--- _id: '9618' abstract: - lang: eng text: The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science. acknowledgement: 'We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.' article_processing_charge: No article_type: original author: - first_name: D. full_name: Bluvstein, D. last_name: Bluvstein - first_name: A. full_name: Omran, A. last_name: Omran - first_name: H. full_name: Levine, H. last_name: Levine - first_name: A. full_name: Keesling, A. last_name: Keesling - first_name: G. full_name: Semeghini, G. last_name: Semeghini - first_name: S. full_name: Ebadi, S. last_name: Ebadi - first_name: T. T. full_name: Wang, T. T. last_name: Wang - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: N. full_name: Maskara, N. last_name: Maskara - first_name: W. W. full_name: Ho, W. W. last_name: Ho - first_name: S. full_name: Choi, S. last_name: Choi - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: M. full_name: Greiner, M. last_name: Greiner - first_name: V. full_name: Vuletić, V. last_name: Vuletić - first_name: M. D. full_name: Lukin, M. D. last_name: Lukin citation: ama: Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530 apa: Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530 chicago: Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530. ieee: D. Bluvstein et al., “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021. ista: Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359. mla: Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530. short: D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359. date_created: 2021-06-29T12:04:05Z date_published: 2021-03-26T00:00:00Z date_updated: 2023-08-10T13:57:07Z day: '26' ddc: - '539' department: - _id: MaSe doi: 10.1126/science.abg2530 ec_funded: 1 external_id: arxiv: - '2012.12276' isi: - '000636043400048' pmid: - '33632894' file: - access_level: open_access checksum: 0b356fd10ab9bb95177d4c047d4e9c1a content_type: application/pdf creator: patrickd date_created: 2021-09-23T14:00:05Z date_updated: 2021-09-23T14:00:05Z file_id: '10040' file_name: scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf file_size: 3671159 relation: main_file success: 1 file_date_updated: 2021-09-23T14:00:05Z has_accepted_license: '1' intvolume: ' 371' isi: 1 issue: '6536' keyword: - Multidisciplinary language: - iso: eng month: '03' oa: 1 oa_version: Preprint page: 1355-1359 pmid: 1 project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: Controlling quantum many-body dynamics in driven Rydberg atom arrays type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 371 year: '2021' ... --- _id: '9657' abstract: - lang: eng text: To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia. article_processing_charge: No article_type: original author: - first_name: Z full_name: Gao, Z last_name: Gao - first_name: Z full_name: Chen, Z last_name: Chen - first_name: Y full_name: Cui, Y last_name: Cui - first_name: M full_name: Ke, M last_name: Ke - first_name: H full_name: Xu, H last_name: Xu - first_name: Q full_name: Xu, Q last_name: Xu - first_name: J full_name: Chen, J last_name: Chen - first_name: Y full_name: Li, Y last_name: Li - first_name: L full_name: Huang, L last_name: Huang - first_name: H full_name: Zhao, H last_name: Zhao - first_name: D full_name: Huang, D last_name: Huang - first_name: S full_name: Mai, S last_name: Mai - first_name: T full_name: Xu, T last_name: Xu - first_name: X full_name: Liu, X last_name: Liu - first_name: S full_name: Li, S last_name: Li - first_name: Y full_name: Guan, Y last_name: Guan - first_name: W full_name: Yang, W last_name: Yang - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: J full_name: Petrášek, J last_name: Petrášek - first_name: J full_name: Zhang, J last_name: Zhang - first_name: X full_name: Chen, X last_name: Chen citation: ama: Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183 apa: Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183 chicago: Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183. ieee: Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021. ista: Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003. mla: Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183. short: Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003. date_created: 2021-07-14T15:32:43Z date_published: 2021-07-07T00:00:00Z date_updated: 2023-08-10T14:01:41Z day: '07' ddc: - '580' department: - _id: JiFr doi: 10.1093/plcell/koab183 external_id: isi: - '000702165300012' pmid: - '34240197' file: - access_level: open_access checksum: 6715712ec306c321f0204c817b7f8ae7 content_type: application/pdf creator: cziletti date_created: 2021-07-19T12:13:34Z date_updated: 2021-07-19T12:13:34Z file_id: '9691' file_name: 2021_PlantCell_Gao.pdf file_size: 10566921 relation: main_file success: 1 file_date_updated: 2021-07-19T12:13:34Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: 2981–3003 pmid: 1 publication: Plant Cell publication_identifier: eissn: - 1532-298x issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: GmPIN-dependent polar auxin transport is involved in soybean nodule 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: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2021' ... --- _id: '9640' abstract: - lang: eng text: 'Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.' acknowledgement: 'K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.' article_number: '4009' article_processing_charge: No article_type: original author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w. ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009. mla: Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w. short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021). date_created: 2021-07-11T22:01:15Z date_published: 2021-06-29T00:00:00Z date_updated: 2023-08-10T14:05:09Z day: '29' ddc: - '510' department: - _id: KrCh doi: 10.1038/s41467-021-24271-w ec_funded: 1 external_id: isi: - '000671752100003' pmid: - '34188036' file: - access_level: open_access checksum: 5767418926a7f7fb76151de29473dae0 content_type: application/pdf creator: cziletti date_created: 2021-07-19T13:02:20Z date_updated: 2021-07-19T13:02:20Z file_id: '9692' file_name: 2021_NatCoom_Tkadlec.pdf file_size: 628992 relation: main_file success: 1 file_date_updated: 2021-07-19T13:02:20Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Fast and strong amplifiers of natural selection 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9656' abstract: - lang: eng text: Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment. acknowledgement: We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: SS full_name: Alotaibi, SS last_name: Alotaibi - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617 apa: Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617 chicago: Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617. ieee: H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021. ista: Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522. mla: Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617. short: H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522. date_created: 2021-07-14T15:29:14Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-08-10T14:02:41Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.17617 ec_funded: 1 external_id: isi: - '000680587100001' pmid: - '34254313' file: - access_level: open_access checksum: 6422a6eb329b52d96279daaee0fcf189 content_type: application/pdf creator: kschuh date_created: 2021-10-07T13:42:47Z date_updated: 2021-10-07T13:42:47Z file_id: '10105' file_name: 2021_NewPhytologist_Han.pdf file_size: 1939800 relation: main_file success: 1 file_date_updated: 2021-10-07T13:42:47Z has_accepted_license: '1' intvolume: ' 232' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 510-522 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646x publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: PIN-mediated polar auxin transport regulations in plant tropic responses 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 232 year: '2021' ... --- _id: '9679' abstract: - lang: eng text: The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment. acknowledgement: We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt. article_number: '065009' article_processing_charge: Yes article_type: original author: - first_name: David full_name: Huber, David last_name: Huber - first_name: Oleksandr V. full_name: Marchukov, Oleksandr V. last_name: Marchukov - first_name: Hans Werner full_name: Hammer, Hans Werner last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576 apa: Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576 chicago: Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576. ieee: D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021. ista: Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009. mla: Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576. short: D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021). date_created: 2021-07-18T22:01:22Z date_published: 2021-06-23T00:00:00Z date_updated: 2023-08-10T13:58:09Z day: '23' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/ac0576 ec_funded: 1 external_id: arxiv: - '2102.04961' isi: - '000664736300001' file: - access_level: open_access checksum: e39164ce7ea228d287cf8924e1a0f9fe content_type: application/pdf creator: cziletti date_created: 2021-07-19T11:47:16Z date_updated: 2021-07-19T11:47:16Z file_id: '9690' file_name: 2021_NewJPhys_Huber.pdf file_size: 3868445 relation: main_file success: 1 file_date_updated: 2021-07-19T11:47:16Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: New Journal of Physics publication_identifier: eissn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Morphology of three-body quantum states from machine 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: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 23 year: '2021' ... --- _id: '9629' abstract: - lang: eng text: Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis. acknowledgement: 'We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).' article_processing_charge: No article_type: original author: - first_name: Qiutan full_name: Yang, Qiutan last_name: Yang - first_name: Shi-lei full_name: Xue, Shi-lei id: 31D2C804-F248-11E8-B48F-1D18A9856A87 last_name: Xue - first_name: Chii Jou full_name: Chan, Chii Jou last_name: Chan - first_name: Markus full_name: Rempfler, Markus last_name: Rempfler - first_name: Dario full_name: Vischi, Dario last_name: Vischi - first_name: Francisca full_name: Maurer-Gutierrez, Francisca last_name: Maurer-Gutierrez - first_name: Takashi full_name: Hiiragi, Takashi last_name: Hiiragi - 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: Prisca full_name: Liberali, Prisca last_name: Liberali citation: ama: Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2 apa: Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2 chicago: Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2. ieee: Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021. ista: Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744. mla: Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2. short: Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744. date_created: 2021-07-04T22:01:25Z date_published: 2021-06-21T00:00:00Z date_updated: 2023-08-10T13:57:36Z day: '21' department: - _id: EdHa doi: 10.1038/s41556-021-00700-2 ec_funded: 1 external_id: isi: - '000664016300003' pmid: - '34155381' intvolume: ' 23' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.05.13.094359 month: '06' oa: 1 oa_version: Preprint page: 733–744 pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton publication: Nature Cell Biology publication_identifier: eissn: - 1476-4679 issn: - 1465-7392 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cell fate coordinates mechano-osmotic forces in intestinal crypt formation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 23 year: '2021' ... --- _id: '9626' abstract: - lang: eng text: SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors. acknowledgement: This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements. article_number: '100452' article_processing_charge: No article_type: original author: - first_name: Lizhong full_name: Su, Lizhong last_name: Su - first_name: Tao full_name: Hong, Tao last_name: Hong - first_name: Dongyang full_name: Wang, Dongyang last_name: Wang - first_name: Sining full_name: Wang, Sining last_name: Wang - first_name: Bingchao full_name: Qin, Bingchao last_name: Qin - first_name: Mengmeng full_name: Zhang, Mengmeng last_name: Zhang - first_name: Xiang full_name: Gao, Xiang last_name: Gao - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Li Dong full_name: Zhao, Li Dong last_name: Zhao citation: ama: Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452 apa: Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452 chicago: Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452. ieee: L. Su et al., “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” Materials Today Physics, vol. 20. Elsevier, 2021. ista: Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452. mla: Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452. short: L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021). date_created: 2021-07-04T22:01:24Z date_published: 2021-06-03T00:00:00Z date_updated: 2023-08-10T13:56:31Z day: '03' department: - _id: MaIb doi: 10.1016/j.mtphys.2021.100452 external_id: isi: - '000703159600010' intvolume: ' 20' isi: 1 language: - iso: eng month: '06' oa_version: None publication: Materials Today Physics publication_identifier: eissn: - 2542-5293 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2021' ... --- _id: '9778' abstract: - lang: eng text: The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses. acknowledged_ssus: - _id: SSU acknowledgement: We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J. article_number: '2912' article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Yuji full_name: Okamoto, Yuji id: 3337E116-F248-11E8-B48F-1D18A9856A87 last_name: Okamoto orcid: 0000-0003-0408-6094 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23153-5 apa: Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5 chicago: Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5. ieee: D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications, vol. 12, no. 1. Springer, 2021. ista: Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912. mla: Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications, vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5. short: D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021). date_created: 2021-08-06T07:22:55Z date_published: 2021-05-18T00:00:00Z date_updated: 2023-08-10T14:16:16Z day: '18' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41467-021-23153-5 ec_funded: 1 external_id: isi: - '000655481800014' file: - access_level: open_access checksum: 6036a8cdae95e1707c2a04d54e325ff4 content_type: application/pdf creator: kschuh date_created: 2021-12-17T11:34:50Z date_updated: 2021-12-17T11:34:50Z file_id: '10563' file_name: 2021_NatureCommunications_Vandael.pdf file_size: 3108845 relation: main_file success: 1 file_date_updated: 2021-12-17T11:34:50Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - general physics and astronomy - general biochemistry - genetics and molecular biology - general chemistry language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/ scopus_import: '1' status: public title: Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9647' abstract: - lang: eng text: 'Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.' acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).' article_processing_charge: No article_type: original author: - first_name: Tatjana full_name: Petrov, Tatjana last_name: Petrov - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin - 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: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023 apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023 chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023. ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021. ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16. mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023. short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16. date_created: 2021-07-11T22:01:18Z date_published: 2021-06-04T00:00:00Z date_updated: 2023-08-10T14:11:19Z day: '04' ddc: - '004' department: - _id: ToHe - _id: CaGu doi: 10.1016/j.tcs.2021.05.023 external_id: isi: - '000710180500002' file: - access_level: open_access checksum: d3aef34cfb13e53bba4cf44d01680793 content_type: application/pdf creator: dernst date_created: 2022-05-12T12:13:27Z date_updated: 2022-05-12T12:13:27Z file_id: '11364' file_name: 2021_TheoreticalComputerScience_Petrov.pdf file_size: 2566504 relation: main_file success: 1 file_date_updated: 2022-05-12T12:13:27Z has_accepted_license: '1' intvolume: ' 893' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1-16 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Long lived transients in gene regulation 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 893 year: '2021' ... --- _id: '9761' abstract: - lang: eng text: 'The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ' acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript. article_number: '1593' article_processing_charge: Yes article_type: original author: - first_name: Nicole A. full_name: Muench, Nicole A. last_name: Muench - first_name: Sonia full_name: Patel, Sonia last_name: Patel - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Ryan J. full_name: Donahue, Ryan J. last_name: Donahue - first_name: Akihiro full_name: Ikeda, Akihiro last_name: Ikeda - first_name: Robert W. full_name: Nickells, Robert W. last_name: Nickells citation: ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593 apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593 chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593. ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021. ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593. mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593. short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021). date_created: 2021-08-01T22:01:22Z date_published: 2021-06-25T00:00:00Z date_updated: 2023-08-10T14:14:53Z day: '25' ddc: - '570' department: - _id: SaSi doi: 10.3390/cells10071593 external_id: isi: - '000678193300001' pmid: - '34201955' file: - access_level: open_access checksum: e0497ce5c77fa3b65a538c7d6e0f6c66 content_type: application/pdf creator: cziletti date_created: 2021-08-04T14:01:30Z date_updated: 2021-08-04T14:01:30Z file_id: '9768' file_name: 2021_Cells_Muench.pdf file_size: 4555611 relation: main_file success: 1 file_date_updated: 2021-08-04T14:01:30Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Cells publication_identifier: eissn: - '20734409' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '9641' abstract: - lang: eng text: At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation. acknowledgement: This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto. article_number: '107486' article_processing_charge: No article_type: original author: - first_name: Felipe full_name: Fredes, Felipe last_name: Fredes - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486 apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486 chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486. ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021. ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486. mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486. short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021). date_created: 2021-07-11T22:01:16Z date_published: 2021-06-30T00:00:00Z date_updated: 2023-08-10T14:10:37Z day: '30' ddc: - '610' department: - _id: RySh doi: 10.1016/j.nlm.2021.107486 ec_funded: 1 external_id: isi: - '000677694900004' pmid: - '34214666' file: - access_level: open_access checksum: 8e8298a9e8c7df146ad23f32c2a63929 content_type: application/pdf creator: cziletti date_created: 2021-07-19T13:46:06Z date_updated: 2021-07-19T13:46:06Z file_id: '9694' file_name: 2021_NeurobLearnMemory_Fredes.pdf file_size: 1994793 relation: main_file success: 1 file_date_updated: 2021-07-19T13:46:06Z has_accepted_license: '1' intvolume: ' 183' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: Neurobiology of Learning and Memory publication_identifier: eissn: - '10959564' issn: - '10747427' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The role of hippocampal mossy cells in novelty detection 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 183 year: '2021' ... --- _id: '9646' abstract: - lang: eng text: We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude. acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).' article_processing_charge: No author: - first_name: Jinyi full_name: Wang, Jinyi last_name: Wang - first_name: Yican full_name: Sun, Yican last_name: Sun - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 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: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102' apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102' chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102. ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186. ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.' mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102. short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186. conference: end_date: 2021-06-26 location: Online name: 'PLDI: Programming Language Design and Implementation' start_date: 2021-06-20 date_created: 2021-07-11T22:01:18Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T14:14:08Z day: '01' department: - _id: KrCh doi: 10.1145/3453483.3454102 ec_funded: 1 external_id: arxiv: - '2011.14617' isi: - '000723661700076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2011.14617 month: '06' oa: 1 oa_version: Preprint page: 1171-1186 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450383912' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Quantitative analysis of assertion violations in probabilistic programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9645' abstract: - lang: eng text: "We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods." acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW). article_processing_charge: No author: - first_name: Ali full_name: Asadi, Ali last_name: Asadi - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Mohammad full_name: Mahdavi, Mohammad last_name: Mahdavi citation: ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076' apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076' chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076. ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787. ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.' mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076. short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787. conference: end_date: 2021-06-26 location: Online name: ' PLDI: Programming Language Design and Implementation' start_date: 2021-06-20 date_created: 2021-07-11T22:01:17Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T14:13:39Z day: '01' department: - _id: KrCh doi: 10.1145/3453483.3454076 ec_funded: 1 external_id: isi: - '000723661700050' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-03183862/ month: '06' oa: 1 oa_version: Submitted Version page: 772-787 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450383912' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Polynomial reachability witnesses via Stellensätze type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9759' acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program. article_number: e1009124 article_processing_charge: Yes article_type: letter_note author: - first_name: Michael John full_name: Bartlett, Michael John last_name: Bartlett - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Adriana full_name: Bankston, Adriana last_name: Bankston - first_name: Sarvenaz full_name: Sarabipour, Sarvenaz last_name: Sarabipour citation: ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124 apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124 chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124. ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021. ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124. mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124. short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021). date_created: 2021-08-01T22:01:21Z date_published: 2021-07-15T00:00:00Z date_updated: 2023-08-10T14:16:46Z day: '15' ddc: - '613' department: - _id: CaHe doi: 10.1371/journal.pcbi.1009124 external_id: isi: - '000677713500008' pmid: - '34264932' file: - access_level: open_access checksum: e56d91f0eeadb36f143a90e2c1b3ab63 content_type: application/pdf creator: cchlebak date_created: 2021-08-05T12:06:49Z date_updated: 2021-08-05T12:06:49Z file_id: '9771' file_name: 2021_PlosCompBio_Bartlett.pdf file_size: 693633 relation: main_file file_date_updated: 2021-08-05T12:06:49Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Computational Biology publication_identifier: eissn: - '15537358' issn: - 1553734X publication_status: published publisher: Public Library of Science scopus_import: '1' status: public title: Ten simple rules to improve academic work- life balance 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '9822' abstract: - lang: eng text: Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science. acknowledgement: We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Themistoklis full_name: Zisis, Themistoklis last_name: Zisis - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Miriam full_name: Balles, Miriam last_name: Balles - first_name: Maibritt full_name: Kretschmer, Maibritt last_name: Kretschmer - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Janina full_name: Lange, Janina last_name: Lange - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Stefan full_name: Zahler, Stefan last_name: Zahler citation: ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850 apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850 chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850. ieee: T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021. ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560. mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850. short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560. date_created: 2021-08-08T22:01:28Z date_published: 2021-08-04T00:00:00Z date_updated: 2023-08-10T14:22:48Z day: '04' ddc: - '620' - '570' department: - _id: MiSi - _id: GaTk - _id: Bio - _id: CaGu doi: 10.1021/acsami.1c09850 ec_funded: 1 external_id: isi: - '000683741400026' pmid: - '34283577' file: - access_level: open_access checksum: b043a91d9f9200e467b970b692687ed3 content_type: application/pdf creator: asandaue date_created: 2021-08-09T09:44:03Z date_updated: 2021-08-09T09:44:03Z file_id: '9833' file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf file_size: 7123293 relation: main_file success: 1 file_date_updated: 2021-08-09T09:44:03Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '30' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 35545–35560 pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - '19448252' issn: - '19448244' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Sequential and switchable patterning for studying cellular processes under spatiotemporal control 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2021' ... --- _id: '9819' abstract: - lang: eng text: Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates. acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019]. article_number: '44' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: B. R. full_name: Mallikarjun, B. R. last_name: Mallikarjun - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Abdallah full_name: Dib, Abdallah last_name: Dib - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Louis full_name: Chevallier, Louis last_name: Chevallier - first_name: Mohamed A. full_name: Elgharib, Mohamed A. last_name: Elgharib - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt citation: ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765' apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765' chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.' ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.' ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.' mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765.' short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:27Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:25:08Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1145/3450626.3459765 external_id: arxiv: - '2103.07658' isi: - '000674930900011' file: - access_level: open_access checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:41:50Z date_updated: 2021-08-09T11:41:50Z file_id: '9834' file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf file_size: 49840741 relation: main_file success: 1 file_date_updated: 2021-08-09T11:41:50Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'PhotoApp: Photorealistic appearance editing of head portraits' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9816' abstract: - lang: eng text: "Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test." acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used. article_number: e0255267 article_processing_charge: Yes article_type: original author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Mathias full_name: Beiglböck, Mathias last_name: Beiglböck - first_name: Anna Nele full_name: Herdina, Anna Nele last_name: Herdina - first_name: Robert full_name: Strassl, Robert last_name: Strassl - first_name: Martin full_name: Posch, Martin last_name: Posch citation: ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267 apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267 chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267. ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267. mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267. short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:26Z date_published: 2021-07-29T00:00:00Z date_updated: 2023-08-10T14:26:32Z day: '29' ddc: - '610' department: - _id: NiBa doi: 10.1371/journal.pone.0255267 external_id: isi: - '000685248200095' pmid: - '34324553' file: - access_level: open_access checksum: ae4df60eb62f4491278588548d0c1f93 content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:52:14Z date_updated: 2021-08-09T11:52:14Z file_id: '9835' file_name: 2021_PLoSONE_Hledík.pdf file_size: 773921 relation: main_file success: 1 file_date_updated: 2021-08-09T11:52:14Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9821' abstract: - lang: eng text: Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode. acknowledgement: We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper. article_number: e0253851 article_processing_charge: Yes article_type: original author: - first_name: Grzegorz full_name: Graff, Grzegorz last_name: Graff - first_name: Beata full_name: Graff, Beata last_name: Graff - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: Dariusz full_name: Gąsecki, Dariusz last_name: Gąsecki - first_name: Krzysztof full_name: Narkiewicz, Krzysztof last_name: Narkiewicz citation: ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851 apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851 chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851. ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851. mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851. short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:28Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-10T14:21:42Z day: '01' ddc: - '006' department: - _id: HeEd doi: 10.1371/journal.pone.0253851 external_id: isi: - '000678124900050' pmid: - '34292957' file: - access_level: open_access checksum: 0277aa155d5db1febd2cb384768bba5f content_type: application/pdf creator: asandaue date_created: 2021-08-09T09:25:41Z date_updated: 2021-08-09T09:25:41Z file_id: '9832' file_name: 2021_PLoSONE_Graff.pdf file_size: 2706919 relation: main_file success: 1 file_date_updated: 2021-08-09T09:25:41Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - '19326203' publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Persistent homology as a new method of the assessment of heart rate variability 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9820' abstract: - lang: eng text: Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design. acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY). article_number: '125' article_processing_charge: No article_type: original author: - first_name: Ana full_name: Serrano, Ana last_name: Serrano - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski citation: ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813' apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., & Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459813' chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.' ieee: 'A. Serrano et al., “The effect of shape and illumination on material perception: Model and applications,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.' ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.' mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.' short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:28Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:20:10Z day: '01' department: - _id: BeBi doi: 10.1145/3450626.3459813 external_id: isi: - '000674930900090' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf month: '08' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'The effect of shape and illumination on material perception: Model and applications' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9818' abstract: - lang: eng text: Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales. acknowledged_ssus: - _id: ScienComp acknowledgement: "We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc." article_number: '168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl - first_name: Rahul full_name: Narain, Rahul last_name: Narain - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816 apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816 chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816. ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021. ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168. mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816. short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:27Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:24:36Z day: '01' department: - _id: GradSch - _id: ChWo doi: 10.1145/3450626.3459816 ec_funded: 1 external_id: isi: - '000674930900132' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3450626.3459816 month: '08' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/knitting-virtual-yarn/ record: - id: '12358' relation: dissertation_contains status: public - id: '9327' relation: software status: public scopus_import: '1' status: public title: Mechanics-aware deformation of yarn pattern geometry type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ...