - first_name: Dominik full_name: Zietlow, Dominik last_name: Zietlow - first_name: Tianjun full_name: Xiao, Tianjun last_name: Xiao - first_name: Carl-Johann Simon-Gabriel full_name: Carl-Johann Simon-Gabriel, Carl-Johann Simon-Gabriel last_name: Carl-Johann Simon-Gabriel - first_name: Tong full_name: He, Tong last_name: He - first_name: Zheng full_name: Zhang, Zheng last_name: Zhang - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Thomas full_name: Brox, Thomas last_name: Brox - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Seitzer M, Horn M, Zadaianchuk A, et al. Bridging the gap to real-world object-centric learning. In: The 11th International Conference on Learning Representations. ; 2023.' apa: Seitzer, M., Horn, M., Zadaianchuk, A., Zietlow, D., Xiao, T., Carl-Johann Simon-Gabriel, C.-J. S.-G., … Locatello, F. (2023). Bridging the gap to real-world object-centric learning. In The 11th International Conference on Learning Representations. Kigali, Rwanda. chicago: Seitzer, Maximilian, Max Horn, Andrii Zadaianchuk, Dominik Zietlow, Tianjun Xiao, Carl-Johann Simon-Gabriel Carl-Johann Simon-Gabriel, Tong He, et al. “Bridging the Gap to Real-World Object-Centric Learning.” In The 11th International Conference on Learning Representations, 2023. ieee: M. Seitzer et al., “Bridging the gap to real-world object-centric learning,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023. ista: 'Seitzer M, Horn M, Zadaianchuk A, Zietlow D, Xiao T, Carl-Johann Simon-Gabriel C-JS-G, He T, Zhang Z, Schölkopf B, Brox T, Locatello F. 2023. Bridging the gap to real-world object-centric learning. The 11th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Seitzer, Maximilian, et al. “Bridging the Gap to Real-World Object-Centric Learning.” The 11th International Conference on Learning Representations, 2023. short: M. Seitzer, M. Horn, A. Zadaianchuk, D. Zietlow, T. Xiao, C.-J.S.-G. Carl-Johann Simon-Gabriel, T. He, Z. Zhang, B. Schölkopf, T. Brox, F. Locatello, in:, The 11th International Conference on Learning Representations, 2023. conference: end_date: 2023-05-05 location: Kigali, Rwanda name: 'ICLR: International Conference on Learning Representations' start_date: 2023-05-01 date_created: 2023-08-22T14:22:41Z date_published: 2023-05-10T00:00:00Z date_updated: 2023-09-13T11:37:03Z day: '10' department: - _id: FrLo extern: '1' external_id: arxiv: - '2209.14860' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2209.14860 month: '05' oa: 1 oa_version: Preprint publication: The 11th International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: Bridging the gap to real-world object-centric learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14219' abstract: - lang: eng text: "In this paper, we show that recent advances in self-supervised feature\r\nlearning enable unsupervised object discovery and semantic segmentation with a\r\nperformance that matches the state of the field on supervised semantic\r\nsegmentation 10 years ago. We propose a methodology based on unsupervised\r\nsaliency masks and self-supervised feature clustering to kickstart object\r\ndiscovery followed by training a semantic segmentation network on pseudo-labels\r\nto bootstrap the system on images with multiple objects. We present results on\r\nPASCAL VOC that go far beyond the current state of the art (50.0 mIoU), and we\r\nreport for the first time results on MS COCO for the whole set of 81 classes:\r\nour method discovers 34 categories with more than $20\\%$ IoU, while obtaining\r\nan average IoU of 19.6 for all 81 categories." article_processing_charge: No author: - first_name: Andrii full_name: Zadaianchuk, Andrii last_name: Zadaianchuk - first_name: Matthaeus full_name: Kleindessner, Matthaeus last_name: Kleindessner - first_name: Yi full_name: Zhu, Yi last_name: Zhu - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Thomas full_name: Brox, Thomas last_name: Brox citation: ama: 'Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. Unsupervised semantic segmentation with self-supervised object-centric representations. In: The 11th International Conference on Learning Representations. ; 2023.' apa: Zadaianchuk, A., Kleindessner, M., Zhu, Y., Locatello, F., & Brox, T. (2023). Unsupervised semantic segmentation with self-supervised object-centric representations. In The 11th International Conference on Learning Representations. Kigali, Rwanda. chicago: Zadaianchuk, Andrii, Matthaeus Kleindessner, Yi Zhu, Francesco Locatello, and Thomas Brox. “Unsupervised Semantic Segmentation with Self-Supervised Object-Centric Representations.” In The 11th International Conference on Learning Representations, 2023. ieee: A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, and T. Brox, “Unsupervised semantic segmentation with self-supervised object-centric representations,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023. ista: 'Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. 2023. Unsupervised semantic segmentation with self-supervised object-centric representations. The 11th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Zadaianchuk, Andrii, et al. “Unsupervised Semantic Segmentation with Self-Supervised Object-Centric Representations.” The 11th International Conference on Learning Representations, 2023. short: A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, T. Brox, in:, The 11th International Conference on Learning Representations, 2023. conference: end_date: 2023-05-05 location: Kigali, Rwanda name: 'ICLR: International Conference on Learning Representations' start_date: 2023-05-01 date_created: 2023-08-22T14:22:58Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-09-13T11:25:43Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2207.05027' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2207.05027 month: '05' oa: 1 oa_version: Preprint publication: The 11th International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: Unsupervised semantic segmentation with self-supervised object-centric representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14333' abstract: - lang: eng text: "As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection." article_number: '2307.09552' article_processing_charge: No author: - first_name: Philipp M. full_name: Faller, Philipp M. last_name: Faller - first_name: Leena Chennuru full_name: Vankadara, Leena Chennuru last_name: Vankadara - first_name: Atalanti A. full_name: Mastakouri, Atalanti A. last_name: Mastakouri - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Dominik full_name: Janzing, Dominik last_name: Janzing citation: ama: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552' apa: 'Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. arXiv. https://doi.org/10.48550/arXiv.2307.09552' chicago: 'Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.' ieee: 'P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” arXiv. .' ista: 'Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.' mla: 'Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.' short: P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.). date_created: 2023-09-13T12:44:59Z date_published: 2023-07-18T00:00:00Z date_updated: 2023-09-13T12:47:53Z day: '18' department: - _id: FrLo doi: 10.48550/arXiv.2307.09552 extern: '1' external_id: arxiv: - '2307.09552' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2307.09552 month: '07' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Self-compatibility: Evaluating causal discovery without ground truth' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14277' abstract: - lang: eng text: Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels. acknowledgement: We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS. article_number: '013001' article_processing_charge: Yes article_type: original author: - first_name: Daniel R full_name: Boocock, Daniel R id: 453AF628-F248-11E8-B48F-1D18A9856A87 last_name: Boocock orcid: 0000-0002-1585-2631 - first_name: Tsuyoshi full_name: Hirashima, Tsuyoshi last_name: Hirashima - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001 apa: Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001 chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001. ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023. ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001. mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001. short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023). date_created: 2023-09-06T08:30:59Z date_published: 2023-07-20T00:00:00Z date_updated: 2023-09-15T06:39:17Z day: '20' ddc: - '570' department: - _id: EdHa doi: 10.1103/prxlife.1.013001 ec_funded: 1 file: - access_level: open_access checksum: f881d98c89eb9f1aa136d7b781511553 content_type: application/pdf creator: dernst date_created: 2023-09-15T06:30:50Z date_updated: 2023-09-15T06:30:50Z file_id: '14335' file_name: 2023_PRXLife_Boocock.pdf file_size: 2559520 relation: main_file success: 1 file_date_updated: 2023-09-15T06:30:50Z has_accepted_license: '1' intvolume: ' 1' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: PRX Life publication_identifier: issn: - 2835-8279 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers 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: 1 year: '2023' ... --- _id: '14314' abstract: - lang: eng text: The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations. acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616). article_number: '113015' article_processing_charge: Yes article_type: original author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 - first_name: Karola full_name: Käfer, Karola id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87 last_name: Käfer - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 2023;42(9). doi:10.1016/j.celrep.2023.113015 apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015 chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015. ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” Cell Reports, vol. 42, no. 9. Elsevier, 2023. ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015. mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier, 2023, doi:10.1016/j.celrep.2023.113015. short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023). date_created: 2023-09-10T22:01:11Z date_published: 2023-09-26T00:00:00Z date_updated: 2023-09-15T07:14:12Z day: '26' ddc: - '570' department: - _id: JoCs doi: 10.1016/j.celrep.2023.113015 ec_funded: 1 external_id: pmid: - '37632747' file: - access_level: open_access checksum: ca77a304fb813c292550b8604b0fb41d content_type: application/pdf creator: dernst date_created: 2023-09-15T07:12:46Z date_updated: 2023-09-15T07:12:46Z file_id: '14337' file_name: 2023_CellPress_Nardin.pdf file_size: 4879455 relation: main_file success: 1 file_date_updated: 2023-09-15T07:12:46Z has_accepted_license: '1' intvolume: ' 42' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 257BBB4C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '607616' name: Inter-and intracellular signalling in schizophrenia publication: Cell Reports publication_identifier: eissn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions 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: 42 year: '2023' ... --- _id: '14315' abstract: - lang: eng text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels. acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.' article_number: RP89066 article_processing_charge: Yes article_type: original author: - first_name: Ukrae H. full_name: Cho, Ukrae H. last_name: Cho - first_name: Martin W full_name: Hetzer, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: Hetzer orcid: 0000-0002-2111-992X citation: ama: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066 apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.89066 chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066. ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12. eLife Sciences Publications, 2023. ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066. mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066. short: U.H. Cho, M. Hetzer, ELife 12 (2023). date_created: 2023-09-10T22:01:11Z date_published: 2023-09-04T00:00:00Z date_updated: 2023-09-15T07:07:10Z day: '04' ddc: - '570' department: - _id: MaHe doi: 10.7554/eLife.89066 external_id: pmid: - '37665327' file: - access_level: open_access checksum: db24bf3d595507387b48d3799c33e289 content_type: application/pdf creator: dernst date_created: 2023-09-15T06:59:10Z date_updated: 2023-09-15T06:59:10Z file_id: '14336' file_name: 2023_eLife_Cho.pdf file_size: 3703097 relation: main_file success: 1 file_date_updated: 2023-09-15T06:59:10Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress 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: 12 year: '2023' ... --- _id: '14319' abstract: - lang: eng text: "We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities." acknowledgement: Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434). article_number: P3.10 article_processing_charge: Yes article_type: original author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos - first_name: David full_name: Fabian, David last_name: Fabian - first_name: Alp full_name: Müyesser, Alp last_name: Müyesser - first_name: Tibor full_name: Szabó, Tibor last_name: Szabó citation: ama: Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3). doi:10.37236/11714 apa: Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714 chicago: Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714. ieee: M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023. ista: Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10. mla: Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:10.37236/11714. short: M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023). date_created: 2023-09-10T22:01:12Z date_published: 2023-07-28T00:00:00Z date_updated: 2023-09-15T08:12:30Z day: '28' ddc: - '510' department: - _id: MaKw doi: 10.37236/11714 ec_funded: 1 external_id: arxiv: - '2212.03100' file: - access_level: open_access checksum: 52c46c8cb329f9aaee9ade01525f317b content_type: application/pdf creator: dernst date_created: 2023-09-15T08:02:09Z date_updated: 2023-09-15T08:02:09Z file_id: '14338' file_name: 2023_elecJournCombinatorics_Anastos.pdf file_size: 247917 relation: main_file success: 1 file_date_updated: 2023-09-15T08:02:09Z has_accepted_license: '1' intvolume: ' 30' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2023' ... --- _id: '14318' abstract: - lang: eng text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice." acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Yican full_name: Sun, Yican last_name: Sun - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: Computer Aided Verification. Vol 13966. Springer Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2' apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In Computer Aided Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2' chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2. ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 16–39. ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.' mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:10.1007/978-3-031-37709-9_2. short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2023-09-10T22:01:12Z date_published: 2023-07-17T00:00:00Z date_updated: 2023-09-20T08:25:57Z day: '17' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-031-37709-9_2 ec_funded: 1 file: - access_level: open_access checksum: 42917e086f8c7699f3bccf84f74fe000 content_type: application/pdf creator: dernst date_created: 2023-09-20T08:24:47Z date_updated: 2023-09-20T08:24:47Z file_id: '14348' file_name: 2023_LNCS_Sun.pdf file_size: 624647 relation: main_file success: 1 file_date_updated: 2023-09-20T08:24:47Z has_accepted_license: '1' intvolume: ' 13966' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 16-39 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Computer Aided Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783031377082' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/boyvolcano/PRR scopus_import: '1' status: public title: Automated tail bound analysis for probabilistic recurrence relations 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: 13966 year: '2023' ... --- _id: '14317' abstract: - lang: eng text: "Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples." acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: S. full_name: Akshay, S. last_name: Akshay - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 citation: ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: International Conference on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5' apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In International Conference on Computer Aided Verification (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5' chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In International Conference on Computer Aided Verification, 13966:86–112. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.' ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 86–112.' ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.' mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” International Conference on Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.' short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2023-09-10T22:01:12Z date_published: 2023-07-17T00:00:00Z date_updated: 2023-09-20T09:04:40Z day: '17' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-031-37709-9_5 ec_funded: 1 file: - access_level: open_access checksum: f143c8eedf609f20f2aad2eeb496d53f content_type: application/pdf creator: dernst date_created: 2023-09-20T08:46:43Z date_updated: 2023-09-20T08:46:43Z file_id: '14349' file_name: 2023_LNCS_Akshay.pdf file_size: 531745 relation: main_file success: 1 file_date_updated: 2023-09-20T08:46:43Z has_accepted_license: '1' intvolume: ' 13966' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 86-112 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: International Conference on Computer Aided Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783031377082' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives' 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: 13966 year: '2023' ... --- _id: '14316' abstract: - lang: eng text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway. article_number: jcs261448 article_processing_charge: No article_type: original author: - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Kaito full_name: Aoshima, Kaito last_name: Aoshima - first_name: Hiroki full_name: Shimamura, Hiroki last_name: Shimamura - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Junko Y. full_name: Toshima, Junko Y. last_name: Toshima - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448 apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., & Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261448 chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448. ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol. 136, no. 17. The Company of Biologists, 2023. ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448. mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448. short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023). date_created: 2023-09-10T22:01:12Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-09-20T09:14:15Z day: '01' department: - _id: DaSi doi: 10.1242/jcs.261448 external_id: pmid: - '37539494' intvolume: ' 136' issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.03.27.534325 month: '09' oa: 1 oa_version: Preprint pmid: 1 publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2023' ... --- _id: '14320' abstract: - lang: eng text: The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance. acknowledgement: A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations. article_number: '125411' article_processing_charge: No article_type: original author: - first_name: Paul M full_name: Henderson, Paul M id: 13C09E74-18D9-11E9-8878-32CFE5697425 last_name: Henderson orcid: 0000-0002-5198-7445 - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Alexander A. full_name: Zibrov, Alexander A. last_name: Zibrov - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411' apa: 'Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.125411' chicago: 'Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.' ieee: 'P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12. American Physical Society, 2023.' ista: 'Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.' mla: 'Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.' short: P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023). date_created: 2023-09-12T07:12:12Z date_published: 2023-09-15T00:00:00Z date_updated: 2023-09-20T09:38:24Z day: '15' department: - _id: MaSe - _id: ChLa - _id: MiLe doi: 10.1103/physrevb.108.125411 external_id: arxiv: - '2210.06310' intvolume: ' 108' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.06310 month: '09' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '12732' abstract: - lang: eng text: "Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 citation: ama: Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732 apa: Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732 chicago: Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732. ieee: P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023. ista: Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. mla: Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732. short: P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023. date_created: 2023-03-17T13:30:48Z date_published: 2023-03-21T00:00:00Z date_updated: 2023-09-20T10:44:12Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:12732 ec_funded: 1 file: - access_level: closed checksum: 5d2de651ef9449c1b8dc27148ca74777 content_type: application/zip creator: pbrighi date_created: 2023-03-23T16:42:56Z date_updated: 2023-03-23T16:42:56Z file_id: '12753' file_name: Thesis_sub_PBrighi.zip file_size: 42167561 relation: source_file - access_level: open_access checksum: 7caa153d4a5b0873a79358787d2dfe1e content_type: application/pdf creator: pbrighi date_created: 2023-03-23T16:43:14Z date_updated: 2023-03-23T16:43:14Z file_id: '12754' file_name: Thesis_PBrighi.pdf file_size: 13977000 relation: main_file success: 1 file_date_updated: 2023-03-23T16:43:14Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa: 1 oa_version: None page: '158' project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11470' relation: part_of_dissertation status: public - id: '8308' relation: part_of_dissertation status: public - id: '11469' relation: part_of_dissertation status: public - id: '12750' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: Ergodicity breaking in disordered and kinetically constrained quantum many-body systems 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: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14334' abstract: - lang: eng text: Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies. acknowledgement: "We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI)." article_number: '093' article_processing_charge: No article_type: original author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 2023;15(3). doi:10.21468/scipostphys.15.3.093 apa: Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093 chicago: Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093. ieee: P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” SciPost Physics, vol. 15, no. 3. SciPost Foundation, 2023. ista: Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093. mla: Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.3.093. short: P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023). date_created: 2023-09-14T13:08:23Z date_published: 2023-09-13T00:00:00Z date_updated: 2023-09-20T10:46:29Z day: '13' ddc: - '530' department: - _id: MaSe doi: 10.21468/scipostphys.15.3.093 ec_funded: 1 external_id: arxiv: - '2210.15607' file: - access_level: open_access checksum: 4cef6a8021f6b6c47ab2f2f2b1387ac2 content_type: application/pdf creator: dernst date_created: 2023-09-20T10:46:10Z date_updated: 2023-09-20T10:46:10Z file_id: '14350' file_name: 2023_SciPostPhysics_Brighi.pdf file_size: 4866506 relation: main_file success: 1 file_date_updated: 2023-09-20T10:46:10Z has_accepted_license: '1' intvolume: ' 15' issue: '3' keyword: - General Physics and Astronomy language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' related_material: record: - id: '12750' relation: earlier_version status: public status: public title: Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models 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: 15 year: '2023' ... --- _id: '14321' abstract: - lang: eng text: We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers. acknowledgement: "We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot." article_number: '104103' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ragheed full_name: Al Hyder, Ragheed id: d1c405be-ae15-11ed-8510-ccf53278162e last_name: Al Hyder - first_name: Alberto full_name: Cappellaro, Alberto id: 9d13b3cb-30a2-11eb-80dc-f772505e8660 last_name: Cappellaro orcid: 0000-0001-6110-2359 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 2023;159(10). doi:10.1063/5.0165806 apa: Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806 chicago: Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806. ieee: R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” The Journal of Chemical Physics, vol. 159, no. 10. AIP Publishing, 2023. ista: Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103. mla: Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806. short: R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023). date_created: 2023-09-13T09:25:09Z date_published: 2023-09-11T00:00:00Z date_updated: 2023-09-20T09:48:12Z day: '11' ddc: - '530' department: - _id: MiLe doi: 10.1063/5.0165806 ec_funded: 1 external_id: arxiv: - '2306.17592' pmid: - '37694742' file: - access_level: open_access checksum: 507ab65ab29e2c987c94cabad7c5370b content_type: application/pdf creator: acappell date_created: 2023-09-13T09:34:20Z date_updated: 2023-09-13T09:34:20Z file_id: '14322' file_name: 104103_1_5.0165806.pdf file_size: 5749653 relation: main_file success: 1 file_date_updated: 2023-09-13T09:34:20Z has_accepted_license: '1' intvolume: ' 159' issue: '10' keyword: - Physical and Theoretical Chemistry - General Physics and Astronomy language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd7b5202-d553-11ed-ba76-9b1c1b258338 grant_number: '101062862' name: Non-equilibrium Field Theory of Molecular Rotations - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Achiral dipoles on a ferromagnet can affect its magnetization direction 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: 159 year: '2023' ... --- _id: '14342' abstract: - lang: eng text: We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors. acknowledgement: The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley. article_number: '091104' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9). doi:10.1063/5.0161713 apa: Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0161713 chicago: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713. ieee: D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” Applied Physics Letters, vol. 123, no. 9. AIP Publishing, 2023. ista: Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104. mla: Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713. short: D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023). date_created: 2023-09-17T22:01:09Z date_published: 2023-08-28T00:00:00Z date_updated: 2023-09-20T11:50:06Z day: '28' ddc: - '530' department: - _id: ZhAl doi: 10.1063/5.0161713 external_id: arxiv: - '2306.09043' file: - access_level: open_access checksum: 89a1b604d58b209fec66c6b6f919ac98 content_type: application/pdf creator: dernst date_created: 2023-09-20T11:36:16Z date_updated: 2023-09-20T11:36:16Z file_id: '14353' file_name: 2023_ApplPhysLetter_Lorenc.pdf file_size: 1486715 relation: main_file success: 1 file_date_updated: 2023-09-20T11:36:16Z has_accepted_license: '1' intvolume: ' 123' issue: '9' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Applied Physics Letters publication_identifier: issn: - 0003-6951 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam 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: 123 year: '2023' ... --- _id: '14341' abstract: - lang: eng text: Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines. acknowledged_ssus: - _id: M-Shop - _id: ScienComp acknowledgement: We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688. article_processing_charge: No article_type: original author: - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74. doi:10.1038/s41586-023-06399-5 apa: Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06399-5 chicago: Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5. ieee: D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023. ista: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74. mla: Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:10.1038/s41586-023-06399-5. short: D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74. date_created: 2023-09-17T22:01:09Z date_published: 2023-09-07T00:00:00Z date_updated: 2023-09-20T12:10:22Z day: '07' department: - _id: BjHo doi: 10.1038/s41586-023-06399-5 external_id: pmid: - '37673988' intvolume: ' 621' issue: '7977' language: - iso: eng month: '09' oa_version: None page: 71-74 pmid: 1 project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows' - _id: 238B8092-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: I04188 name: Instabilities in pulsating pipe flow of Newtonian and complex fluids publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://www.ista.ac.at/en/news/pumping-like-the-heart/ scopus_import: '1' status: public title: Turbulence suppression by cardiac-cycle-inspired driving of pipe flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 621 year: '2023' ... --- _id: '13120' abstract: - lang: eng text: 'We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.' acknowledgement: "Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. " alternative_title: - LIPIcs article_number: '15' article_processing_charge: No author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette citation: ama: 'Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15' apa: 'Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15' chicago: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15. ieee: M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268. ista: 'Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.' mla: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15. short: M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-08-04 location: Bialystok, Poland name: 'ITP: International Conference on Interactive Theorem Proving' start_date: 2023-07-31 date_created: 2023-06-05T07:29:05Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-09-25T11:04:29Z day: '27' ddc: - '000' department: - _id: GradSch - _id: VlKo doi: 10.4230/LIPIcs.ITP.2023.15 external_id: arxiv: - '2302.06420' file: - access_level: open_access checksum: 773a0197f05b67feaa6cb1e17ec3642d content_type: application/pdf creator: dernst date_created: 2023-08-07T11:55:43Z date_updated: 2023-08-07T11:55:43Z file_id: '13982' file_name: 2023_LIPIcS_Dvorak.pdf file_size: 715976 relation: main_file success: 1 file_date_updated: 2023-08-07T11:55:43Z has_accepted_license: '1' intvolume: ' 268' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: 14th International Conference on Interactive Theorem Proving publication_identifier: eissn: - 1868-8969 isbn: - '9783959772846' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: link: - relation: software url: https://github.com/madvorak/grammars/tree/publish scopus_import: '1' status: public title: Closure properties of general grammars - formally verified 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: 268 year: '2023' ... --- _id: '13969' abstract: - lang: eng text: "Bundling crossings is a strategy which can enhance the readability\r\nof graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany two edges have at most one common point which can be a common vertex or a\r\ncrossing. Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation of the bundled crossing number of a good drawing with no toothed\r\nhole. In general the number of toothed holes has to be added to the 8-approximation.\r\nIn the special case of circular drawings the approximation factor is 8, this improves\r\nupon the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce. We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe pseudosegments is bipartite and has no toothed hole." acknowledgement: This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1. An extended abstract of this paper has been published in the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395. article_processing_charge: Yes article_type: original author: - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Stefan full_name: Felsner, Stefan last_name: Felsner citation: ama: Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629 apa: Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00629 chicago: Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications. Brown University, 2023. https://doi.org/10.7155/jgaa.00629. ieee: A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University, pp. 433–457, 2023. ista: Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 27(6), 433–457. mla: Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6, Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629. short: A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications 27 (2023) 433–457. date_created: 2023-08-06T22:01:11Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-09-25T10:56:10Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.7155/jgaa.00629 ec_funded: 1 external_id: arxiv: - '2109.14892' file: - access_level: open_access checksum: 9c30d2b8e324cc1c904f2aeec92013a3 content_type: application/pdf creator: dernst date_created: 2023-08-07T08:00:48Z date_updated: 2023-08-07T08:00:48Z file_id: '13979' file_name: 2023_JourGraphAlgorithms_Arroyo.pdf file_size: 865774 relation: main_file success: 1 file_date_updated: 2023-08-07T08:00:48Z has_accepted_license: '1' intvolume: ' 27' issue: '6' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 433-457 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Graph Algorithms and Applications publication_identifier: issn: - 1526-1719 publication_status: published publisher: Brown University quality_controlled: '1' related_material: record: - id: '11185' relation: earlier_version status: public scopus_import: '1' status: public title: Approximating the bundled crossing number 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: 27 year: '2023' ... --- _id: '14344' abstract: - lang: eng text: We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively, each being best possible in its own setting. article_processing_charge: No author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos citation: ama: 'Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88' apa: 'Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88' chicago: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch88. ieee: M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, vol. 2023, pp. 2286–2323. ista: 'Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.' mla: Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:10.1137/1.9781611977554.ch88. short: M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323. conference: end_date: 2023-01-25 location: Florence, Italy name: 'SODA: Symposium on Discrete Algorithms' start_date: 2023-01-22 date_created: 2023-09-17T22:01:10Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-09-25T09:13:41Z day: '01' department: - _id: MaKw doi: 10.1137/1.9781611977554.ch88 external_id: arxiv: - '2111.14759' intvolume: ' 2023' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2111.14759 month: '01' oa: 1 oa_version: Preprint page: 2286-2323 publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: isbn: - '9781611977554' publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Fast algorithms for solving the Hamilton cycle problem with high probability type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '12710' abstract: - lang: eng text: Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes. acknowledgement: B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science. article_number: '2206110' article_processing_charge: No article_type: review author: - first_name: Barbara full_name: Schamberger, Barbara last_name: Schamberger - first_name: Ricardo full_name: Ziege, Ricardo last_name: Ziege - first_name: Karine full_name: Anselme, Karine last_name: Anselme - first_name: Martine full_name: Ben Amar, Martine last_name: Ben Amar - first_name: Michał full_name: Bykowski, Michał last_name: Bykowski - first_name: André P.G. full_name: Castro, André P.G. last_name: Castro - first_name: Amaia full_name: Cipitria, Amaia last_name: Cipitria - first_name: Rhoslyn A. full_name: Coles, Rhoslyn A. last_name: Coles - first_name: Rumiana full_name: Dimova, Rumiana last_name: Dimova - first_name: Michaela full_name: Eder, Michaela last_name: Eder - first_name: Sebastian full_name: Ehrig, Sebastian last_name: Ehrig - first_name: Luis M. full_name: Escudero, Luis M. last_name: Escudero - first_name: Myfanwy E. full_name: Evans, Myfanwy E. last_name: Evans - first_name: Paulo R. full_name: Fernandes, Paulo R. last_name: Fernandes - first_name: Peter full_name: Fratzl, Peter last_name: Fratzl - first_name: Liesbet full_name: Geris, Liesbet last_name: Geris - first_name: Notburga full_name: Gierlinger, Notburga last_name: Gierlinger - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Aleš full_name: Iglič, Aleš last_name: Iglič - first_name: Jacob J.K. full_name: Kirkensgaard, Jacob J.K. last_name: Kirkensgaard - first_name: Philip full_name: Kollmannsberger, Philip last_name: Kollmannsberger - first_name: Łucja full_name: Kowalewska, Łucja last_name: Kowalewska - first_name: Nicholas A. full_name: Kurniawan, Nicholas A. last_name: Kurniawan - first_name: Ioannis full_name: Papantoniou, Ioannis last_name: Papantoniou - first_name: Laurent full_name: Pieuchot, Laurent last_name: Pieuchot - first_name: Tiago H.V. full_name: Pires, Tiago H.V. last_name: Pires - first_name: Lars D. full_name: Renner, Lars D. last_name: Renner - first_name: Andrew O. full_name: Sageman-Furnas, Andrew O. last_name: Sageman-Furnas - first_name: Gerd E. full_name: Schröder-Turk, Gerd E. last_name: Schröder-Turk - first_name: Anupam full_name: Sengupta, Anupam last_name: Sengupta - first_name: Vikas R. full_name: Sharma, Vikas R. last_name: Sharma - first_name: Antonio full_name: Tagua, Antonio last_name: Tagua - first_name: Caterina full_name: Tomba, Caterina last_name: Tomba - first_name: Xavier full_name: Trepat, Xavier last_name: Trepat - first_name: Sarah L. full_name: Waters, Sarah L. last_name: Waters - first_name: Edwina F. full_name: Yeo, Edwina F. last_name: Yeo - first_name: Andreas full_name: Roschger, Andreas last_name: Roschger - first_name: Cécile M. full_name: Bidan, Cécile M. last_name: Bidan - first_name: John W.C. full_name: Dunlop, John W.C. last_name: Dunlop citation: ama: 'Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110' apa: 'Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110' chicago: 'Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.' ieee: 'B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.' ista: 'Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.' mla: 'Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.' short: B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023). date_created: 2023-03-05T23:01:06Z date_published: 2023-03-29T00:00:00Z date_updated: 2023-09-26T10:56:46Z day: '29' ddc: - '570' department: - _id: EdHa doi: 10.1002/adma.202206110 external_id: isi: - '000941068900001' pmid: - '36461812' file: - access_level: open_access checksum: 5c04d68130e97a0ecd1ca27fbc15a246 content_type: application/pdf creator: dernst date_created: 2023-09-26T10:51:56Z date_updated: 2023-09-26T10:51:56Z file_id: '14373' file_name: 2023_AdvancedMaterials_Schamberger.pdf file_size: 2898063 relation: main_file success: 1 file_date_updated: 2023-09-26T10:51:56Z has_accepted_license: '1' intvolume: ' 35' isi: 1 issue: '13' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Curvature in biological systems: Its quantification, emergence, and implications across the scales' 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: 35 year: '2023' ... --- _id: '13340' abstract: - lang: eng text: Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation. acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)]. article_processing_charge: No article_type: original author: - first_name: Julius full_name: Gemen, Julius last_name: Gemen - first_name: Jonathan R. full_name: Church, Jonathan R. last_name: Church - first_name: Tero-Petri full_name: Ruoko, Tero-Petri last_name: Ruoko - first_name: Nikita full_name: Durandin, Nikita last_name: Durandin - first_name: Michał J. full_name: Białek, Michał J. last_name: Białek - first_name: Maren full_name: Weissenfels, Maren last_name: Weissenfels - first_name: Moran full_name: Feller, Moran last_name: Feller - first_name: Miri full_name: Kazes, Miri last_name: Kazes - first_name: Veniamin A. full_name: Borin, Veniamin A. last_name: Borin - first_name: Magdalena full_name: Odaybat, Magdalena last_name: Odaybat - first_name: Rishir full_name: Kalepu, Rishir last_name: Kalepu - first_name: Yael full_name: Diskin-Posner, Yael last_name: Diskin-Posner - first_name: Dan full_name: Oron, Dan last_name: Oron - first_name: Matthew J. full_name: Fuchter, Matthew J. last_name: Fuchter - first_name: Arri full_name: Priimagi, Arri last_name: Priimagi - first_name: Igor full_name: Schapiro, Igor last_name: Schapiro - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059 apa: Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adh9059 chicago: Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059. ieee: J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization under confinement,” Science, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023. ista: Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363. mla: Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059. short: J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363. date_created: 2023-08-01T08:26:15Z date_published: 2023-09-22T00:00:00Z date_updated: 2023-10-03T08:11:26Z day: '22' department: - _id: RaKl doi: 10.1126/science.adh9059 intvolume: ' 381' issue: '6664' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2023-gq2h0 month: '09' oa: 1 oa_version: Preprint page: 1357-1363 publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Disequilibrating azoarenes by visible-light sensitization under confinement type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 381 year: '2023' ... --- _id: '12705' abstract: - lang: eng text: The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system. acknowledgement: We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France. article_number: '074905' article_processing_charge: No article_type: original author: - first_name: Valerio full_name: Sorichetti, Valerio id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b last_name: Sorichetti orcid: 0000-0002-9645-6576 - first_name: Andrea full_name: Ninarello, Andrea last_name: Ninarello - first_name: José full_name: Ruiz-Franco, José last_name: Ruiz-Franco - first_name: Virginie full_name: Hugouvieux, Virginie last_name: Hugouvieux - first_name: Emanuela full_name: Zaccarelli, Emanuela last_name: Zaccarelli - first_name: Cristian full_name: Micheletti, Cristian last_name: Micheletti - first_name: Walter full_name: Kob, Walter last_name: Kob - first_name: Lorenzo full_name: Rovigatti, Lorenzo last_name: Rovigatti citation: ama: Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 2023;158(7). doi:10.1063/5.0134271 apa: Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271 chicago: Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271. ieee: V. Sorichetti et al., “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” Journal of Chemical Physics, vol. 158, no. 7. American Institute of Physics, 2023. ista: Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905. mla: Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271. short: V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023). date_created: 2023-03-05T23:01:05Z date_published: 2023-02-21T00:00:00Z date_updated: 2023-10-03T11:31:51Z day: '21' department: - _id: AnSa doi: 10.1063/5.0134271 external_id: arxiv: - '2211.04810' isi: - '000936943800002' pmid: - '36813705' intvolume: ' 158' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.04810 month: '02' oa: 1 oa_version: Preprint pmid: 1 publication: Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: American Institute of Physics quality_controlled: '1' scopus_import: '1' status: public title: Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 158 year: '2023' ... --- _id: '12738' abstract: - lang: eng text: We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies. acknowledgement: Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Stefanie full_name: Mohr, Stefanie last_name: Mohr - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. Formal Methods in System Design. 2023. doi:10.1007/s10703-023-00411-4 apa: Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2023). Stochastic games with lexicographic objectives. Formal Methods in System Design. Springer Nature. https://doi.org/10.1007/s10703-023-00411-4 chicago: Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design. Springer Nature, 2023. https://doi.org/10.1007/s10703-023-00411-4. ieee: K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” Formal Methods in System Design. Springer Nature, 2023. ista: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic games with lexicographic objectives. Formal Methods in System Design. mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design, Springer Nature, 2023, doi:10.1007/s10703-023-00411-4. short: K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design (2023). date_created: 2023-03-19T23:00:59Z date_published: 2023-03-08T00:00:00Z date_updated: 2023-10-03T11:36:13Z day: '08' ddc: - '000' department: - _id: KrCh doi: 10.1007/s10703-023-00411-4 ec_funded: 1 external_id: isi: - '000946174300001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10703-023-00411-4 month: '03' oa: 1 oa_version: Published Version project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Formal Methods in System Design publication_identifier: eissn: - 1572-8102 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8272' relation: earlier_version status: public scopus_import: '1' status: public title: Stochastic games with lexicographic objectives 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 year: '2023' ... --- _id: '14279' abstract: - lang: eng text: "The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt." article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 citation: ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960 apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960 chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960. ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023. ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960. mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960. short: M.C. Ucar, (2023). date_created: 2023-09-06T08:39:25Z date_published: 2023-07-11T00:00:00Z date_updated: 2023-10-03T11:42:58Z day: '11' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.8133960 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8133960 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14274' relation: used_in_publication status: public status: public title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration" 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '10405' abstract: - lang: eng text: 'We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. ' acknowledgement: L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023. ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034. mla: Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028. short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034. date_created: 2021-12-05T23:01:41Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-10-04T09:22:55Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1002/cpa.22028 ec_funded: 1 external_id: arxiv: - '1912.04100' isi: - '000724652500001' file: - access_level: open_access checksum: 8346bc2642afb4ccb7f38979f41df5d9 content_type: application/pdf creator: dernst date_created: 2023-10-04T09:21:48Z date_updated: 2023-10-04T09:21:48Z file_id: '14388' file_name: 2023_CommPureMathematics_Cipolloni.pdf file_size: 803440 relation: main_file success: 1 file_date_updated: 2023-10-04T09:21:48Z has_accepted_license: '1' intvolume: ' 76' isi: 1 issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 946-1034 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Communications on Pure and Applied Mathematics publication_identifier: eissn: - 1097-0312 issn: - 0010-3640 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices 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: 76 year: '2023' ... --- _id: '10770' abstract: - lang: eng text: Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings. acknowledgement: "The authors would like to acknowledge stimulating email discussions with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors would like to acknowledge partial support from the Australian Research Council under the Discovery grant DP180101602 and support by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411." article_processing_charge: No article_type: original author: - first_name: Thomas full_name: Graham, Thomas last_name: Graham - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina - first_name: Jerzy A. full_name: Filar, Jerzy A. last_name: Filar citation: ama: Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 2023;13:231-264. doi:10.1007/s13235-022-00425-3 apa: Graham, T., Kleshnina, M., & Filar, J. A. (2023). Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. Springer Nature. https://doi.org/10.1007/s13235-022-00425-3 chicago: Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications. Springer Nature, 2023. https://doi.org/10.1007/s13235-022-00425-3. ieee: T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey of games with incompetent players,” Dynamic Games and Applications, vol. 13. Springer Nature, pp. 231–264, 2023. ista: Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 13, 231–264. mla: Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications, vol. 13, Springer Nature, 2023, pp. 231–64, doi:10.1007/s13235-022-00425-3. short: T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023) 231–264. date_created: 2022-02-20T23:01:32Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-10-04T09:24:30Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1007/s13235-022-00425-3 ec_funded: 1 external_id: isi: - '000753777100001' file: - access_level: open_access checksum: cd53b07e96f9030ddb348f305e5b58c7 content_type: application/pdf creator: dernst date_created: 2022-02-21T08:54:17Z date_updated: 2022-02-21T08:54:17Z file_id: '10781' file_name: 2022_DynamicGamesApplic_Graham.pdf file_size: 1890512 relation: main_file success: 1 file_date_updated: 2022-02-21T08:54:17Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 231-264 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Dynamic Games and Applications publication_identifier: eissn: - 2153-0793 issn: - 2153-0785 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Where do mistakes lead? A survey of games with incompetent players 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: '2023' ... --- _id: '10145' abstract: - lang: eng text: We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique. acknowledgement: The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lorenzo full_name: Dello Schiavo, Lorenzo id: ECEBF480-9E4F-11EA-B557-B0823DDC885E last_name: Dello Schiavo orcid: 0000-0002-9881-6870 citation: ama: Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y apa: Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y chicago: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis. Springer Nature, 2023. https://doi.org/10.1007/s11118-021-09951-y. ieee: L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615, 2023. ista: Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615. mla: Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature, 2023, pp. 573–615, doi:10.1007/s11118-021-09951-y. short: L. Dello Schiavo, Potential Analysis 58 (2023) 573–615. date_created: 2021-10-17T22:01:17Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-10-04T09:19:12Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s11118-021-09951-y ec_funded: 1 external_id: arxiv: - '2003.01366' isi: - '000704213400001' file: - access_level: open_access checksum: 625526482be300ca7281c91c30d41725 content_type: application/pdf creator: dernst date_created: 2023-10-04T09:18:59Z date_updated: 2023-10-04T09:18:59Z file_id: '14387' file_name: 2023_PotentialAnalysis_DelloSchiavo.pdf file_size: 806391 relation: main_file success: 1 file_date_updated: 2023-10-04T09:18:59Z has_accepted_license: '1' intvolume: ' 58' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 573-615 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Potential Analysis publication_identifier: eissn: - 1572-929X issn: - 0926-2601 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Ergodic decomposition of Dirichlet forms via direct integrals and applications 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: 58 year: '2023' ... --- _id: '12669' abstract: - lang: eng text: The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader. article_number: koac346 article_processing_charge: No article_type: original author: - first_name: Pablo A full_name: Manavella, Pablo A last_name: Manavella - first_name: Micaela A full_name: Godoy Herz, Micaela A last_name: Godoy Herz - first_name: Alberto R full_name: Kornblihtt, Alberto R last_name: Kornblihtt - first_name: Reed full_name: Sorenson, Reed last_name: Sorenson - first_name: Leslie E full_name: Sieburth, Leslie E last_name: Sieburth - first_name: Kentaro full_name: Nakaminami, Kentaro last_name: Nakaminami - first_name: Motoaki full_name: Seki, Motoaki last_name: Seki - first_name: Yiliang full_name: Ding, Yiliang last_name: Ding - first_name: Qianwen full_name: Sun, Qianwen last_name: Sun - first_name: Hunseung full_name: Kang, Hunseung last_name: Kang - first_name: Federico D full_name: Ariel, Federico D last_name: Ariel - first_name: Martin full_name: Crespi, Martin last_name: Crespi - first_name: Axel J full_name: Giudicatti, Axel J last_name: Giudicatti - first_name: Qiang full_name: Cai, Qiang last_name: Cai - first_name: Hailing full_name: Jin, Hailing last_name: Jin - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Yijun full_name: Qi, Yijun last_name: Qi - first_name: Craig S full_name: Pikaard, Craig S last_name: Pikaard citation: ama: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346' apa: 'Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac346' chicago: 'Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koac346.' ieee: 'P. A. Manavella et al., “Beyond transcription: compelling open questions in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University Press, 2023.' ista: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.' mla: 'Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:10.1093/plcell/koac346.' short: P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023). date_created: 2023-02-23T09:14:59Z date_published: 2023-06-01T00:00:00Z date_updated: 2023-10-04T09:48:43Z day: '01' department: - _id: XiFe doi: 10.1093/plcell/koac346 extern: '1' external_id: pmid: - '36477566' intvolume: ' 35' issue: '6' keyword: - Cell Biology - Plant Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/plcell/koac346 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Beyond transcription: compelling open questions in plant RNA biology' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2023' ... --- _id: '11706' abstract: - lang: eng text: 'We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. ' acknowledgement: "This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Anita full_name: Liebenau, Anita last_name: Liebenau - first_name: Letícia full_name: Mattos, Letícia last_name: Mattos - first_name: Walner full_name: Mendonca Dos Santos, Walner id: 12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd last_name: Mendonca Dos Santos - first_name: Jozef full_name: Skokan, Jozef last_name: Skokan citation: ama: Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 2023;62(4):1035-1055. doi:10.1002/rsa.21106 apa: Liebenau, A., Mattos, L., Mendonca dos Santos, W., & Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.21106 chicago: Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106. ieee: A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” Random Structures and Algorithms, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023. ista: Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055. mla: Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106. short: A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055. date_created: 2022-07-31T22:01:49Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-10-04T09:38:45Z day: '01' ddc: - '510' department: - _id: MaKw doi: 10.1002/rsa.21106 external_id: isi: - '000828530400001' file: - access_level: open_access checksum: 3a5969d0c512aef01c30f3dc81c6d59b content_type: application/pdf creator: dernst date_created: 2023-10-04T09:37:26Z date_updated: 2023-10-04T09:37:26Z file_id: '14389' file_name: 2023_RandomStructureAlgorithms_Liebenau.pdf file_size: 1362334 relation: main_file success: 1 file_date_updated: 2023-10-04T09:37:26Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1035-1055 publication: Random Structures and Algorithms publication_identifier: eissn: - 1098-2418 issn: - 1042-9832 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Asymmetric Ramsey properties of random graphs involving cliques and cycles 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: 62 year: '2023' ... --- _id: '12707' abstract: - lang: eng text: We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail. article_processing_charge: No article_type: original author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Yuanyuan full_name: Xu, Yuanyuan id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3 last_name: Xu orcid: 0000-0003-1559-1205 citation: ama: Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 2023;29(2):1063-1079. doi:10.3150/22-BEJ1490 apa: Erdös, L., & Xu, Y. (2023). Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/22-BEJ1490 chicago: Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2023. https://doi.org/10.3150/22-BEJ1490. ieee: L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue of Wigner matrices,” Bernoulli, vol. 29, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1063–1079, 2023. ista: Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079. mla: Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” Bernoulli, vol. 29, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2023, pp. 1063–79, doi:10.3150/22-BEJ1490. short: L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079. date_created: 2023-03-05T23:01:05Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-10-04T10:21:07Z day: '01' department: - _id: LaEr doi: 10.3150/22-BEJ1490 ec_funded: 1 external_id: arxiv: - '2112.12093 ' isi: - '000947270100008' intvolume: ' 29' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2112.12093 month: '05' oa: 1 oa_version: Preprint page: 1063-1079 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Bernoulli publication_identifier: issn: - 1350-7265 publication_status: published publisher: Bernoulli Society for Mathematical Statistics and Probability quality_controlled: '1' scopus_import: '1' status: public title: Small deviation estimates for the largest eigenvalue of Wigner matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2023' ... --- _id: '12837' abstract: - lang: eng text: As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues. acknowledgement: 'We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).' article_processing_charge: No article_type: original author: - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra - first_name: Amrita full_name: Singh, Amrita id: 76250f9f-3a21-11eb-9a80-a6180a0d7958 last_name: Singh - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 2023;19:1050-1058. doi:10.1038/s41567-023-01977-w apa: Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w chicago: Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w. ieee: L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023. ista: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058. mla: Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:10.1038/s41567-023-01977-w. short: L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058. date_created: 2023-04-16T22:01:09Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-10-04T11:14:05Z day: '01' ddc: - '570' department: - _id: EdHa - _id: AnKi doi: 10.1038/s41567-023-01977-w ec_funded: 1 external_id: isi: - '000964029300003' file: - access_level: open_access checksum: 858225a4205b74406e5045006cdd853f content_type: application/pdf creator: dernst date_created: 2023-10-04T11:13:28Z date_updated: 2023-10-04T11:13:28Z file_id: '14392' file_name: 2023_NaturePhysics_Boncanegra.pdf file_size: 5532285 relation: main_file success: 1 file_date_updated: 2023-10-04T11:13:28Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1050-1058 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F07802 name: Morphogen control of growth and pattern in the spinal cord - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13081' relation: dissertation_contains status: public scopus_import: '1' status: public title: Cell cycle dynamics control fluidity of the developing mouse neuroepithelium 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: 19 year: '2023' ... --- _id: '13081' abstract: - lang: eng text: During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis. acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra citation: ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081 apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081 chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081. ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023. ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081. short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T19:10:42Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-10-04T11:14:04Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:13081 file: - access_level: closed checksum: 74f3f89e59a0189bee53ebfad9c1b9af content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lbocaneg date_created: 2023-05-25T06:32:12Z date_updated: 2023-05-25T06:32:12Z file_id: '13089' file_name: Thesis_final_LauraBocanegra.docx file_size: 25615534 relation: source_file - access_level: closed checksum: c6cdef6323eacfb4b7a8af20f32eae97 content_type: application/pdf creator: lbocaneg date_created: 2023-05-25T06:32:16Z date_updated: 2023-05-25T06:32:16Z embargo: 2024-05-31 embargo_to: open_access file_id: '13090' file_name: TotalFinal_Thesis_LauraBocanegraArx.pdf file_size: 12386046 relation: main_file file_date_updated: 2023-05-25T06:32:16Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '93' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9349' relation: part_of_dissertation status: public - id: '12837' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Epithelial dynamics during mouse neural tube development 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: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12863' abstract: - lang: eng text: In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems. acknowledgement: 'The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”' article_processing_charge: No article_type: original author: - first_name: Vlatka full_name: Filipović Marijić, Vlatka last_name: Filipović Marijić - first_name: Nesrete full_name: Krasnici, Nesrete id: cb5852d4-287f-11ed-baf0-bc1dd2d5c745 last_name: Krasnici - first_name: Damir full_name: Valić, Damir last_name: Valić - first_name: Damir full_name: Kapetanović, Damir last_name: Kapetanović - first_name: Irena full_name: Vardić Smrzlić, Irena last_name: Vardić Smrzlić - first_name: Maja full_name: Jordanova, Maja last_name: Jordanova - first_name: Katerina full_name: Rebok, Katerina last_name: Rebok - first_name: Sheriban full_name: Ramani, Sheriban last_name: Ramani - first_name: Vasil full_name: Kostov, Vasil last_name: Kostov - first_name: Rodne full_name: Nastova, Rodne last_name: Nastova - first_name: Zrinka full_name: Dragun, Zrinka last_name: Dragun citation: ama: Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2 apa: Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2 chicago: Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2. ieee: V. Filipović Marijić et al., “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” Environmental Science and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023. ista: Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521. mla: Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2. short: V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521. date_created: 2023-04-23T22:01:03Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-10-04T11:23:10Z day: '01' department: - _id: LifeSc doi: 10.1007/s11356-023-26844-2 external_id: isi: - '000970917900012' pmid: - '37055686' intvolume: ' 30' isi: 1 language: - iso: eng month: '05' oa_version: None page: 63510-63521 pmid: 1 publication: Environmental Science and Pollution Research publication_identifier: eissn: - 1614-7499 issn: - 0944-1344 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2023' ...