--- _id: '9911' abstract: - lang: eng text: A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics. acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg. article_processing_charge: Yes article_type: original author: - first_name: Glyn full_name: Nelson, Glyn last_name: Nelson - first_name: Ulrike full_name: Boehm, Ulrike last_name: Boehm - first_name: Steve full_name: Bagley, Steve last_name: Bagley - first_name: Peter full_name: Bajcsy, Peter last_name: Bajcsy - first_name: Johanna full_name: Bischof, Johanna last_name: Bischof - first_name: Claire M. full_name: Brown, Claire M. last_name: Brown - first_name: Aurélien full_name: Dauphin, Aurélien last_name: Dauphin - first_name: Ian M. full_name: Dobbie, Ian M. last_name: Dobbie - first_name: John E. full_name: Eriksson, John E. last_name: Eriksson - first_name: Orestis full_name: Faklaris, Orestis last_name: Faklaris - first_name: Julia full_name: Fernandez-Rodriguez, Julia last_name: Fernandez-Rodriguez - first_name: Alexia full_name: Ferrand, Alexia last_name: Ferrand - first_name: Laurent full_name: Gelman, Laurent last_name: Gelman - first_name: Ali full_name: Gheisari, Ali last_name: Gheisari - first_name: Hella full_name: Hartmann, Hella last_name: Hartmann - first_name: Christian full_name: Kukat, Christian last_name: Kukat - first_name: Alex full_name: Laude, Alex last_name: Laude - first_name: Miso full_name: Mitkovski, Miso last_name: Mitkovski - first_name: Sebastian full_name: Munck, Sebastian last_name: Munck - first_name: Alison J. full_name: North, Alison J. last_name: North - first_name: Tobias M. full_name: Rasse, Tobias M. last_name: Rasse - first_name: Ute full_name: Resch-Genger, Ute last_name: Resch-Genger - first_name: Lucas C. full_name: Schuetz, Lucas C. last_name: Schuetz - first_name: Arne full_name: Seitz, Arne last_name: Seitz - first_name: Caterina full_name: Strambio-De-Castillia, Caterina last_name: Strambio-De-Castillia - first_name: Jason R. full_name: Swedlow, Jason R. last_name: Swedlow - first_name: Ioannis full_name: Alexopoulos, Ioannis last_name: Alexopoulos - first_name: Karin full_name: Aumayr, Karin last_name: Aumayr - first_name: Sergiy full_name: Avilov, Sergiy last_name: Avilov - first_name: Gert Jan full_name: Bakker, Gert Jan last_name: Bakker - first_name: Rodrigo R. full_name: Bammann, Rodrigo R. last_name: Bammann - first_name: Andrea full_name: Bassi, Andrea last_name: Bassi - first_name: Hannes full_name: Beckert, Hannes last_name: Beckert - first_name: Sebastian full_name: Beer, Sebastian last_name: Beer - first_name: Yury full_name: Belyaev, Yury last_name: Belyaev - first_name: Jakob full_name: Bierwagen, Jakob last_name: Bierwagen - first_name: Konstantin A. full_name: Birngruber, Konstantin A. last_name: Birngruber - first_name: Manel full_name: Bosch, Manel last_name: Bosch - first_name: Juergen full_name: Breitlow, Juergen last_name: Breitlow - first_name: Lisa A. full_name: Cameron, Lisa A. last_name: Cameron - first_name: Joe full_name: Chalfoun, Joe last_name: Chalfoun - first_name: James J. full_name: Chambers, James J. last_name: Chambers - first_name: Chieh Li full_name: Chen, Chieh Li last_name: Chen - first_name: Eduardo full_name: Conde-Sousa, Eduardo last_name: Conde-Sousa - first_name: Alexander D. full_name: Corbett, Alexander D. last_name: Corbett - first_name: Fabrice P. full_name: Cordelieres, Fabrice P. last_name: Cordelieres - first_name: Elaine Del full_name: Nery, Elaine Del last_name: Nery - first_name: Ralf full_name: Dietzel, Ralf last_name: Dietzel - first_name: Frank full_name: Eismann, Frank last_name: Eismann - first_name: Elnaz full_name: Fazeli, Elnaz last_name: Fazeli - first_name: Andreas full_name: Felscher, Andreas last_name: Felscher - first_name: Hans full_name: Fried, Hans last_name: Fried - first_name: Nathalie full_name: Gaudreault, Nathalie last_name: Gaudreault - first_name: Wah Ing full_name: Goh, Wah Ing last_name: Goh - first_name: Thomas full_name: Guilbert, Thomas last_name: Guilbert - first_name: Roland full_name: Hadleigh, Roland last_name: Hadleigh - first_name: Peter full_name: Hemmerich, Peter last_name: Hemmerich - first_name: Gerhard A. full_name: Holst, Gerhard A. last_name: Holst - first_name: Michelle S. full_name: Itano, Michelle S. last_name: Itano - first_name: Claudia B. full_name: Jaffe, Claudia B. last_name: Jaffe - first_name: Helena K. full_name: Jambor, Helena K. last_name: Jambor - first_name: Stuart C. full_name: Jarvis, Stuart C. last_name: Jarvis - first_name: Antje full_name: Keppler, Antje last_name: Keppler - first_name: David full_name: Kirchenbuechler, David last_name: Kirchenbuechler - first_name: Marcel full_name: Kirchner, Marcel last_name: Kirchner - first_name: Norio full_name: Kobayashi, Norio last_name: Kobayashi - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Susanne full_name: Kunis, Susanne last_name: Kunis - first_name: Judith full_name: Lacoste, Judith last_name: Lacoste - first_name: Marco full_name: Marcello, Marco last_name: Marcello - first_name: Gabriel G. full_name: Martins, Gabriel G. last_name: Martins - first_name: Daniel J. full_name: Metcalf, Daniel J. last_name: Metcalf - first_name: Claire A. full_name: Mitchell, Claire A. last_name: Mitchell - first_name: Joshua full_name: Moore, Joshua last_name: Moore - first_name: Tobias full_name: Mueller, Tobias last_name: Mueller - first_name: Michael S. full_name: Nelson, Michael S. last_name: Nelson - first_name: Stephen full_name: Ogg, Stephen last_name: Ogg - first_name: Shuichi full_name: Onami, Shuichi last_name: Onami - first_name: Alexandra L. full_name: Palmer, Alexandra L. last_name: Palmer - first_name: Perrine full_name: Paul-Gilloteaux, Perrine last_name: Paul-Gilloteaux - first_name: Jaime A. full_name: Pimentel, Jaime A. last_name: Pimentel - first_name: Laure full_name: Plantard, Laure last_name: Plantard - first_name: Santosh full_name: Podder, Santosh last_name: Podder - first_name: Elton full_name: Rexhepaj, Elton last_name: Rexhepaj - first_name: Arnaud full_name: Royon, Arnaud last_name: Royon - first_name: Markku A. full_name: Saari, Markku A. last_name: Saari - first_name: Damien full_name: Schapman, Damien last_name: Schapman - first_name: Vincent full_name: Schoonderwoert, Vincent last_name: Schoonderwoert - first_name: Britta full_name: Schroth-Diez, Britta last_name: Schroth-Diez - first_name: Stanley full_name: Schwartz, Stanley last_name: Schwartz - first_name: Michael full_name: Shaw, Michael last_name: Shaw - first_name: Martin full_name: Spitaler, Martin last_name: Spitaler - first_name: Martin T. full_name: Stoeckl, Martin T. last_name: Stoeckl - first_name: Damir full_name: Sudar, Damir last_name: Sudar - first_name: Jeremie full_name: Teillon, Jeremie last_name: Teillon - first_name: Stefan full_name: Terjung, Stefan last_name: Terjung - first_name: Roland full_name: Thuenauer, Roland last_name: Thuenauer - first_name: Christian D. full_name: Wilms, Christian D. last_name: Wilms - first_name: Graham D. full_name: Wright, Graham D. last_name: Wright - first_name: Roland full_name: Nitschke, Roland last_name: Nitschke citation: ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041' apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041' chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.' ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.' ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.' mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.' short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73. date_created: 2021-08-15T22:01:29Z date_published: 2021-08-11T00:00:00Z date_updated: 2025-06-12T06:29:47Z day: '11' department: - _id: Bio doi: 10.1111/jmi.13041 external_id: isi: - '000683702700001' pmid: - '34214188' intvolume: ' 284' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jmi.13041 month: '08' oa: 1 oa_version: Published Version page: 56-73 pmid: 1 publication: Journal of Microscopy publication_identifier: eissn: - 1365-2818 issn: - 0022-2720 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 284 year: '2021' ... --- _id: '9912' abstract: - lang: eng text: "In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via \U0001D441≪\U0001D440 channels, the density \U0001D70C of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio \U0001D719:=\U0001D441/\U0001D440≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit \U0001D719→0, we recover the formula for the density \U0001D70C that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any \U0001D719<1 but in the borderline case \U0001D719=1 an anomalous \U0001D706−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries." acknowledgement: The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks. article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Yuriy full_name: Nemish, Yuriy id: 4D902E6A-F248-11E8-B48F-1D18A9856A87 last_name: Nemish orcid: 0000-0002-7327-856X citation: ama: Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6 apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . Springer Nature. https://doi.org/10.1007/s00023-021-01085-6 chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6. ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature, pp. 4205–4269, 2021. ista: Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269. mla: Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:10.1007/s00023-021-01085-6. short: L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269. date_created: 2021-08-15T22:01:29Z date_published: 2021-12-01T00:00:00Z date_updated: 2025-04-15T08:04:59Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00023-021-01085-6 ec_funded: 1 external_id: arxiv: - '1911.05112' isi: - '000681531500001' file: - access_level: open_access checksum: 8d6bac0e2b0a28539608b0538a8e3b38 content_type: application/pdf creator: dernst date_created: 2022-05-12T12:50:27Z date_updated: 2022-05-12T12:50:27Z file_id: '11365' file_name: 2021_AnnHenriPoincare_Erdoes.pdf file_size: 1162454 relation: main_file success: 1 file_date_updated: 2022-05-12T12:50:27Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4205–4269 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: 'Annales Henri Poincaré ' publication_identifier: eissn: - 1424-0661 issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Scattering in quantum dots via noncommutative rational functions 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: 22 year: '2021' ... --- _id: '9933' abstract: - lang: eng text: "In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto." acknowledgement: This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411. article_processing_charge: No arxiv: 1 author: - first_name: Artur full_name: Czumaj, Artur last_name: Czumaj - first_name: Peter full_name: Davies, Peter id: 11396234-BB50-11E9-B24C-90FCE5697425 last_name: Davies orcid: 0000-0002-5646-9524 - first_name: Merav full_name: Parter, Merav last_name: Parter citation: ama: 'Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:481–491. doi:10.1145/3465084.3467903' apa: 'Czumaj, A., Davies, P., & Parter, M. (2021). Component stability in low-space massively parallel computation. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 481–491). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467903' chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 481–491. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467903. ieee: A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 481–491. ista: 'Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.' mla: Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491, doi:10.1145/3465084.3467903. short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-08-17T18:11:16Z date_published: 2021-07-21T00:00:00Z date_updated: 2025-04-14T07:43:49Z day: '21' department: - _id: DaAl doi: 10.1145/3465084.3467903 ec_funded: 1 external_id: arxiv: - '2106.01880' isi: - '000744439800049' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2106.01880 month: '07' oa: 1 oa_version: Submitted Version page: 481–491 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - '9781450385480' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Component stability in low-space massively parallel computation type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9935' abstract: - lang: eng text: "We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before." acknowledgement: This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411. article_processing_charge: No author: - first_name: Artur full_name: Czumaj, Artur last_name: Czumaj - first_name: Peter full_name: Davies, Peter id: 11396234-BB50-11E9-B24C-90FCE5697425 last_name: Davies orcid: 0000-0002-5646-9524 - first_name: Merav full_name: Parter, Merav last_name: Parter citation: ama: 'Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:469–479. doi:10.1145/3465084.3467937' apa: 'Czumaj, A., Davies, P., & Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 469–479). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467937' chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 469–479. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467937. ieee: A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 469–479. ista: 'Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.' mla: Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479, doi:10.1145/3465084.3467937. short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Symposium on Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-08-17T18:14:15Z date_published: 2021-07-21T00:00:00Z date_updated: 2025-04-14T07:43:49Z day: '21' department: - _id: DaAl doi: 10.1145/3465084.3467937 ec_funded: 1 external_id: isi: - '000744439800048' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://wrap.warwick.ac.uk/153753 month: '07' oa: 1 oa_version: Submitted Version page: 469–479 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - 978-1-4503-8548-0 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Improved deterministic (Δ+1) coloring in low-space MPC type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9946' abstract: - lang: eng text: We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs. acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper. alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Fabian full_name: Mühlböck, Fabian id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425 last_name: Mühlböck orcid: 0000-0003-1548-0177 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946 apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946 chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946. ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021. ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p. mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946. short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021. date_created: 2021-08-20T20:00:37Z date_published: 2021-09-01T00:00:00Z date_updated: 2025-04-15T06:55:00Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.15479/AT:ISTA:9946 file: - access_level: open_access checksum: 0f9aafd59444cb6bdca6925d163ab946 content_type: application/pdf creator: fmuehlbo date_created: 2021-08-20T19:59:44Z date_updated: 2021-09-03T12:34:28Z file_id: '9948' file_name: differentialmonitoring-techreport.pdf file_size: '320453' relation: main_file file_date_updated: 2021-09-03T12:34:28Z has_accepted_license: '1' keyword: - run-time verification - software engineering - implicit specification language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '17' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria related_material: record: - id: '10108' relation: shorter_version status: public - id: '9281' relation: other status: public status: public title: Differential monitoring type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9949' article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949 apa: Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949 chicago: Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949. ieee: B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021. ista: Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949. mla: Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949. short: B. Vicoso, (2021). date_created: 2021-08-21T13:44:22Z date_published: 2021-08-24T00:00:00Z date_updated: 2025-04-15T07:49:47Z day: '24' department: - _id: BeVi doi: 10.15479/AT:ISTA:9949 file: - access_level: open_access checksum: 90461837eed66beac6fa302993cf0ca9 content_type: application/zip creator: bvicoso date_created: 2021-08-21T13:43:59Z date_updated: 2021-08-21T13:43:59Z file_id: '9950' file_name: Data.zip file_size: 139188306 relation: main_file success: 1 file_date_updated: 2021-08-21T13:43:59Z has_accepted_license: '1' month: '08' oa: 1 oa_version: None publisher: Institute of Science and Technology Austria related_material: record: - id: '10166' relation: used_in_publication status: public status: public title: Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9951' abstract: - lang: eng text: "There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model." acknowledgement: We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Martin full_name: Töpfer, Martin id: 4B865388-F248-11E8-B48F-1D18A9856A87 last_name: Töpfer - first_name: Przemysław full_name: Uznański, Przemysław last_name: Uznański citation: ama: 'Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:55-65. doi:10.1145/3465084.3467915' apa: 'Alistarh, D.-A., Töpfer, M., & Uznański, P. (2021). Comparison dynamics in population protocols. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 55–65). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467915' chicago: Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 55–65. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467915. ieee: D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 55–65. ista: 'Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.' mla: Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65, doi:10.1145/3465084.3467915. short: D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65. conference: end_date: 2021-07-30 location: Virtual, Italy name: 'PODC: Symposium on Principles of Distributed Computing' start_date: 2021-07-26 date_created: 2021-08-22T22:01:20Z date_published: 2021-07-21T00:00:00Z date_updated: 2023-08-11T10:56:04Z day: '21' department: - _id: DaAl doi: 10.1145/3465084.3467915 external_id: isi: - '000744439800005' isi: 1 language: - iso: eng month: '07' oa_version: None page: 55-65 publication: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing publication_identifier: isbn: - '9781450385480' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Comparison dynamics in population protocols type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9952' abstract: - lang: eng text: Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry. acknowledgement: We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support. article_number: jcs255018 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Agathe full_name: Chaigne, Agathe last_name: Chaigne - first_name: Matthew B. full_name: Smith, Matthew B. last_name: Smith - first_name: R. L. full_name: Cavestany, R. L. last_name: Cavestany - 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: Kevin J. full_name: Chalut, Kevin J. last_name: Chalut - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch citation: ama: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 2021;134(14). doi:10.1242/jcs.255018 apa: Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.255018 chicago: Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of Biologists, 2021. https://doi.org/10.1242/jcs.255018. ieee: A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists, 2021. ista: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018. mla: Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:10.1242/jcs.255018. short: A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021). date_created: 2021-08-22T22:01:20Z date_published: 2021-07-01T00:00:00Z date_updated: 2025-07-10T12:02:07Z day: '01' ddc: - '570' department: - _id: EdHa doi: 10.1242/jcs.255018 external_id: isi: - '000681395800008' file: - access_level: open_access checksum: f086f9d7cb63b2474c01921cb060c513 content_type: application/pdf creator: asandaue date_created: 2021-08-23T07:32:20Z date_updated: 2021-08-23T07:32:20Z file_id: '9954' file_name: 2021_JournalOfCellScience_Chaigne.pdf file_size: 8651724 relation: main_file success: 1 file_date_updated: 2021-08-23T07:32:20Z has_accepted_license: '1' intvolume: ' 134' isi: 1 issue: '14' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Three-dimensional geometry controls division symmetry in stem cell colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2021' ... --- _id: '9953' abstract: - lang: eng text: Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress. acknowledgement: We acknowledge that Université Laval stands on the traditional and unceded land of the Huron-Wendat peoples; and that the University of Victoria exists on the territory of the Lekwungen peoples and that the Songhees, Esquimalt and WSÁNEÆ peoples have relationships to this land. We thank Emmanuel Planel for the access to the epifluorescence microscope and Julie-Christine Lévesque at the Bioimaging Platform of CRCHU de Québec-Université Laval for technical assistance. We also thank the Centre for Advanced Materials and Related Technology for the access to the confocal microscope with Airyscan. K.P. was supported by a doctoral scholarship from Fonds de Recherche du Québec – Santé (FRQS), an excellence award from Fondation du CHU de Québec, as well as from Centre Thématique de Recherche en Neurosciences and from Fondation Famille-Choquette. K.B. was supported by excellence scholarships from Université Laval and Fondation du CHU de Québec. S.G. is supported by FIRC-AIRC fellowship for Italy 22329/2018 and by Pilot ARISLA NKINALS 2019. C.W.H. and J.C.S. were supported by postdoctoral fellowships from FRQS. This study was funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant (RGPIN-2014-05308) awarded to M.E.T., by ERANET neuron 2017 MicroSynDep to M.E.T. and I.B., and by the Italian Ministry of Health, grant RF-2018-12367249 to I.B, by PRIN 2017, AIRC 2019 and Ministero della Salute RF2018 to C.L. M.E.T. is a Tier II Canada Research Chair in Neurobiology of Aging and Cognition. article_processing_charge: No article_type: original author: - first_name: Katherine full_name: Picard, Katherine last_name: Picard - first_name: Kanchan full_name: Bisht, Kanchan last_name: Bisht - first_name: Silvia full_name: Poggini, Silvia last_name: Poggini - first_name: Stefano full_name: Garofalo, Stefano last_name: Garofalo - first_name: Maria Teresa full_name: Golia, Maria Teresa last_name: Golia - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Fatima full_name: Abdallah, Fatima last_name: Abdallah - first_name: Naomi full_name: Ciano Albanese, Naomi last_name: Ciano Albanese - first_name: Irmgard full_name: Amrein, Irmgard last_name: Amrein - first_name: Nathalie full_name: Vernoux, Nathalie last_name: Vernoux - first_name: Kaushik full_name: Sharma, Kaushik last_name: Sharma - first_name: Chin Wai full_name: Hui, Chin Wai last_name: Hui - first_name: Julie full_name: C. Savage, Julie last_name: C. Savage - first_name: Cristina full_name: Limatola, Cristina last_name: Limatola - first_name: Davide full_name: Ragozzino, Davide last_name: Ragozzino - first_name: Laura full_name: Maggi, Laura last_name: Maggi - first_name: Igor full_name: Branchi, Igor last_name: Branchi - first_name: Marie Ève full_name: Tremblay, Marie Ève last_name: Tremblay citation: ama: Picard K, Bisht K, Poggini S, et al. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 2021;97:423-439. doi:10.1016/j.bbi.2021.07.022 apa: Picard, K., Bisht, K., Poggini, S., Garofalo, S., Golia, M. T., Basilico, B., … Tremblay, M. È. (2021). Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. Elsevier. https://doi.org/10.1016/j.bbi.2021.07.022 chicago: Picard, Katherine, Kanchan Bisht, Silvia Poggini, Stefano Garofalo, Maria Teresa Golia, Bernadette Basilico, Fatima Abdallah, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity. Elsevier, 2021. https://doi.org/10.1016/j.bbi.2021.07.022. ieee: K. Picard et al., “Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice,” Brain, Behavior, and Immunity, vol. 97. Elsevier, pp. 423–439, 2021. ista: Picard K, Bisht K, Poggini S, Garofalo S, Golia MT, Basilico B, Abdallah F, Ciano Albanese N, Amrein I, Vernoux N, Sharma K, Hui CW, C. Savage J, Limatola C, Ragozzino D, Maggi L, Branchi I, Tremblay MÈ. 2021. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 97, 423–439. mla: Picard, Katherine, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” Brain, Behavior, and Immunity, vol. 97, Elsevier, 2021, pp. 423–39, doi:10.1016/j.bbi.2021.07.022. short: K. Picard, K. Bisht, S. Poggini, S. Garofalo, M.T. Golia, B. Basilico, F. Abdallah, N. Ciano Albanese, I. Amrein, N. Vernoux, K. Sharma, C.W. Hui, J. C. Savage, C. Limatola, D. Ragozzino, L. Maggi, I. Branchi, M.È. Tremblay, Brain, Behavior, and Immunity 97 (2021) 423–439. date_created: 2021-08-22T22:01:21Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-10-03T09:49:18Z day: '01' department: - _id: GaNo doi: 10.1016/j.bbi.2021.07.022 external_id: isi: - '000702878400007' pmid: - '34343616' intvolume: ' 97' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf month: '10' oa: 1 oa_version: Submitted Version page: 423-439 pmid: 1 publication: Brain, Behavior, and Immunity publication_identifier: issn: - 0889-1591 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2021' ... --- _id: '9957' abstract: - lang: eng text: The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects. acknowledgement: "We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital." article_processing_charge: No arxiv: 1 author: - first_name: Mallikarjun full_name: B R, Mallikarjun last_name: B R - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Tae-Hyun full_name: Oh, Tae-Hyun last_name: Oh - 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: Mohamed full_name: Elgharib, Mohamed last_name: Elgharib - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt citation: ama: 'B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476' apa: 'B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. https://doi.org/10.1109/CVPR46437.2021.00476' chicago: B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476. ieee: M. B R et al., “Monocular reconstruction of neural face reflectance fields,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800. ista: 'B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.' mla: B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476. short: M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800. conference: end_date: 2021-06-25 location: Nashville, TN, United States; Virtual name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2021-06-20 date_created: 2021-08-24T06:03:00Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-11T11:08:35Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1109/CVPR46437.2021.00476 external_id: arxiv: - '2008.10247' isi: - '000739917304096' file: - access_level: open_access checksum: 961db0bde76dd87cf833930080bb9f38 content_type: application/pdf creator: bbickel date_created: 2021-08-24T06:02:15Z date_updated: 2021-08-24T06:02:15Z file_id: '9958' file_name: R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf file_size: 4746649 relation: main_file file_date_updated: 2021-08-24T06:02:15Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Preprint page: 4791-4800 publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - 978-166544509-2 issn: - 1063-6919 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Monocular reconstruction of neural face reflectance fields type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9960' abstract: - lang: eng text: The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars. acknowledgement: We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini, Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.); the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories and Gauge-Gravity Correspondence – Grant No. DE-SC0021013. article_number: '090602' article_processing_charge: No article_type: letter_note arxiv: 1 author: - first_name: N. full_name: Maskara, N. last_name: Maskara - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: W. W. full_name: Ho, W. W. last_name: Ho - first_name: D. full_name: Bluvstein, D. last_name: Bluvstein - first_name: S. full_name: Choi, S. last_name: Choi - first_name: M. D. full_name: Lukin, M. D. last_name: Lukin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: 'Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602' apa: 'Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M. D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602' chicago: 'Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M. D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.' ieee: 'N. Maskara et al., “Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving,” Physical Review Letters, vol. 127, no. 9. American Physical Society, 2021.' ista: 'Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M. 2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving. Physical Review Letters. 127(9), 090602.' mla: 'Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters, vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.' short: N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021). date_created: 2021-08-28T08:08:58Z date_published: 2021-08-27T00:00:00Z date_updated: 2025-04-14T07:52:05Z day: '27' department: - _id: MaSe doi: 10.1103/PhysRevLett.127.090602 ec_funded: 1 external_id: arxiv: - '2102.13160' isi: - '000692200100002' intvolume: ' 127' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2102.13160 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 127 year: '2021' ... --- _id: '9961' abstract: - lang: eng text: The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems. acknowledgement: "We thank S. Garratt for useful comments on the manuscript. This work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A., Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1 and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations were performed on the Baobab cluster of the University\r\nof Geneva." article_number: L081112 article_processing_charge: No article_type: letter_note arxiv: 1 author: - first_name: Michael full_name: Sonner, Michael last_name: Sonner - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin citation: ama: Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 2021;104(8). doi:10.1103/PhysRevB.104.L081112 apa: Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112 chicago: Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112. ieee: M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across the many-body localization transition in Floquet systems,” Physical Review B, vol. 104, no. 8. American Physical Society, 2021. ista: Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body localization transition in Floquet systems. Physical Review B. 104(8), L081112. mla: Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112, American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112. short: M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021). date_created: 2021-08-28T16:44:55Z date_published: 2021-08-15T00:00:00Z date_updated: 2025-04-14T07:52:05Z day: '15' department: - _id: MaSe doi: 10.1103/PhysRevB.104.L081112 ec_funded: 1 external_id: arxiv: - '2012.15676' isi: - '000689734500009' intvolume: ' 104' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.15676 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Thouless energy across the many-body localization transition in Floquet systems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '9973' abstract: - lang: eng text: In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors. acknowledgement: Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Melchior full_name: Wirth, Melchior id: 88644358-0A0E-11EA-8FA5-49A33DDC885E last_name: Wirth orcid: 0000-0002-0519-4241 - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4 apa: Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4 chicago: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04199-4. ieee: M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” Communications in Mathematical Physics, vol. 387. Springer Nature, pp. 761–791, 2021. ista: Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791. mla: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4. short: M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791. corr_author: '1' date_created: 2021-08-30T10:07:44Z date_published: 2021-08-30T00:00:00Z date_updated: 2025-06-12T06:30:13Z day: '30' ddc: - '621' department: - _id: JaMa doi: 10.1007/s00220-021-04199-4 ec_funded: 1 external_id: arxiv: - '2007.13506' isi: - '000691214200001' pmid: - '34776525' file: - access_level: open_access checksum: 8a602f916b1c2b0dc1159708b7cb204b content_type: application/pdf creator: cchlebak date_created: 2021-09-08T07:34:24Z date_updated: 2021-09-08T09:46:34Z file_id: '9990' file_name: 2021_CommunMathPhys_Wirth.pdf file_size: 505971 relation: main_file file_date_updated: 2021-09-08T09:46:34Z has_accepted_license: '1' intvolume: ' 387' isi: 1 keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 761–791 pmid: 1 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Complete gradient estimates of quantum Markov semigroups tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 387 year: '2021' ... --- _id: '9978' abstract: - lang: eng text: Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents. acknowledgement: 'This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ' article_processing_charge: No author: - first_name: Deqing full_name: Cao, Deqing last_name: Cao - first_name: Xiaoxiao full_name: Shen, Xiaoxiao last_name: Shen - first_name: Aiping full_name: Wang, Aiping last_name: Wang - first_name: Fengjiao full_name: Yu, Fengjiao last_name: Yu - first_name: Yuping full_name: Wu, Yuping last_name: Wu - first_name: Siqi full_name: Shi, Siqi last_name: Shi - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen citation: ama: Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1 apa: Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1 chicago: Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square. Research Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1. ieee: D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square. ista: Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, 10.21203/rs.3.rs-750965/v1. mla: Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1. short: D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.). corr_author: '1' date_created: 2021-08-31T12:54:16Z date_published: 2021-08-18T00:00:00Z date_updated: 2024-10-09T21:01:46Z day: '18' ddc: - '541' department: - _id: StFr doi: 10.21203/rs.3.rs-750965/v1 file: - access_level: open_access checksum: 1878e91c29d5769ed5a827b0b7addf00 content_type: application/pdf creator: cchlebak date_created: 2021-08-31T14:02:19Z date_updated: 2021-08-31T14:02:19Z file_id: '9979' file_name: 2021_ResearchSquare_Cao.pdf file_size: 1019662 relation: main_file success: 1 file_date_updated: 2021-08-31T14:02:19Z has_accepted_license: '1' keyword: - Catalysis - Energy engineering - Materials theory and modeling language: - iso: eng month: '08' oa: 1 oa_version: Preprint page: '21' publication: Research Square publication_identifier: eissn: - 2693-5015 publication_status: submitted publisher: Research Square related_material: record: - id: '10813' relation: later_version status: public status: public title: Sharp kinetic acceleration potentials during mediated redox catalysis of insulators 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: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9980' abstract: - lang: eng text: Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film. acknowledgement: "This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge TU Graz for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University\r\n6 of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2-1863. S.A.F. is indebted to IST Austria for support. " article_processing_charge: No author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Sara Drvarič full_name: Talian, Sara Drvarič last_name: Talian - first_name: Alen full_name: Vizintin, Alen last_name: Vizintin - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Robert full_name: Dominko, Robert last_name: Dominko - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Vanessa full_name: Wood, Vanessa last_name: Wood citation: ama: Prehal C, Talian SD, Vizintin A, et al. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. Research Square. doi:10.21203/rs.3.rs-818607/v1 apa: Prehal, C., Talian, S. D., Vizintin, A., Amenitsch, H., Dominko, R., Freunberger, S. A., & Wood, V. (n.d.). Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. Research Square. https://doi.org/10.21203/rs.3.rs-818607/v1 chicago: Prehal, Christian, Sara Drvarič Talian, Alen Vizintin, Heinz Amenitsch, Robert Dominko, Stefan Alexander Freunberger, and Vanessa Wood. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-818607/v1. ieee: C. Prehal et al., “Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries,” Research Square. . ista: Prehal C, Talian SD, Vizintin A, Amenitsch H, Dominko R, Freunberger SA, Wood V. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. Research Square, 10.21203/rs.3.rs-818607/v1. mla: Prehal, Christian, et al. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” Research Square, doi:10.21203/rs.3.rs-818607/v1. short: C. Prehal, S.D. Talian, A. Vizintin, H. Amenitsch, R. Dominko, S.A. Freunberger, V. Wood, Research Square (n.d.). date_created: 2021-09-02T08:45:00Z date_published: 2021-08-16T00:00:00Z date_updated: 2021-12-03T10:35:42Z day: '16' ddc: - '621' department: - _id: StFr doi: 10.21203/rs.3.rs-818607/v1 keyword: - Li2S - Lithium Sulphur Batteries - SAXS - WAXS language: - iso: eng main_file_link: - open_access: '1' url: https://www.researchsquare.com/article/rs-818607/v1 month: '08' oa: 1 oa_version: Preprint page: '21' publication: Research Square publication_status: submitted status: public title: Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries 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: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9981' abstract: - lang: eng text: "The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments." article_number: '048' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Stefano full_name: De Nicola, Stefano id: 42832B76-F248-11E8-B48F-1D18A9856A87 last_name: De Nicola orcid: 0000-0002-4842-6671 citation: ama: De Nicola S. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048 apa: De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.11.3.048 chicago: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics. SciPost Foundation, 2021. https://doi.org/10.21468/scipostphys.11.3.048. ieee: S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost Foundation, 2021. ista: De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048. mla: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost Foundation, 2021, doi:10.21468/scipostphys.11.3.048. short: S. De Nicola, SciPost Physics 11 (2021). date_created: 2021-09-02T11:49:47Z date_published: 2021-09-02T00:00:00Z date_updated: 2025-05-14T10:51:45Z day: '02' ddc: - '519' department: - _id: MaSe doi: 10.21468/scipostphys.11.3.048 ec_funded: 1 external_id: arxiv: - '2103.16468' isi: - '000692534200001' file: - access_level: open_access checksum: e4ec69d893e31811efc6093cb6ea8eb7 content_type: application/pdf creator: cchlebak date_created: 2021-09-02T14:05:43Z date_updated: 2021-09-02T14:05:43Z file_id: '9984' file_name: 2021_SciPostPhys_DeNicola.pdf file_size: 373833 relation: main_file success: 1 file_date_updated: 2021-09-02T14:05:43Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '3' keyword: - General Physics and Astronomy language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: SciPost Physics publication_identifier: eissn: - 2666-9366 issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' scopus_import: '1' status: public title: Importance sampling scheme for the stochastic simulation of quantum spin dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2021' ... --- _id: '9985' abstract: - lang: eng text: AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity. acknowledgement: The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1). article_number: '5083' article_processing_charge: Yes article_type: original author: - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alexandra full_name: Pinggera, Alexandra last_name: Pinggera - first_name: Hinze full_name: Ho, Hinze last_name: Ho - first_name: Ingo H. full_name: Greger, Ingo H. last_name: Greger citation: ama: Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-25281-4 apa: Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4 chicago: Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4. ieee: J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021. ista: Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083. mla: Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4. short: J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021). date_created: 2021-09-05T22:01:23Z date_published: 2021-08-23T00:00:00Z date_updated: 2023-08-11T11:07:51Z day: '23' ddc: - '612' department: - _id: PeJo doi: 10.1038/s41467-021-25281-4 external_id: isi: - '000687672000006' pmid: - '34426577 ' file: - access_level: open_access checksum: 1bf4f6a561f96bc426d754de9cb57710 content_type: application/pdf creator: cchlebak date_created: 2021-09-08T12:57:06Z date_updated: 2021-09-08T12:57:06Z file_id: '9991' file_name: 2021_NatureCommunications_Watson.pdf file_size: 18310502 relation: main_file success: 1 file_date_updated: 2021-09-08T12:57:06Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9986' abstract: - lang: eng text: Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth. acknowledgement: "We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n" article_number: '9222' article_processing_charge: Yes article_type: original author: - first_name: Silvia Melina full_name: Velasquez, Silvia Melina last_name: Velasquez - first_name: Xiaoyuan full_name: Guo, Xiaoyuan last_name: Guo - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Bibek full_name: Aryal, Bibek last_name: Aryal - first_name: Peter full_name: Venhuizen, Peter last_name: Venhuizen - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Kai Alexander full_name: Dünser, Kai Alexander last_name: Dünser - first_name: Martin full_name: Darino, Martin last_name: Darino - first_name: Aleš full_name: Pӗnčík, Aleš last_name: Pӗnčík - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Maria full_name: Kalyna, Maria last_name: Kalyna - first_name: Gregory full_name: Mouille, Gregory last_name: Mouille - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Rishikesh P. full_name: Bhalerao, Rishikesh P. last_name: Bhalerao - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine-Vehn citation: ama: Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222 apa: Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222 chicago: Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222. ieee: S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021. ista: Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222. mla: Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222. short: S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021). corr_author: '1' date_created: 2021-09-05T22:01:24Z date_published: 2021-08-26T00:00:00Z date_updated: 2024-10-09T21:00:50Z day: '26' ddc: - '575' department: - _id: EvBe doi: 10.3390/ijms22179222 external_id: isi: - '000694347100001' pmid: - '34502129' file: - access_level: open_access checksum: 6b7055cf89f1b7ed8594c3fdf56f000b content_type: application/pdf creator: cchlebak date_created: 2021-09-06T12:50:19Z date_updated: 2021-09-07T09:04:53Z file_id: '9988' file_name: 2021_IntJMolecularSciences_Velasquez.pdf file_size: 2162247 relation: main_file file_date_updated: 2021-09-07T09:04:53Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '17' keyword: - auxin - growth - cell wall - xyloglucans - hypocotyls - gravitropism language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: eissn: - 1422-0067 issn: - 1661-6596 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2021' ... --- _id: '9998' abstract: - lang: eng text: We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice. acknowledgement: 'First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).' article_number: '87' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Peter full_name: Koroteev, Peter last_name: Koroteev - first_name: Petr full_name: Pushkar, Petr id: 151DCEB6-9EC3-11E9-8480-ABECE5697425 last_name: Pushkar - first_name: Andrey V. full_name: Smirnov, Andrey V. last_name: Smirnov - first_name: Anton M. full_name: Zeitlin, Anton M. last_name: Zeitlin citation: ama: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3 apa: Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-021-00698-3 chicago: Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica. Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3. ieee: P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27, no. 5. Springer Nature, 2021. ista: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87. mla: Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021, doi:10.1007/s00029-021-00698-3. short: P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021). date_created: 2021-09-12T22:01:22Z date_published: 2021-08-30T00:00:00Z date_updated: 2025-04-15T06:53:09Z day: '30' ddc: - '530' department: - _id: TaHa doi: 10.1007/s00029-021-00698-3 external_id: isi: - '000692795200001' file: - access_level: open_access checksum: beadc5a722ffb48190e1e63ee2dbfee5 content_type: application/pdf creator: cchlebak date_created: 2021-09-13T11:31:34Z date_updated: 2021-09-13T11:31:34Z file_id: '10010' file_name: 2021_SelectaMath_Koroteev.pdf file_size: 584648 relation: main_file success: 1 file_date_updated: 2021-09-13T11:31:34Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Selecta Mathematica publication_identifier: eissn: - 1420-9020 issn: - 1022-1824 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantum K-theory of quiver varieties and many-body systems 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: 27 year: '2021' ... --- _id: '9999' abstract: - lang: eng text: 'The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site.' article_number: e66483 article_processing_charge: Yes article_type: original author: - first_name: Eduardo full_name: Pulgar, Eduardo last_name: Pulgar - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Néstor full_name: Guerrero, Néstor last_name: Guerrero - first_name: Loreto full_name: López, Loreto last_name: López - first_name: Susana full_name: Márquez, Susana last_name: Márquez - first_name: Steffen full_name: Härtel, Steffen last_name: Härtel - first_name: Rodrigo full_name: Soto, Rodrigo last_name: Soto - first_name: Carl Philipp full_name: Heisenberg, Carl Philipp last_name: Heisenberg - first_name: Miguel L. full_name: Concha, Miguel L. last_name: Concha citation: ama: Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 2021;10. doi:10.7554/eLife.66483 apa: Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.66483 chicago: Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.66483. ieee: E. Pulgar et al., “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483. mla: Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife, vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483. short: E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021). date_created: 2021-09-12T22:01:23Z date_published: 2021-08-27T00:00:00Z date_updated: 2025-04-14T07:46:58Z day: '27' ddc: - '570' department: - _id: CaHe doi: 10.7554/eLife.66483 ec_funded: 1 external_id: isi: - '000700428500001' pmid: - '34448451' file: - access_level: open_access checksum: a3f82b0499cc822ac1eab48a01f3f57e content_type: application/pdf creator: dernst date_created: 2022-05-13T08:03:37Z date_updated: 2022-05-13T08:03:37Z file_id: '11371' file_name: 2021_eLife_Pulgar.pdf file_size: 9010446 relation: main_file success: 1 file_date_updated: 2022-05-13T08:03:37Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - cell delamination - apical constriction - dragging - mechanical forces - collective 18 locomotion - dorsal forerunner cells - zebrafish language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism 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' ...