--- _id: '17061' abstract: - lang: eng text: Across many domains of interaction, both natural and artificial, individuals use past experience to shape future behaviors. The results of such learning processes depend on what individuals wish to maximize. A natural objective is one’s own success. However, when two such “selfish” learners interact with each other, the outcome can be detrimental to both, especially when there are conflicts of interest. Here, we explore how a learner can align incentives with a selfish opponent. Moreover, we consider the dynamics that arise when learning rules themselves are subject to evolutionary pressure. By combining extensive simulations and analytical techniques, we demonstrate that selfish learning is unstable in most classical two-player repeated games. If evolution operates on the level of long-run payoffs, selection instead favors learning rules that incorporate social (other-regarding) preferences. To further corroborate these results, we analyze data from a repeated prisoner’s dilemma experiment. We find that selfish learning is insufficient to explain human behavior when there is a trade-off between payoff maximization and fairness. acknowledgement: The authors are grateful to Jörg Oechssler for many helpful comments. A.M. was supported by a Simons Postdoctoral Fellowship (Math+X) at the University of Pennsylvania; K.C. was supported by the European Research Council Consolidator Grant 863818 (ForM-SMArt); and C.H. was supported by the European Research Council Starting Grant 850529 (E-DIRECT). article_number: pgac141 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Alex full_name: McAvoy, Alex last_name: McAvoy - first_name: Julian full_name: Kates-Harbeck, Julian last_name: Kates-Harbeck - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X citation: ama: McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 2022;1(4). doi:10.1093/pnasnexus/pgac141 apa: McAvoy, A., Kates-Harbeck, J., Chatterjee, K., & Hilbe, C. (2022). Evolutionary instability of selfish learning in repeated games. PNAS Nexus. Oxford University Press. https://doi.org/10.1093/pnasnexus/pgac141 chicago: McAvoy, Alex, Julian Kates-Harbeck, Krishnendu Chatterjee, and Christian Hilbe. “Evolutionary Instability of Selfish Learning in Repeated Games.” PNAS Nexus. Oxford University Press, 2022. https://doi.org/10.1093/pnasnexus/pgac141. ieee: A. McAvoy, J. Kates-Harbeck, K. Chatterjee, and C. Hilbe, “Evolutionary instability of selfish learning in repeated games,” PNAS Nexus, vol. 1, no. 4. Oxford University Press, 2022. ista: McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. 2022. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 1(4), pgac141. mla: McAvoy, Alex, et al. “Evolutionary Instability of Selfish Learning in Repeated Games.” PNAS Nexus, vol. 1, no. 4, pgac141, Oxford University Press, 2022, doi:10.1093/pnasnexus/pgac141. short: A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022). date_created: 2024-05-28T14:23:12Z date_published: 2022-09-01T00:00:00Z date_updated: 2025-06-11T13:54:20Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1093/pnasnexus/pgac141 ec_funded: 1 external_id: arxiv: - '2105.06199' pmid: - '36714856' file: - access_level: open_access checksum: 79a8e3e4be7e8a2b407b4efddd65f3f3 content_type: application/pdf creator: dernst date_created: 2024-08-06T07:33:30Z date_updated: 2024-08-06T07:33:30Z file_id: '17400' file_name: 2022_PNASNexus_McAvoy.pdf file_size: 2410962 relation: main_file success: 1 file_date_updated: 2024-08-06T07:33:30Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: PNAS Nexus publication_identifier: issn: - 2752-6542 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/alexmcavoy/fmtl/ scopus_import: '1' status: public title: Evolutionary instability of selfish learning in repeated games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2022' ... --- _id: '17062' acknowledgement: "Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF “Lise Meitner Fellowship”" article_number: '159' article_processing_charge: No author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: ama: 'Ibáñez M, Liu Y, Calcabrini M. The importance of surface adsorbates in solution-processed thermoelectric materials. In: Proceedings of the NanoGe Spring Meeting 2022. Fundació Scito; 2022. doi:10.29363/nanoge.nsm.2022.159' apa: 'Ibáñez, M., Liu, Y., & Calcabrini, M. (2022). The importance of surface adsorbates in solution-processed thermoelectric materials. In Proceedings of the nanoGe Spring Meeting 2022. Spain/Virtual: Fundació Scito. https://doi.org/10.29363/nanoge.nsm.2022.159' chicago: Ibáñez, Maria, Yu Liu, and Mariano Calcabrini. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” In Proceedings of the NanoGe Spring Meeting 2022. Fundació Scito, 2022. https://doi.org/10.29363/nanoge.nsm.2022.159. ieee: M. Ibáñez, Y. Liu, and M. Calcabrini, “The importance of surface adsorbates in solution-processed thermoelectric materials,” in Proceedings of the nanoGe Spring Meeting 2022, Spain/Virtual, 2022. ista: 'Ibáñez M, Liu Y, Calcabrini M. 2022. The importance of surface adsorbates in solution-processed thermoelectric materials. Proceedings of the nanoGe Spring Meeting 2022. SNI: Semiconductor Nanocrystals, 159.' mla: Ibáñez, Maria, et al. “The Importance of Surface Adsorbates in Solution-Processed Thermoelectric Materials.” Proceedings of the NanoGe Spring Meeting 2022, 159, Fundació Scito, 2022, doi:10.29363/nanoge.nsm.2022.159. short: M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting 2022, Fundació Scito, 2022. conference: end_date: 2022-03-11 location: Spain/Virtual name: 'SNI: Semiconductor Nanocrystals' start_date: 2022-03-07 corr_author: '1' date_created: 2024-05-29T05:38:47Z date_published: 2022-02-07T00:00:00Z date_updated: 2025-04-15T06:54:34Z day: '07' department: - _id: MaIb doi: 10.29363/nanoge.nsm.2022.159 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.29363/nanoge.nsm.2022.159 month: '02' oa: 1 oa_version: Published Version project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Proceedings of the nanoGe Spring Meeting 2022 publication_status: published publisher: Fundació Scito quality_controlled: '1' related_material: record: - id: '10123' relation: earlier_version status: public status: public title: The importance of surface adsorbates in solution-processed thermoelectric materials type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '17063' abstract: - lang: eng text: This workshop continued a biannual series of workshops at Oberwolfach on dynamical systems that started with a meeting organized by Moser and Zehnder in 1981. Workshops in this series focus on new results and developments in dynamical systems and related areas of mathematics, with symplectic geometry playing an important role in recent years in connection with Hamiltonian dynamics. In this year special emphasis was placed on various kinds of spectra (in contact geometry, in Riemannian geometry, in dynamical systems and in symplectic topology) and their applications to dynamics. article_processing_charge: No article_type: original author: - first_name: Marie-Claude full_name: Arnaud, Marie-Claude last_name: Arnaud - first_name: Helmut W. full_name: Hofer, Helmut W. last_name: Hofer - first_name: Michael full_name: Hutchings, Michael last_name: Hutchings - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. Dynamische Systeme. Oberwolfach Reports. 2022;18(3):1735-1803. doi:10.4171/owr/2021/33 apa: Arnaud, M.-C., Hofer, H. W., Hutchings, M., & Kaloshin, V. (2022). Dynamische Systeme. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2021/33 chicago: Arnaud, Marie-Claude, Helmut W. Hofer, Michael Hutchings, and Vadim Kaloshin. “Dynamische Systeme.” Oberwolfach Reports. European Mathematical Society, 2022. https://doi.org/10.4171/owr/2021/33. ieee: M.-C. Arnaud, H. W. Hofer, M. Hutchings, and V. Kaloshin, “Dynamische Systeme,” Oberwolfach Reports, vol. 18, no. 3. European Mathematical Society, pp. 1735–1803, 2022. ista: Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. 2022. Dynamische Systeme. Oberwolfach Reports. 18(3), 1735–1803. mla: Arnaud, Marie-Claude, et al. “Dynamische Systeme.” Oberwolfach Reports, vol. 18, no. 3, European Mathematical Society, 2022, pp. 1735–803, doi:10.4171/owr/2021/33. short: M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803. corr_author: '1' date_created: 2024-05-29T06:01:19Z date_published: 2022-11-26T00:00:00Z date_updated: 2024-08-06T07:28:50Z day: '26' department: - _id: VaKa doi: 10.4171/owr/2021/33 intvolume: ' 18' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.4171/OWR/2021/33 month: '11' oa: 1 oa_version: Published Version page: 1735-1803 publication: Oberwolfach Reports publication_identifier: eissn: - 1660-8941 issn: - 1660-8933 publication_status: published publisher: European Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamische Systeme type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2022' ... --- _id: '17065' abstract: - lang: eng text: Past work on optimizing fabrication plans given a carpentry design can provide Pareto-optimal plans trading off between material waste, fabrication time, precision, and other considerations. However, when developing fabrication plans, experts rarely restrict to a single design, instead considering families of design variations, sometimes adjusting designs to simplify fabrication. Jointly exploring the design and fabrication plan spaces for each design is intractable using current techniques. We present a new approach to jointly optimize design and fabrication plans for carpentered objects. To make this bi-level optimization tractable, we adapt recent work from program synthesis based on equality graphs (e-graphs), which encode sets of equivalent programs. Our insight is that subproblems within our bi-level problem share significant substructures. By representing both designs and fabrication plans in a new bag of parts (BOP) e-graph, we amortize the cost of optimizing design components shared among multiple candidates. Even using BOP e-graphs, the optimization space grows quickly in practice. Hence, we also show how a feedback-guided search strategy dubbed Iterative Contraction and Expansion on E-graphs (ICEE) can keep the size of the e-graph manageable and direct the search towards promising candidates. We illustrate the advantages of our pipeline through examples from the carpentry domain. acknowledgement: The authors would like to thank anonymous reviewers for their helpful feedback; Haomiao Wu for her contribution to the algorithm development in the early stage of the project; Elias Baldwin, David Tsay, Alexander Lefort, and Qiyang Tan for helping the experiments. article_number: '32' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Haisen full_name: Zhao, Haisen id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4 last_name: Zhao orcid: 0000-0002-6389-1045 - first_name: Max full_name: Willsey, Max last_name: Willsey - first_name: Amy full_name: Zhu, Amy last_name: Zhu - first_name: Chandrakana full_name: Nandi, Chandrakana last_name: Nandi - first_name: Zachary full_name: Tatlock, Zachary last_name: Tatlock - first_name: Justin full_name: Solomon, Justin last_name: Solomon - first_name: Adriana full_name: Schulz, Adriana last_name: Schulz citation: ama: Zhao H, Willsey M, Zhu A, et al. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 2022;41(3). doi:10.1145/3508499 apa: Zhao, H., Willsey, M., Zhu, A., Nandi, C., Tatlock, Z., Solomon, J., & Schulz, A. (2022). Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3508499 chicago: Zhao, Haisen, Max Willsey, Amy Zhu, Chandrakana Nandi, Zachary Tatlock, Justin Solomon, and Adriana Schulz. “Co-Optimization of Design and Fabrication Plans for Carpentry.” ACM Transactions on Graphics. Association for Computing Machinery, 2022. https://doi.org/10.1145/3508499. ieee: H. Zhao et al., “Co-optimization of design and fabrication plans for carpentry,” ACM Transactions on Graphics, vol. 41, no. 3. Association for Computing Machinery, 2022. ista: Zhao H, Willsey M, Zhu A, Nandi C, Tatlock Z, Solomon J, Schulz A. 2022. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 41(3), 32. mla: Zhao, Haisen, et al. “Co-Optimization of Design and Fabrication Plans for Carpentry.” ACM Transactions on Graphics, vol. 41, no. 3, 32, Association for Computing Machinery, 2022, doi:10.1145/3508499. short: H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz, ACM Transactions on Graphics 41 (2022). date_created: 2024-05-29T06:09:23Z date_published: 2022-03-09T00:00:00Z date_updated: 2024-08-06T07:03:14Z day: '09' department: - _id: BeBi doi: 10.1145/3508499 external_id: arxiv: - '2107.12265' intvolume: ' 41' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2107.12265 month: '03' oa: 1 oa_version: Preprint publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Co-optimization of design and fabrication plans for carpentry type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2022' ... --- _id: '17066' abstract: - lang: eng text: A cell’s size affects the likelihood that it will die. But how is cell size controlled in this context and how does cell size impact commitment to the cell death fate? We present evidence that the caspase CED-3 interacts with the RhoGEF ECT-2 in Caenorhabditis elegans neuroblasts that generate “unwanted” cells. We propose that this interaction promotes polar actomyosin contractility, which leads to unequal neuroblast division and the generation of a daughter cell that is below the critical “lethal” size threshold. Furthermore, we find that hyperactivation of ECT-2 RhoGEF reduces the sizes of unwanted cells. Importantly, this suppresses the “cell death abnormal” phenotype caused by the partial loss of ced-3 caspase and therefore increases the likelihood that unwanted cells die. A putative null mutation of ced-3 caspase, however, is not suppressed, which indicates that cell size affects CED-3 caspase activation and/or activity. Therefore, we have uncovered novel sequential and reciprocal interactions between the apoptosis pathway and cell size that impact a cell’s commitment to the cell death fate. acknowledgement: "We thank members of the Conradt, Lambie, and Hajnal labs for discussions and comments on the manuscript. We thank M. Bauer, L. Jocham, N. Lebedeva, and L. McGuinness for excellent technical support; A. Hajnal and T. Kohlbrenner (University of Zurich, Switzerland) for allele zh135; and H.R. Horvitz (Massachusetts of Technology, USA) for plasmid pET-CED-3.\r\nSome strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (https://orip.nih.gov/) (P40 OD010440). This work was supported by UCL (Capital Equipment Fund, CEF2), a predoctoral fellowship from the China Scholarship Council (https://www.csc.edu.cn/) to HW, a predoctoral fellowship from the Studienstiftung des Deutschen Volkes (https://www.studienstiftung.de/) to NM, a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to BC (RSWF\\R1\\180008), the Deutsche Forschungsgemeinschaft (https://www.dfg.de/en/index.jsp) (ZA619/3-1 and ZA619/3-2 to EZ; C0204/10-1 and EXC114 to BC), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 to BC). " article_number: e3001786 article_processing_charge: Yes article_type: original author: - first_name: Aditya full_name: Sethi, Aditya last_name: Sethi - first_name: Hai full_name: Wei, Hai last_name: Wei - first_name: Nikhil full_name: Mishra, Nikhil id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E last_name: Mishra orcid: 0000-0002-6425-5788 - first_name: Ioannis full_name: Segos, Ioannis last_name: Segos - first_name: Eric J. full_name: Lambie, Eric J. last_name: Lambie - first_name: Esther full_name: Zanin, Esther last_name: Zanin - first_name: Barbara full_name: Conradt, Barbara last_name: Conradt citation: ama: Sethi A, Wei H, Mishra N, et al. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 2022;20(10). doi:10.1371/journal.pbio.3001786 apa: Sethi, A., Wei, H., Mishra, N., Segos, I., Lambie, E. J., Zanin, E., & Conradt, B. (2022). A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001786 chicago: Sethi, Aditya, Hai Wei, Nikhil Mishra, Ioannis Segos, Eric J. Lambie, Esther Zanin, and Barbara Conradt. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001786. ieee: A. Sethi et al., “A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans,” PLOS Biology, vol. 20, no. 10. Public Library of Science, 2022. ista: Sethi A, Wei H, Mishra N, Segos I, Lambie EJ, Zanin E, Conradt B. 2022. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 20(10), e3001786. mla: Sethi, Aditya, et al. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology, vol. 20, no. 10, e3001786, Public Library of Science, 2022, doi:10.1371/journal.pbio.3001786. short: A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt, PLOS Biology 20 (2022). date_created: 2024-05-29T06:09:34Z date_published: 2022-10-06T00:00:00Z date_updated: 2024-08-06T07:08:54Z day: '06' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pbio.3001786 external_id: pmid: - '36201522' file: - access_level: open_access checksum: a7b46460b7819c196028481cc18a7c85 content_type: application/pdf creator: dernst date_created: 2024-08-06T07:07:52Z date_updated: 2024-08-06T07:07:52Z file_id: '17399' file_name: 2022_PlosBio_Sethi.pdf file_size: 2515388 relation: main_file success: 1 file_date_updated: 2024-08-06T07:07:52Z has_accepted_license: '1' intvolume: ' 20' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Biology publication_identifier: issn: - 1545-7885 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans 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: 20 year: '2022' ... --- _id: '17067' abstract: - lang: eng text: 'Human doublecortin (DCX) mutations are associated with severe brain malformations leading to aberrant neuron positioning (heterotopia), intellectual disability and epilepsy. DCX is a microtubule-associated protein which plays a key role during neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO) mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons are also more excitable than wild-type (WT) cells. To further identify abnormalities, we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural levels. Severe defects were observed in mitochondria, affecting number and distribution. Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally organized. Transcriptome analyses from laser microdissected hippocampal tissue at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue showed that organelle defects are persistent throughout life. Locomotor activity and fear memory of young and mature adults were also abnormal: Dcx KO mice consistently performed less well than WT littermates, with defects becoming more severe with age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can lead to permanent organelle anomalies contributing to abnormal adult behavior.' acknowledgement: "We thank Sylvie Dumont for initial aid with laser microdissection and G. Martinez-Lorenzana for experimental help with electron microscopy. We thank the animal experimentation facility and cellular and tissue imaging platforms at the Institut du Fer à Moulin, supported also by the Région Ile de France and the FRC Rotary. The Francis lab was associated with the BioPsy Labex project and the Ecole des Neurosciences de Paris Ile-de-France (ENP) network. Our salaries and lab were supported by Inserm, the Centre national de la recherche scientifique (CNRS) and Sorbonne University. The Francis group obtained the following funding contributing to this project: the European Union (EU- HEALTH-2013, DESIRE, N° 60253), the JTC 2015 Neurodevelopmental Disorders affiliated with the French Agence National de la Recherche (for \r\nNEURON8-Full- 815-006 STEM-MCD, to FF), E-Rare-3, the ERA-Net for Research on Rare Diseases affiliated with the French ANR (ERARE18-049), the European Cooperation on Science and Technology (COST Action CA16118)." article_number: '105702' article_processing_charge: Yes article_type: original author: - first_name: Melissa A full_name: Stouffer, Melissa A id: 4C9372C4-F248-11E8-B48F-1D18A9856A87 last_name: Stouffer - first_name: R. full_name: Khalaf-Nazzal, R. last_name: Khalaf-Nazzal - first_name: C. full_name: Cifuentes-Diaz, C. last_name: Cifuentes-Diaz - first_name: G. full_name: Albertini, G. last_name: Albertini - first_name: E. full_name: Bandet, E. last_name: Bandet - first_name: G. full_name: Grannec, G. last_name: Grannec - first_name: V. full_name: Lavilla, V. last_name: Lavilla - first_name: J.-F. full_name: Deleuze, J.-F. last_name: Deleuze - first_name: R. full_name: Olaso, R. last_name: Olaso - first_name: M. full_name: Nosten-Bertrand, M. last_name: Nosten-Bertrand - first_name: F. full_name: Francis, F. last_name: Francis citation: ama: Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, et al. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. 2022;168. doi:10.1016/j.nbd.2022.105702 apa: Stouffer, M. A., Khalaf-Nazzal, R., Cifuentes-Diaz, C., Albertini, G., Bandet, E., Grannec, G., … Francis, F. (2022). Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. Elsevier. https://doi.org/10.1016/j.nbd.2022.105702 chicago: Stouffer, Melissa A, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” Neurobiology of Disease. Elsevier, 2022. https://doi.org/10.1016/j.nbd.2022.105702. ieee: M. A. Stouffer et al., “Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells,” Neurobiology of Disease, vol. 168. Elsevier, 2022. ista: Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, Albertini G, Bandet E, Grannec G, Lavilla V, Deleuze J-F, Olaso R, Nosten-Bertrand M, Francis F. 2022. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. 168, 105702. mla: Stouffer, Melissa A., et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” Neurobiology of Disease, vol. 168, 105702, Elsevier, 2022, doi:10.1016/j.nbd.2022.105702. short: M.A. Stouffer, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, J.-F. Deleuze, R. Olaso, M. Nosten-Bertrand, F. Francis, Neurobiology of Disease 168 (2022). date_created: 2024-05-29T06:10:05Z date_published: 2022-06-15T00:00:00Z date_updated: 2024-08-06T06:57:39Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.nbd.2022.105702 external_id: pmid: - '35339680' file: - access_level: open_access checksum: b705d3d23d0b424ba29920be7ab64c23 content_type: application/pdf creator: dernst date_created: 2024-08-06T06:54:24Z date_updated: 2024-08-06T06:54:24Z file_id: '17398' file_name: 2022_NeurobioDisease_Stouffer.pdf file_size: 8890818 relation: main_file success: 1 file_date_updated: 2024-08-06T06:54:24Z has_accepted_license: '1' intvolume: ' 168' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Neurobiology of Disease publication_identifier: issn: - 0969-9961 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 168 year: '2022' ... --- _id: '17068' abstract: - lang: eng text: In plants, the antagonism between growth and defense is hardwired by hormonal signaling. The perception of pathogen-associated molecular patterns (PAMPs) from invading microorganisms inhibits auxin signaling and plant growth. Conversely, pathogens manipulate auxin signaling to promote disease, but how this hormone inhibits immunity is not fully understood. Ustilago maydis is a maize pathogen that induces auxin signaling in its host. We characterized a U. maydis effector protein, Naked1 (Nkd1), that is translocated into the host nucleus. Through its native ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, Nkd1 binds to the transcriptional co-repressors TOPLESS/TOPLESS-related (TPL/TPRs) and prevents the recruitment of a transcriptional repressor involved in hormonal signaling, leading to the de-repression of auxin and jasmonate signaling and thereby promoting susceptibility to (hemi)biotrophic pathogens. A moderate upregulation of auxin signaling inhibits the PAMP-triggered reactive oxygen species (ROS) burst, an early defense response. Thus, our findings establish a clear mechanism for auxin-induced pathogen susceptibility. Engineered Nkd1 variants with increased expression or increased EAR-mediated TPL/TPR binding trigger typical salicylic-acid-mediated defense reactions, leading to pathogen resistance. This implies that moderate binding of Nkd1 to TPL is a result of a balancing evolutionary selection process to enable TPL manipulation while avoiding host recognition. acknowledgement: "The research leading to these results received funding from the European Research Council under the European Union Seventh Framework Programme ERC-2013-STG grant agreement \r\n335691; the Austrian Science Fund (FWF) P27818-B22,I 3033-B22; the Austrian Academy of Sciences (OEAW); and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2070-390732324.\r\nWe would like to thank the GMI/IMBA/IMP core facilities for excellent technical support, especially the BioOptics and Molecular Biology Services. We thank the Plant Sciences and Next Generation Sequencing Facilities at the Vienna BioCenter Core Facilities GmbH (VBCF). We are grateful to the Jirí Friml and Jürgen Kleine-Vehn laboratories for providing useful A. thaliana lines. We thank Mathias Madalinski for peptide synthesis and Dr. J. Matthew Watson for proofreading and valuable feedback on the manuscript. The authors declare no competing interests." article_number: '100269' article_processing_charge: Yes article_type: original author: - first_name: Fernando full_name: Navarrete, Fernando last_name: Navarrete - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Aleksandra E. full_name: Kornienko, Aleksandra E. last_name: Kornienko - first_name: Indira full_name: Saado, Indira last_name: Saado - first_name: Mamoona full_name: Khan, Mamoona last_name: Khan - first_name: Khong-Sam full_name: Chia, Khong-Sam last_name: Chia - first_name: Martin A. full_name: Darino, Martin A. last_name: Darino - first_name: Janos full_name: Bindics, Janos last_name: Bindics - first_name: Armin full_name: Djamei, Armin last_name: Djamei citation: ama: Navarrete F, Gallei MC, Kornienko AE, et al. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 2022;3(2). doi:10.1016/j.xplc.2021.100269 apa: Navarrete, F., Gallei, M. C., Kornienko, A. E., Saado, I., Khan, M., Chia, K.-S., … Djamei, A. (2022). TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2021.100269 chicago: Navarrete, Fernando, Michelle C Gallei, Aleksandra E. Kornienko, Indira Saado, Mamoona Khan, Khong-Sam Chia, Martin A. Darino, Janos Bindics, and Armin Djamei. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” Plant Communications. Elsevier, 2022. https://doi.org/10.1016/j.xplc.2021.100269. ieee: F. Navarrete et al., “TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1,” Plant Communications, vol. 3, no. 2. Elsevier, 2022. ista: Navarrete F, Gallei MC, Kornienko AE, Saado I, Khan M, Chia K-S, Darino MA, Bindics J, Djamei A. 2022. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 3(2), 100269. mla: Navarrete, Fernando, et al. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” Plant Communications, vol. 3, no. 2, 100269, Elsevier, 2022, doi:10.1016/j.xplc.2021.100269. short: F. Navarrete, M.C. Gallei, A.E. Kornienko, I. Saado, M. Khan, K.-S. Chia, M.A. Darino, J. Bindics, A. Djamei, Plant Communications 3 (2022). date_created: 2024-05-29T06:10:22Z date_published: 2022-03-14T00:00:00Z date_updated: 2024-08-05T10:27:03Z day: '14' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2021.100269 external_id: pmid: - '35529945' file: - access_level: open_access checksum: 1eeb6ee65419e4aa34627fea6857f343 content_type: application/pdf creator: dernst date_created: 2024-08-05T10:26:29Z date_updated: 2024-08-05T10:26:29Z file_id: '17393' file_name: 2022_PlantComm_Navarrete.pdf file_size: 3216686 relation: main_file success: 1 file_date_updated: 2024-08-05T10:26:29Z has_accepted_license: '1' intvolume: ' 3' issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Communications publication_identifier: issn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1 tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2022' ... --- OA_place: repository OA_type: green _id: '17069' abstract: - lang: eng text: Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact with pollen tube–specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this polytubey block. The same combination of RALF (rapid alkalinization factor) peptides and receptor complexes controls pollen tube reception and rupture inside the targeted ovule. Pollen tube rupture releases the polytubey block at the septum, which allows the emergence of secondary pollen tubes upon fertilization failure. Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated by the same signaling components to guarantee and optimize reproductive success. acknowledgement: "We thank D. Ye for providing fer-4 and myb97 myb101 myb120 mutant seeds; L. Smith for sharing anj, herk1, anj herk1, and fer anj herk1 mutant seeds; J. F. Harper for providing aca9 mutant seeds; and C. Li and Q. Duan for sharing fer+/− mutant seeds.\r\nL.-J.Q. was funded by the National Natural Science Foundation of China (grant nos. 31991202, 31830004, 31620103903, and 31621001), S.Z. was supported by the Young Elite Scientists Sponsorship Program by the China Association of Science and Technology (2019QNRC001), Z.G. was supported by a NSFC Young Scientists Fund (31900161), A.Y.C. was funded by the US Natural Science Foundation (IOS-1645854, MCB-1715764, and MCB-0955910), J.D. was funded by the National Institute of Health (R01GM109080), and T.D. was supported by the German Research Foundation DFG (SFB924)." article_processing_charge: No article_type: original author: - first_name: Sheng full_name: Zhong, Sheng last_name: Zhong - first_name: Ling full_name: Li, Ling last_name: Li - first_name: Zhijuan full_name: Wang, Zhijuan last_name: Wang - first_name: Zengxiang full_name: Ge, Zengxiang id: f43371a3-09ff-11eb-8013-bd0c6a2f6de8 last_name: Ge orcid: 0000-0001-9381-3577 - first_name: Qiyun full_name: Li, Qiyun last_name: Li - first_name: Andrea full_name: Bleckmann, Andrea last_name: Bleckmann - first_name: Jizong full_name: Wang, Jizong last_name: Wang - first_name: Zihan full_name: Song, Zihan last_name: Song - first_name: Yihao full_name: Shi, Yihao last_name: Shi - first_name: Tianxu full_name: Liu, Tianxu last_name: Liu - first_name: Luhan full_name: Li, Luhan last_name: Li - first_name: Huabin full_name: Zhou, Huabin last_name: Zhou - first_name: Yanyan full_name: Wang, Yanyan last_name: Wang - first_name: Li full_name: Zhang, Li last_name: Zhang - first_name: Hen-Ming full_name: Wu, Hen-Ming last_name: Wu - first_name: Luhua full_name: Lai, Luhua last_name: Lai - first_name: Hongya full_name: Gu, Hongya last_name: Gu - first_name: Juan full_name: Dong, Juan last_name: Dong - first_name: Alice Y. full_name: Cheung, Alice Y. last_name: Cheung - first_name: Thomas full_name: Dresselhaus, Thomas last_name: Dresselhaus - first_name: Li-Jia full_name: Qu, Li-Jia last_name: Qu citation: ama: Zhong S, Li L, Wang Z, et al. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 2022;375(6578):290-296. doi:10.1126/science.abl4683 apa: Zhong, S., Li, L., Wang, Z., Ge, Z., Li, Q., Bleckmann, A., … Qu, L.-J. (2022). RALF peptide signaling controls the polytubey block in Arabidopsis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abl4683 chicago: Zhong, Sheng, Ling Li, Zhijuan Wang, Zengxiang Ge, Qiyun Li, Andrea Bleckmann, Jizong Wang, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abl4683. ieee: S. Zhong et al., “RALF peptide signaling controls the polytubey block in Arabidopsis,” Science, vol. 375, no. 6578. American Association for the Advancement of Science, pp. 290–296, 2022. ista: Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu T, Li L, Zhou H, Wang Y, Zhang L, Wu H-M, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus T, Qu L-J. 2022. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 375(6578), 290–296. mla: Zhong, Sheng, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” Science, vol. 375, no. 6578, American Association for the Advancement of Science, 2022, pp. 290–96, doi:10.1126/science.abl4683. short: S. Zhong, L. Li, Z. Wang, Z. Ge, Q. Li, A. Bleckmann, J. Wang, Z. Song, Y. Shi, T. Liu, L. Li, H. Zhou, Y. Wang, L. Zhang, H.-M. Wu, L. Lai, H. Gu, J. Dong, A.Y. Cheung, T. Dresselhaus, L.-J. Qu, Science 375 (2022) 290–296. date_created: 2024-05-29T06:11:10Z date_published: 2022-01-20T00:00:00Z date_updated: 2025-04-24T11:39:46Z day: '20' department: - _id: JiFr doi: 10.1126/science.abl4683 external_id: pmid: - '35050671' intvolume: ' 375' issue: '6578' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003 month: '01' oa: 1 oa_version: Submitted Version page: 290-296 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: RALF peptide signaling controls the polytubey block in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 375 year: '2022' ... --- _id: '17070' abstract: - lang: eng text: We investigate the formation of magnetic Bose polaron, an impurity atom dressed by spin-wave excitations, in a one-dimensional spinor Bose gas. Within an effective potential model, the impurity is strongly confined by the host excitations which can even overcome the impurity-medium repulsion leading to a self-localized quasi-particle state. The phase diagram of the attractive and self-bound repulsive magnetic polaron, repulsive non-magnetic (Fröhlich-type) polaron and impurity-medium phase-separation regimes is explored with respect to the Rabi-coupling between the spin components, spin–spin interactions and impurity-medium coupling. The residue of such magnetic polarons decreases substantially in both strong attractive and repulsive branches with strong impurity-spin interactions, illustrating significant dressing of the impurity. The impurity can be used to probe and maneuver the spin polarization of the magnetic medium while suppressing ferromagnetic spin–spin correlations. It is shown that mean-field theory fails as the spinor gas approaches immiscibility since the generated spin-wave excitations are prominent. Our findings illustrate that impurities can be utilized to generate controllable spin–spin correlations and magnetic polaron states which can be realized with current cold atom setups. article_number: '083030' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: S I full_name: Mistakidis, S I last_name: Mistakidis - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: F full_name: Grusdt, F last_name: Grusdt - first_name: P full_name: Schmelcher, P last_name: Schmelcher - first_name: H R full_name: Sadeghpour, H R last_name: Sadeghpour citation: ama: 'Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 2022;24(8). doi:10.1088/1367-2630/ac836c' apa: 'Mistakidis, S. I., Koutentakis, G., Grusdt, F., Schmelcher, P., & Sadeghpour, H. R. (2022). Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac836c' chicago: 'Mistakidis, S I, Georgios Koutentakis, F Grusdt, P Schmelcher, and H R Sadeghpour. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac836c.' ieee: 'S. I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, and H. R. Sadeghpour, “Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron,” New Journal of Physics, vol. 24, no. 8. IOP Publishing, 2022.' ista: 'Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. 2022. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 24(8), 083030.' mla: 'Mistakidis, S. I., et al. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics, vol. 24, no. 8, 083030, IOP Publishing, 2022, doi:10.1088/1367-2630/ac836c.' short: S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour, New Journal of Physics 24 (2022). date_created: 2024-05-29T06:11:35Z date_published: 2022-09-08T00:00:00Z date_updated: 2024-07-31T12:14:55Z day: '08' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/ac836c external_id: arxiv: - '2204.10960' file: - access_level: open_access checksum: 85776a9d3abe163b33b322c8e346752a content_type: application/pdf creator: dernst date_created: 2024-07-31T12:13:16Z date_updated: 2024-07-31T12:13:16Z file_id: '17358' file_name: 2022_NewJournPhysics_Mistakidis.pdf file_size: 4201283 relation: main_file success: 1 file_date_updated: 2024-07-31T12:13:16Z has_accepted_license: '1' intvolume: ' 24' issue: '8' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_identifier: issn: - 1367-2630 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron' 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: 24 year: '2022' ... --- _id: '17071' abstract: - lang: eng text: "The eukaryotic nucleus pro­tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg­est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf­fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma­tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal­lenge for structural biologists.\r\nConsiderable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra­tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc­tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf­fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight­forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol­ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination.\r\nIn this study, we used artificial intelligence (AI)–based prediction to generate an exten­sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac­terized. Benchmarking against previous and unpublished x-ray and cryo–electron micros­copy structures revealed unprecedented accu­racy. We obtained well-resolved cryo–electron tomographic maps of both the constricted and dilated conformational states of the hu­man NPC. Using integrative modeling, we fit­ted the structural models of individual NUPs into the cryo–electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf­fold. We elucidated in great detail how mem­brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en­vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension\r\nOur 70-MDa atomically re­solved model covers >90% of the human NPC scaffold. It captures conforma­tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy­namic model of the NPC. Our study exempli­fies how AI-based structure prediction may accelerate the elucidation of subcellular ar­chitecture at atomic resolution." acknowledgement: "We acknowledge support from the Electron Microscopy Core Facility (EMCF) and IT services of European Molecular Biology Laboratory (EMBL) Heidelberg. We thank S. Welsch at the Central Electron Microscopy Facility of the Max Planck Institute of Biophysics for technical expertise. We thank T. Hoffman and R. Alves for help with the AlphaFold installation.\r\nFunding: M.B. acknowledges funding by EMBL, the Max Planck Society, and the European Research Council (ComplexAssembly 724349). J.K. acknowledges funding from the Federal Ministry of Education and Research of Germany (FKZ 031L0100). The work by M.S. and G.H. on computer simulations was supported by the Max Planck Society. M.S. was supported by the EMBL Interdisciplinary Postdoc Programme under Marie Curie COFUND actions. M.S. and G.H. were supported by the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) DynaMem program of the State of Hessen." article_number: abm9506 article_processing_charge: No article_type: original author: - first_name: Shyamal full_name: Mosalaganti, Shyamal last_name: Mosalaganti - first_name: Agnieszka full_name: Obarska-Kosinska, Agnieszka last_name: Obarska-Kosinska - first_name: Marc full_name: Siggel, Marc last_name: Siggel - first_name: Reiya full_name: Taniguchi, Reiya last_name: Taniguchi - first_name: Beata full_name: Turoňová, Beata last_name: Turoňová - first_name: Christian E. full_name: Zimmerli, Christian E. last_name: Zimmerli - first_name: Katarzyna full_name: Buczak, Katarzyna last_name: Buczak - first_name: Florian full_name: Schmidt, Florian id: A2EF226A-AF19-11E9-924C-0525E6697425 last_name: Schmidt - first_name: Erica full_name: Margiotta, Erica last_name: Margiotta - first_name: Marie-Therese full_name: Mackmull, Marie-Therese last_name: Mackmull - first_name: Wim J. H. full_name: Hagen, Wim J. H. last_name: Hagen - first_name: Gerhard full_name: Hummer, Gerhard last_name: Hummer - first_name: Jan full_name: Kosinski, Jan last_name: Kosinski - first_name: Martin full_name: Beck, Martin last_name: Beck citation: ama: Mosalaganti S, Obarska-Kosinska A, Siggel M, et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 2022;376(6598). doi:10.1126/science.abm9506 apa: Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., … Beck, M. (2022). AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abm9506 chicago: Mosalaganti, Shyamal, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turoňová, Christian E. Zimmerli, Katarzyna Buczak, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abm9506. ieee: S. Mosalaganti et al., “AI-based structure prediction empowers integrative structural analysis of human nuclear pores,” Science, vol. 376, no. 6598. American Association for the Advancement of Science, 2022. ista: Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt F, Margiotta E, Mackmull M-T, Hagen WJH, Hummer G, Kosinski J, Beck M. 2022. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 376(6598), abm9506. mla: Mosalaganti, Shyamal, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science, vol. 376, no. 6598, abm9506, American Association for the Advancement of Science, 2022, doi:10.1126/science.abm9506. short: S. Mosalaganti, A. Obarska-Kosinska, M. Siggel, R. Taniguchi, B. Turoňová, C.E. Zimmerli, K. Buczak, F. Schmidt, E. Margiotta, M.-T. Mackmull, W.J.H. Hagen, G. Hummer, J. Kosinski, M. Beck, Science 376 (2022). date_created: 2024-05-29T06:12:02Z date_published: 2022-06-10T00:00:00Z date_updated: 2024-07-31T12:10:32Z day: '10' department: - _id: MaJö doi: 10.1126/science.abm9506 external_id: pmid: - '35679397' intvolume: ' 376' issue: '6598' language: - iso: eng month: '06' oa_version: None pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: AI-based structure prediction empowers integrative structural analysis of human nuclear pores type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 376 year: '2022' ... --- _id: '17072' abstract: - lang: eng text: The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery. acknowledgement: We thank A. L. Horwich, K. Chakraborty, and B. Schuler for providing plasmids, and R. van Leeuwen, M. Mayer, J. van Zon, W. Noorduin, and P. R. ten Wolde for comments and critical reading of the manuscript. Work in the group of S.J.T. was supported by the Netherlands Organization for Scientific Research (NWO). Work in the group of H.S.R. was supported by a grant from the NIH (R01GM114405). article_number: eabl6293 article_processing_charge: Yes article_type: original author: - first_name: Mohsin M. full_name: Naqvi, Mohsin M. last_name: Naqvi - first_name: Mario full_name: Avellaneda Sarrió, Mario id: DC4BA84C-56E6-11EA-AD5D-348C3DDC885E last_name: Avellaneda Sarrió orcid: 0000-0001-6406-524X - first_name: Andrew full_name: Roth, Andrew last_name: Roth - first_name: Eline J. full_name: Koers, Eline J. last_name: Koers - first_name: Antoine full_name: Roland, Antoine last_name: Roland - first_name: Vanda full_name: Sunderlikova, Vanda last_name: Sunderlikova - first_name: Günter full_name: Kramer, Günter last_name: Kramer - first_name: Hays S. full_name: Rye, Hays S. last_name: Rye - first_name: Sander J. full_name: Tans, Sander J. last_name: Tans citation: ama: Naqvi MM, Avellaneda Sarrió M, Roth A, et al. Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. 2022;8(9). doi:10.1126/sciadv.abl6293 apa: Naqvi, M. M., Avellaneda Sarrió, M., Roth, A., Koers, E. J., Roland, A., Sunderlikova, V., … Tans, S. J. (2022). Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abl6293 chicago: Naqvi, Mohsin M., Mario Avellaneda Sarrió, Andrew Roth, Eline J. Koers, Antoine Roland, Vanda Sunderlikova, Günter Kramer, Hays S. Rye, and Sander J. Tans. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” Science Advances. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.abl6293. ieee: M. M. Naqvi et al., “Protein chain collapse modulation and folding stimulation by GroEL-ES,” Science Advances, vol. 8, no. 9. American Association for the Advancement of Science, 2022. ista: Naqvi MM, Avellaneda Sarrió M, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. 2022. Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. 8(9), eabl6293. mla: Naqvi, Mohsin M., et al. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” Science Advances, vol. 8, no. 9, eabl6293, American Association for the Advancement of Science, 2022, doi:10.1126/sciadv.abl6293. short: M.M. Naqvi, M. Avellaneda Sarrió, A. Roth, E.J. Koers, A. Roland, V. Sunderlikova, G. Kramer, H.S. Rye, S.J. Tans, Science Advances 8 (2022). date_created: 2024-05-29T06:12:19Z date_published: 2022-03-01T00:00:00Z date_updated: 2024-08-05T08:30:29Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1126/sciadv.abl6293 external_id: pmid: - '35245117' file: - access_level: open_access checksum: 9511579306cce7e04107d3d6389ed614 content_type: application/pdf creator: dernst date_created: 2024-07-31T12:01:51Z date_updated: 2024-07-31T12:01:51Z file_id: '17357' file_name: 2022_ScienceAdv_Naqvi.pdf file_size: 2404150 relation: main_file success: 1 file_date_updated: 2024-07-31T12:01:51Z has_accepted_license: '1' intvolume: ' 8' issue: '9' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Protein chain collapse modulation and folding stimulation by GroEL-ES 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: 8 year: '2022' ... --- _id: '17075' abstract: - lang: eng text: Disorders associated with the malfunction of amino acid transporters mainly affect the function of the intestine, kidney, brain, and liver. Mutations of brain amino acid transporters, for example, alter neuronal excitability (e.g., episodic ataxia due to SLC1A3 (EAAT1) defect and hyperekplexia due to SLC6A5 (GLYT2) deficiency) or brain development (SLC1A1 (EAAT3), SLC3A2/SLC7A5 (CD98hc/LAT1), and SLC1A4 (ASCT1) deficiencies). Mutations of renal and intestinal amino acid transporters SLC3A1/SLC7A9 (rBAT/b0,+AT) and SLC1A1 (EAAT3) cause renal problems (cystinuria and dicarboxylic aminoaciduria, respectively) and malabsorption that can affect whole-body homoeostasis (Hartnup disorder SLC6A19 (B0AT1), lysinuric protein intolerance SLC3A2/SLC7A7 (CD98hc/y+LAT1), and hyperdibasic aminoaciduria type 1). Mutations in the neuronal system A amino acid transporter SLC38A8 (SNAT8) cause eye developmental and visual defects. Inborn errors associated with mitochondrial SLC25 family members such as SLC25A12 (neuronal- and muscle-specific mitochondrial aspartate/glutamate transporter 1; AGC1) (global cerebral hypomyelination), SLC25A13 (aspartate/glutamate transporter 2) (citrin deficiency), SLC25A15 (ornithine-citrulline carrier 2) (homocitrullinuria, hyperornithinemia, and hyperammonemia syndrome), and SLC25A22 (mitochondrial glutamate/H+ symporter 1, GC1) (neonatal myoclonic epilepsy) will be dealt within Chap. 43 (defects of mitochondrial carriers). acknowledgement: The authors thank Dr. Christian Lueck (Canberra Hospital) for clarification of differential diagnosis in cases of episodic ataxia. The authors thank Dr. Rafael Artuch (Hospital San Joan de Deu, Barcelona) for reference values of plasma amino acid concentration. The authors also thank Lisa Kraus (Institute of Science and Technology-Austria) and Dr. Susanna Bodoy (IRB-Barcelona) that helped in preparing tables and bibliography. article_processing_charge: No author: - first_name: Manuel full_name: Palacín, Manuel last_name: Palacín - first_name: Stefan full_name: Bröer, Stefan last_name: Bröer - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Palacín M, Bröer S, Novarino G. Amino Acid Transport Defects. In: Blau N, Vici CD, Ferreira CR, Vianey-Saban C, van Karnebeek CDM, eds. Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. 2nd ed. Cham: Springer Nature; 2022:291-312. doi:10.1007/978-3-030-67727-5_18' apa: 'Palacín, M., Bröer, S., & Novarino, G. (2022). Amino Acid Transport Defects. In N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, & C. D. M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases (2nd ed., pp. 291–312). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-67727-5_18' chicago: 'Palacín, Manuel, Stefan Bröer, and Gaia Novarino. “Amino Acid Transport Defects.” In Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, edited by Nenad Blau, Carlo Dionisi Vici, Carlos R. Ferreira, Christine Vianey-Saban, and Clara D.M. van Karnebeek, 2nd ed., 291–312. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67727-5_18.' ieee: 'M. Palacín, S. Bröer, and G. Novarino, “Amino Acid Transport Defects,” in Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 2nd ed., N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, and C. D. M. van Karnebeek, Eds. Cham: Springer Nature, 2022, pp. 291–312.' ista: 'Palacín M, Bröer S, Novarino G. 2022.Amino Acid Transport Defects. In: Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. , 291–312.' mla: Palacín, Manuel, et al. “Amino Acid Transport Defects.” Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, edited by Nenad Blau et al., 2nd ed., Springer Nature, 2022, pp. 291–312, doi:10.1007/978-3-030-67727-5_18. short: M. Palacín, S. Bröer, G. Novarino, in:, N. Blau, C.D. Vici, C.R. Ferreira, C. Vianey-Saban, C.D.M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 2nd ed., Springer Nature, Cham, 2022, pp. 291–312. date_created: 2024-05-29T06:13:04Z date_published: 2022-02-22T00:00:00Z date_updated: 2024-07-31T11:45:50Z day: '22' department: - _id: GaNo doi: 10.1007/978-3-030-67727-5_18 edition: '2' editor: - first_name: Nenad full_name: Blau, Nenad last_name: Blau - first_name: Carlo Dionisi full_name: Vici, Carlo Dionisi last_name: Vici - first_name: 'Carlos R. ' full_name: 'Ferreira, Carlos R. ' last_name: Ferreira - first_name: Christine full_name: Vianey-Saban, Christine last_name: Vianey-Saban - first_name: Clara D.M. full_name: van Karnebeek, Clara D.M. last_name: van Karnebeek language: - iso: eng month: '02' oa_version: None page: 291-312 place: Cham publication: Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases publication_identifier: eisbn: - '9783030677275' isbn: - '9783030677268' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Amino Acid Transport Defects type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '17076' abstract: - lang: eng text: "Introduction: The levels of many blood proteins are associated with Alzheimer's disease (AD) or its pathological hallmarks. Elucidating the molecular factors that control circulating levels of these proteins may help to identify proteins associated with disease risk mechanisms.\r\n\r\nMethods: Genome-wide and epigenome-wide studies (nindividuals ≤1064) were performed on plasma levels of 282 AD-associated proteins, identified by a structured literature review. Bayesian penalized regression estimated contributions of genetic and epigenetic variation toward inter-individual differences in plasma protein levels. Mendelian randomization (MR) and co-localization tested associations between proteins and disease-related phenotypes.\r\n\r\nResults: Sixty-four independent genetic and 26 epigenetic loci were associated with 45 proteins. Novel findings included an association between plasma triggering receptor expressed on myeloid cells 2 (TREM2) levels and a polymorphism and cytosine-phosphate-guanine (CpG) site within the MS4A4A locus. Higher plasma tubulin-specific chaperone A (TBCA) and TREM2 levels were significantly associated with lower AD risk.\r\n\r\nDiscussion: Our data inform the regulation of biomarker levels and their relationships with AD." acknowledgement: This research was funded in whole, or in part, by Wellcome [108890/Z/15/Z, 104036/Z/14/Z]. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The authors are grateful to the families who took part in this study, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the wider Generation Scotland team. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. Genotyping and DNA methylation profiling of the Generation Scotland samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland, and was funded by the Medical Research Council (MRC) UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” ([STRADL] Reference [104036/Z/14/Z]). Andrew M. McIntosh is supported by Wellcome [104036/Z/14/Z, 216767/Z/19/Z, 220857/Z/20/Z], United Kingdom Research and Innovation (UKRI) MRC [MC_PC_17209, MR/S035818/1] and the European Union H2020 [SEP-210574971]. Ian J. Deary received support from Age UK, Wellcome, and the Medical Research Council. David J. Porteous is supported by Wellcome as prinicpal investigator (PI), and MRC and National Institute for Health Research (NIHR) grants as co-PI, made to the University of Edinburgh. Robert F. Hillary and Danni A. Gadd are supported by funding from the Wellcome 4-year PhD in Translational Neuroscience—training the next generation of basic neuroscientists to embrace clinical research [108890/Z/15/Z]. Daniel L. McCartney and Riccardo E. Marioni are supported by Alzheimer's Research UK major project grant ARUK-PG2017B-10. Riccardo E. Marioni is supported by Alzheimer's Society major project grant AS-PG-19b-010. Proteomic analyses in STRADL were supported by Dementias Platform UK (DPUK). DPUK funded this work through core grant support from the Medical Research Council [MR/L023784/2]. Kathryn L. Evans was supported by a grant from Alzheimer's Research UK, paid to the University of Edinburgh. Alejo J. Nevado-Holgado was funded by a Horizon 2020 Virtual Brain Cloud project (H2020-SC1-DTH-2018-1), in addition to funding from the MRC, UK Rosetrees, and King Abdullah University of Science and Technology, Saudi Arabia. Caroline Hayward is supported by an MRC University Unit Programme Grant MC_UU_00007/10 (QTL in Health and Disease). Liu Shi is funded by DPUK through MRC [MR/L023784/2] and the UK Medical Research Council Award to the University of Oxford [MC_PC_17215]. Liu Shi received support from the NIHR Biomedical Research Centre at Oxford Health NHS Foundation Trust. Matthew R. Robinson is funded by a Swiss National Science Foundation Eccellenza Grant [PCEGP3-181181]. article_number: e12280 article_processing_charge: Yes article_type: original author: - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Danni A. full_name: Gadd, Danni A. last_name: Gadd - first_name: Daniel L. full_name: McCartney, Daniel L. last_name: McCartney - first_name: Liu full_name: Shi, Liu last_name: Shi - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Rosie M. full_name: Walker, Rosie M. last_name: Walker - first_name: Craig W. full_name: Ritchie, Craig W. last_name: Ritchie - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Alejo J. full_name: Nevado‐Holgado, Alejo J. last_name: Nevado‐Holgado - first_name: Caroline full_name: Hayward, Caroline last_name: Hayward - first_name: David J. full_name: Porteous, David J. last_name: Porteous - first_name: Andrew M. full_name: McIntosh, Andrew M. last_name: McIntosh - first_name: Simon full_name: Lovestone, Simon last_name: Lovestone - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni citation: ama: 'Hillary RF, Gadd DA, McCartney DL, et al. Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer’s disease implicate TBCA and TREM2 in disease risk. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring. 2022;14(1). doi:10.1002/dad2.12280' apa: 'Hillary, R. F., Gadd, D. A., McCartney, D. L., Shi, L., Campbell, A., Walker, R. M., … Marioni, R. E. (2022). Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer’s disease implicate TBCA and TREM2 in disease risk. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring. Wiley. https://doi.org/10.1002/dad2.12280' chicago: 'Hillary, Robert F., Danni A. Gadd, Daniel L. McCartney, Liu Shi, Archie Campbell, Rosie M. Walker, Craig W. Ritchie, et al. “Genome‐ and Epigenome‐wide Studies of Plasma Protein Biomarkers for Alzheimer’s Disease Implicate TBCA and TREM2 in Disease Risk.” Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring. Wiley, 2022. https://doi.org/10.1002/dad2.12280.' ieee: 'R. F. Hillary et al., “Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer’s disease implicate TBCA and TREM2 in disease risk,” Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, vol. 14, no. 1. Wiley, 2022.' ista: 'Hillary RF, Gadd DA, McCartney DL, Shi L, Campbell A, Walker RM, Ritchie CW, Deary IJ, Evans KL, Nevado‐Holgado AJ, Hayward C, Porteous DJ, McIntosh AM, Lovestone S, Robinson MR, Marioni RE. 2022. Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer’s disease implicate TBCA and TREM2 in disease risk. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring. 14(1), e12280.' mla: 'Hillary, Robert F., et al. “Genome‐ and Epigenome‐wide Studies of Plasma Protein Biomarkers for Alzheimer’s Disease Implicate TBCA and TREM2 in Disease Risk.” Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, vol. 14, no. 1, e12280, Wiley, 2022, doi:10.1002/dad2.12280.' short: 'R.F. Hillary, D.A. Gadd, D.L. McCartney, L. Shi, A. Campbell, R.M. Walker, C.W. Ritchie, I.J. Deary, K.L. Evans, A.J. Nevado‐Holgado, C. Hayward, D.J. Porteous, A.M. McIntosh, S. Lovestone, M.R. Robinson, R.E. Marioni, Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring 14 (2022).' date_created: 2024-05-29T06:13:25Z date_published: 2022-04-20T00:00:00Z date_updated: 2024-07-31T11:33:50Z day: '20' ddc: - '570' department: - _id: MaRo doi: 10.1002/dad2.12280 external_id: pmid: - '35475137' file: - access_level: open_access checksum: 49c8597b588ef1c63897703a32b7967b content_type: application/pdf creator: dernst date_created: 2024-07-31T11:27:29Z date_updated: 2024-07-31T11:27:29Z file_id: '17356' file_name: 2023_AlzheimersDementia_Hillary.pdf file_size: 975181 relation: main_file success: 1 file_date_updated: 2024-07-31T11:27:29Z has_accepted_license: '1' intvolume: ' 14' issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: 'Alzheimer''s & Dementia: Diagnosis, Assessment & Disease Monitoring' publication_identifier: eissn: - 2352-8729 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2022' ... --- _id: '17077' abstract: - lang: eng text: "Resolving a conjecture of Füredi from 1988, we prove that with high probability, the random graph \U0001D53E(\U0001D45B, 1/2) admits a friendly bisection of its vertex set, i.e., a\r\npartition of its vertex set into two parts whose sizes differ by at most one in which\r\n\U0001D45B − \U0001D45C(\U0001D45B) vertices have more neighbours in their own part as across. Our proof is constructive, and in the process, we develop a new method to study stochastic processes\r\ndriven by degree information in random graphs; this involves combining enumeration\r\ntechniques with an abstract second moment argument." acknowledgement: "We thank the referees for extensive comments which helped improve the paper substantially.\r\nThe first author was supported in part by NSF grants DMS-1954395 and DMS-1953799. The second author was supported by NSF grant DMS-1953990. The third author was supported by NSF grant DMS180052. The fourth and fifth authors were both supported by NSF Graduate Research Fellowship Program DGE-1745302." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Asaf full_name: Ferber, Asaf last_name: Ferber - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Bhargav full_name: Narayanan, Bhargav last_name: Narayanan - first_name: Ashwin full_name: Sah, Ashwin last_name: Sah - first_name: Mehtaab full_name: Sawhney, Mehtaab last_name: Sawhney citation: ama: Ferber A, Kwan MA, Narayanan B, Sah A, Sawhney M. Friendly bisections of random graphs. Communications of the American Mathematical Society. 2022;2(10):380-416. doi:10.1090/cams/13 apa: Ferber, A., Kwan, M. A., Narayanan, B., Sah, A., & Sawhney, M. (2022). Friendly bisections of random graphs. Communications of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/cams/13 chicago: Ferber, Asaf, Matthew Alan Kwan, Bhargav Narayanan, Ashwin Sah, and Mehtaab Sawhney. “Friendly Bisections of Random Graphs.” Communications of the American Mathematical Society. American Mathematical Society, 2022. https://doi.org/10.1090/cams/13. ieee: A. Ferber, M. A. Kwan, B. Narayanan, A. Sah, and M. Sawhney, “Friendly bisections of random graphs,” Communications of the American Mathematical Society, vol. 2, no. 10. American Mathematical Society, pp. 380–416, 2022. ista: Ferber A, Kwan MA, Narayanan B, Sah A, Sawhney M. 2022. Friendly bisections of random graphs. Communications of the American Mathematical Society. 2(10), 380–416. mla: Ferber, Asaf, et al. “Friendly Bisections of Random Graphs.” Communications of the American Mathematical Society, vol. 2, no. 10, American Mathematical Society, 2022, pp. 380–416, doi:10.1090/cams/13. short: A. Ferber, M.A. Kwan, B. Narayanan, A. Sah, M. Sawhney, Communications of the American Mathematical Society 2 (2022) 380–416. corr_author: '1' date_created: 2024-05-29T06:13:37Z date_published: 2022-12-20T00:00:00Z date_updated: 2024-07-15T08:06:05Z day: '20' ddc: - '500' department: - _id: MaKw doi: 10.1090/cams/13 external_id: arxiv: - '2105.13337' file: - access_level: open_access checksum: 719861e76f5bce3d0362d8171daa26fc content_type: application/pdf creator: cchlebak date_created: 2024-07-12T12:55:02Z date_updated: 2024-07-12T12:55:02Z file_id: '17230' file_name: 2022_CommAMS_Ferber.pdf file_size: 335965 relation: main_file success: 1 file_date_updated: 2024-07-12T12:55:02Z has_accepted_license: '1' intvolume: ' 2' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '12' oa: 1 oa_version: Published Version page: 380-416 publication: Communications of the American Mathematical Society publication_identifier: issn: - 2692-3688 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: Friendly bisections of random graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2022' ... --- _id: '17084' abstract: - lang: eng text: 'Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which exchanges the tokens at the two endpoints of an edge of the graph. In parallel token swapping, the goal is to use the fewest rounds, each of which consists of one or more swaps on the edges of a matching. We prove that both of these problems remain NP-hard when the graph is restricted to be a tree. These token swapping problems have been studied by disparate groups of researchers in discrete mathematics, theoretical computer science, robot motion planning, game theory, and engineering. Previous work establishes NP-completeness on general graphs (for both problems), constant-factor approximation algorithms, and some poly-time exact algorithms for simple graph classes such as cliques, stars, paths, and cycles. Sequential and parallel token swapping on trees were first studied over thirty years ago (as "sorting with a transposition tree") and over twenty-five years ago (as "routing permutations via matchings"), yet their complexities were previously unknown. We also show limitations on approximation of sequential token swapping on trees: we identify a broad class of algorithms that encompass all three known polynomial-time algorithms that achieve the best known approximation factor (which is 2) and show that no such algorithm can achieve an approximation factor less than 2.' acknowledgement: "g Anna Lubiw: Supported by the Natural Sciences and Engineering Research Council of\r\nCanada (NSERC). Jayson Lynch: Supported by the Natural Sciences and Engineering Research Council of Canada (NSERC). Zuzana Masárová: Supported by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. Virginia Vassilevska Williams: Supported by an NSF CAREER Award, NSF Grants CCF-1528078, CCF-1514339 and CCF-1909429, a BSF Grant BSF:2012338, a Google Research Fellowship and a Sloan Research Fellowship.\r\nNicole Wein: Supported by a grant to DIMACS from the Simons Foundation (820931). This work was done while the author was at MIT.\r\nThis research was initiated at the 34th Bellairs Winter Workshop on Computational Geometry, co-organized by Erik Demaine and Godfried Toussaint, held on March 22–29,\r\n2019 in Holetown, Barbados. We thank the other participants of that workshop for providing a\r\nstimulating research environment." alternative_title: - LIPIcs article_number: '3' article_processing_charge: Yes arxiv: 1 author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Erik D. full_name: Demaine, Erik D. last_name: Demaine - first_name: Matias full_name: Korman, Matias last_name: Korman - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Jayson full_name: Lynch, Jayson last_name: Lynch - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Mikhail full_name: Rudoy, Mikhail last_name: Rudoy - first_name: Virginia full_name: Vassilevska Williams, Virginia last_name: Vassilevska Williams - first_name: Nicole full_name: Wein, Nicole last_name: Wein citation: ama: 'Aichholzer O, Demaine ED, Korman M, et al. Hardness of token swapping on trees. In: 30th Annual European Symposium on Algorithms. Vol 244. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.ESA.2022.3' apa: 'Aichholzer, O., Demaine, E. D., Korman, M., Lubiw, A., Lynch, J., Masárová, Z., … Wein, N. (2022). Hardness of token swapping on trees. In 30th Annual European Symposium on Algorithms (Vol. 244). Berlin/Potsdam, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2022.3' chicago: Aichholzer, Oswin, Erik D. Demaine, Matias Korman, Anna Lubiw, Jayson Lynch, Zuzana Masárová, Mikhail Rudoy, Virginia Vassilevska Williams, and Nicole Wein. “Hardness of Token Swapping on Trees.” In 30th Annual European Symposium on Algorithms, Vol. 244. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.ESA.2022.3. ieee: O. Aichholzer et al., “Hardness of token swapping on trees,” in 30th Annual European Symposium on Algorithms, Berlin/Potsdam, Germany, 2022, vol. 244. ista: 'Aichholzer O, Demaine ED, Korman M, Lubiw A, Lynch J, Masárová Z, Rudoy M, Vassilevska Williams V, Wein N. 2022. Hardness of token swapping on trees. 30th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 244, 3.' mla: Aichholzer, Oswin, et al. “Hardness of Token Swapping on Trees.” 30th Annual European Symposium on Algorithms, vol. 244, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.ESA.2022.3. short: O. Aichholzer, E.D. Demaine, M. Korman, A. Lubiw, J. Lynch, Z. Masárová, M. Rudoy, V. Vassilevska Williams, N. Wein, in:, 30th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. conference: end_date: 2022-09-09 location: Berlin/Potsdam, Germany name: 'ESA: European Symposium on Algorithms' start_date: 2022-09-05 corr_author: '1' date_created: 2024-05-29T06:27:16Z date_published: 2022-09-01T00:00:00Z date_updated: 2025-04-15T07:16:56Z day: '01' ddc: - '510' department: - _id: HeEd - _id: UlWa doi: 10.4230/LIPIcs.ESA.2022.3 external_id: arxiv: - '2103.06707' file: - access_level: open_access checksum: a1fbd3e7baad510fbcb998cf4a7d9f7f content_type: application/pdf creator: dernst date_created: 2024-08-12T08:51:44Z date_updated: 2024-08-12T08:51:44Z file_id: '17420' file_name: 2022_LIPIcS_Aichholzer.pdf file_size: 1406071 relation: main_file success: 1 file_date_updated: 2024-08-12T08:51:44Z has_accepted_license: '1' intvolume: ' 244' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication: 30th Annual European Symposium on Algorithms publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Hardness of token swapping on trees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 244 year: '2022' ... --- _id: '17085' abstract: - lang: eng text: Mosses are a cosmopolitan group of land plants, sister to vascular plants, with a high potential for molecular and cell biological research. The species Physcomitrium patens has helped gaining better understanding of the biological processes of the plant cell, and it has become a central system to understand water-to-land plant transition through 2D-to-3D growth transition, regulation of asymmetric cell division, shoot apical cell establishment and maintenance, phyllotaxis and regeneration. P. patens was the first fully sequenced moss in 2008, with the latest annotated release in 2018. It has been shown that many gene functions and networks are conserved in mosses when compared to angiosperms. Importantly, this model organism has a simplified and accessible body structure that facilitates close tracking in time and space with the support of live cell imaging set-ups and multiple reporter lines. This has become possible thanks to its fully established molecular toolkit, with highly efficient PEG-assisted, CRISPR/Cas9 and RNAi transformation and silencing protocols, among others. Here we provide examples on how mosses exhibit advantages over vascular plants to study several processes and their future potential to answer some other outstanding questions in plant cell biology. acknowledgement: 'The authors would like to thank Dr. Jeroen de Keijzer and Dr. Tijs Ketelaar for their thoughtful and detailed review of the manuscript. Also, the funding agencies Technology, Knowledge and Innovation, division Horticulture and Propagating Material (TKI T&U) and the Dutch Research Council (NWO) (reference number: TKILWV20.390) for funding JFC and the ERC grant to Prof. J. Friml (reference number: PR1023ERC02) for funding HT. The authors would like to sincerely apologise for the literature not cited that may be relevant for this chapter and is not present due to space constraints.' article_processing_charge: No author: - first_name: Jordi full_name: Floriach-Clark, Jordi last_name: Floriach-Clark - first_name: Han full_name: Tang, Han id: 19BDF720-25A0-11EA-AC6E-928F3DDC885E last_name: Tang orcid: 0000-0001-6152-6637 - first_name: Viola full_name: Willemsen, Viola last_name: Willemsen citation: ama: 'Floriach-Clark J, Tang H, Willemsen V. Mosses: Accessible Systems for Plant Development Studies. In: Abdurakhmonov IY, ed. Model Organisms in Plant Genetics. IntechOpen; 2022. doi:10.5772/intechopen.100535' apa: 'Floriach-Clark, J., Tang, H., & Willemsen, V. (2022). Mosses: Accessible Systems for Plant Development Studies. In I. Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics. IntechOpen. https://doi.org/10.5772/intechopen.100535' chicago: 'Floriach-Clark, Jordi, Han Tang, and Viola Willemsen. “Mosses: Accessible Systems for Plant Development Studies.” In Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov. IntechOpen, 2022. https://doi.org/10.5772/intechopen.100535.' ieee: 'J. Floriach-Clark, H. Tang, and V. Willemsen, “Mosses: Accessible Systems for Plant Development Studies,” in Model Organisms in Plant Genetics, I. Y. Abdurakhmonov, Ed. IntechOpen, 2022.' ista: 'Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .' mla: 'Floriach-Clark, Jordi, et al. “Mosses: Accessible Systems for Plant Development Studies.” Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov, IntechOpen, 2022, doi:10.5772/intechopen.100535.' short: J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022. date_created: 2024-05-29T06:35:13Z date_published: 2022-06-23T00:00:00Z date_updated: 2025-05-14T11:20:40Z day: '23' department: - _id: JiFr doi: 10.5772/intechopen.100535 ec_funded: 1 editor: - first_name: Ibrokhim Y. full_name: Abdurakhmonov, Ibrokhim Y. last_name: Abdurakhmonov language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5772/intechopen.100535 month: '06' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Model Organisms in Plant Genetics publication_identifier: isbn: - '9781839697500' publication_status: published publisher: IntechOpen quality_controlled: '1' status: public title: 'Mosses: Accessible Systems for Plant Development Studies' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '17086' abstract: - lang: eng text: 'We consider a high-dimensional mean estimation problem over a binary hidden Markov model, which illuminates the interplay between memory in data, sample size, dimension, and signal strength in statistical inference. In this model, an estimator observes n samples of a d-dimensional parameter vector θ∗∈Rd, multiplied by a random sign Si (1≤i≤n), and corrupted by isotropic standard Gaussian noise. The sequence of signs {Si}i∈[n]∈{−1,1}n is drawn from a stationary homogeneous Markov chain with flip probability δ∈[0,1/2]. As δ varies, this model smoothly interpolates two well-studied models: the Gaussian Location Model for which δ=0 and the Gaussian Mixture Model for which δ=1/2. Assuming that the estimator knows δ, we establish a nearly minimax optimal (up to logarithmic factors) estimation error rate, as a function of ∥θ∗∥,δ,d,n. We then provide an upper bound to the case of estimating δ, assuming a (possibly inaccurate) knowledge of θ∗. The bound is proved to be tight when θ∗ is an accurately known constant. These results are then combined to an algorithm which estimates θ∗ with δ unknown a priori, and theoretical guarantees on its error are stated.' acknowledgement: "Part of this work was done when YZ was a postdoc at Technion where he received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of of NW was supported in part by the Israel Science Foundation (ISF) under Grant 1782/22. NW is grateful to Guy Bresler for introducing him to this problem, for the initial ideas that led to this research, and for many helpful discussions on the topic." alternative_title: - NeurIPS article_processing_charge: No arxiv: 1 author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Nir full_name: Weinberger, Nir last_name: Weinberger citation: ama: 'Zhang Y, Weinberger N. Mean estimation in high-dimensional binary Markov Gaussian mixture models. In: 36th Conference on Neural Information Processing Systems. Vol 35. ML Research Press; 2022.' apa: 'Zhang, Y., & Weinberger, N. (2022). Mean estimation in high-dimensional binary Markov Gaussian mixture models. In 36th Conference on Neural Information Processing Systems (Vol. 35). New Orleans, LA, United States: ML Research Press.' chicago: Zhang, Yihan, and Nir Weinberger. “Mean Estimation in High-Dimensional Binary Markov Gaussian Mixture Models.” In 36th Conference on Neural Information Processing Systems, Vol. 35. ML Research Press, 2022. ieee: Y. Zhang and N. Weinberger, “Mean estimation in high-dimensional binary Markov Gaussian mixture models,” in 36th Conference on Neural Information Processing Systems, New Orleans, LA, United States, 2022, vol. 35. ista: 'Zhang Y, Weinberger N. 2022. Mean estimation in high-dimensional binary Markov Gaussian mixture models. 36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, NeurIPS, vol. 35.' mla: Zhang, Yihan, and Nir Weinberger. “Mean Estimation in High-Dimensional Binary Markov Gaussian Mixture Models.” 36th Conference on Neural Information Processing Systems, vol. 35, ML Research Press, 2022. short: Y. Zhang, N. Weinberger, in:, 36th Conference on Neural Information Processing Systems, ML Research Press, 2022. conference: end_date: 2022-12-09 location: New Orleans, LA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2022-11-28 corr_author: '1' date_created: 2024-05-29T06:37:16Z date_published: 2022-12-01T00:00:00Z date_updated: 2024-08-05T09:48:58Z day: '01' ddc: - '000' department: - _id: MaMo external_id: arxiv: - '2206.02455' file: - access_level: open_access checksum: 05f6f9f8fc34e224e0cad045b9489030 content_type: application/pdf creator: dernst date_created: 2024-08-05T09:44:49Z date_updated: 2024-08-05T09:44:49Z file_id: '17392' file_name: 2022_NeurIPS_Zhang.pdf file_size: 476307 relation: main_file success: 1 file_date_updated: 2024-08-05T09:44:49Z has_accepted_license: '1' intvolume: ' 35' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: 36th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9781713871088' publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Mean estimation in high-dimensional binary Markov Gaussian mixture models type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2022' ... --- _id: '17088' abstract: - lang: eng text: 'In this paper, we consider the problem of sparsifying BERT models, which are a key building block for natural language processing, in order to reduce their storage and computational cost. We introduce the Optimal BERT Surgeon (oBERT), an efficient and accurate pruning method based on approximate second-order information, which we show to yield state-of-the-art results in both stages of language tasks: pre-training and fine-tuning. Specifically, oBERT extends existing work on second-order pruning by allowing for pruning weight blocks, and is the first such method that is applicable at BERT scale. Second, we investigate compounding compression approaches to obtain highly compressed but accurate models for deployment on edge devices. These models significantly push boundaries of the current state-of-the-art sparse BERT models with respect to all metrics: model size, inference speed and task accuracy. For example, relative to the dense BERT-base, we obtain 10x model size compression with < 1% accuracy drop, 10x CPU-inference speedup with < 2% accuracy drop, and 29x CPU-inference speedup with < 7.5% accuracy drop. Our code, fully integrated with Transformers and SparseML, is available at https://github.com/neuralmagic/sparseml/tree/main/research/optimal_BERT_surgeon_oBERT.' article_processing_charge: Yes arxiv: 1 author: - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Daniel full_name: Campos, Daniel last_name: Campos - first_name: Tuan full_name: Nguyen, Tuan last_name: Nguyen - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Mark full_name: Kurtz, Mark last_name: Kurtz - first_name: Benjamin full_name: Fineran, Benjamin last_name: Fineran - first_name: Michael full_name: Goin, Michael last_name: Goin - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Kurtic E, Campos D, Nguyen T, et al. The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. In: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing. Association for Computational Linguistics; 2022:4163-4181. doi:10.18653/v1/2022.emnlp-main.279' apa: 'Kurtic, E., Campos, D., Nguyen, T., Frantar, E., Kurtz, M., Fineran, B., … Alistarh, D.-A. (2022). The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing (pp. 4163–4181). Abu Dhabi, United Arab Emirates: Association for Computational Linguistics. https://doi.org/10.18653/v1/2022.emnlp-main.279' chicago: 'Kurtic, Eldar, Daniel Campos, Tuan Nguyen, Elias Frantar, Mark Kurtz, Benjamin Fineran, Michael Goin, and Dan-Adrian Alistarh. “The Optimal BERT Surgeon: Scalable and Accurate Second-Order Pruning for Large Language Models.” In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 4163–81. Association for Computational Linguistics, 2022. https://doi.org/10.18653/v1/2022.emnlp-main.279.' ieee: 'E. Kurtic et al., “The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models,” in Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Abu Dhabi, United Arab Emirates, 2022, pp. 4163–4181.' ista: 'Kurtic E, Campos D, Nguyen T, Frantar E, Kurtz M, Fineran B, Goin M, Alistarh D-A. 2022. The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing. EMNLP: Conference on Empirical Methods in Natural Language Processing, 4163–4181.' mla: 'Kurtic, Eldar, et al. “The Optimal BERT Surgeon: Scalable and Accurate Second-Order Pruning for Large Language Models.” Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics, 2022, pp. 4163–81, doi:10.18653/v1/2022.emnlp-main.279.' short: E. Kurtic, D. Campos, T. Nguyen, E. Frantar, M. Kurtz, B. Fineran, M. Goin, D.-A. Alistarh, in:, Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics, 2022, pp. 4163–4181. conference: end_date: 2022-12-11 location: Abu Dhabi, United Arab Emirates name: 'EMNLP: Conference on Empirical Methods in Natural Language Processing' start_date: 2022-12-07 corr_author: '1' date_created: 2024-05-29T06:40:55Z date_published: 2022-12-01T00:00:00Z date_updated: 2024-07-31T11:05:32Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.18653/v1/2022.emnlp-main.279 external_id: arxiv: - '2203.07259' file: - access_level: open_access checksum: c47b9edd8a9f743ac77a593de6d2e84a content_type: application/pdf creator: dernst date_created: 2024-07-31T11:03:34Z date_updated: 2024-07-31T11:03:34Z file_id: '17354' file_name: 2022_EMNLP_Kurtic.pdf file_size: 522563 relation: main_file success: 1 file_date_updated: 2024-07-31T11:03:34Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4163-4181 publication: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing publication_status: published publisher: Association for Computational Linguistics quality_controlled: '1' related_material: link: - relation: software url: https://github.com/neuralmagic/sparseml/tree/main/research/optimal_BERT_surgeon_oBERT scopus_import: '1' status: public title: 'The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '7791' abstract: - lang: eng text: Extending a result of Milena Radnovic and Serge Tabachnikov, we establish conditionsfor two different non-symmetric norms to define the same billiard reflection law. acknowledgement: AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). RK was supported by the Federal professorship program Grant 1.456.2016/1.4 and the Russian Foundation for Basic Research Grants 18-01-00036 and 19-01-00169. Open access funding provided by Institute of Science and Technology (IST Austria). The authors thank Alexey Balitskiy, Milena Radnović, and Serge Tabachnikov for useful discussions. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Roman full_name: Karasev, Roman last_name: Karasev citation: ama: Akopyan A, Karasev R. When different norms lead to same billiard trajectories? European Journal of Mathematics. 2022;8(4):1309-1312. doi:10.1007/s40879-020-00405-0 apa: Akopyan, A., & Karasev, R. (2022). When different norms lead to same billiard trajectories? European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-020-00405-0 chicago: Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” European Journal of Mathematics. Springer Nature, 2022. https://doi.org/10.1007/s40879-020-00405-0. ieee: A. Akopyan and R. Karasev, “When different norms lead to same billiard trajectories?,” European Journal of Mathematics, vol. 8, no. 4. Springer Nature, pp. 1309–1312, 2022. ista: Akopyan A, Karasev R. 2022. When different norms lead to same billiard trajectories? European Journal of Mathematics. 8(4), 1309–1312. mla: Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” European Journal of Mathematics, vol. 8, no. 4, Springer Nature, 2022, pp. 1309–12, doi:10.1007/s40879-020-00405-0. short: A. Akopyan, R. Karasev, European Journal of Mathematics 8 (2022) 1309–1312. corr_author: '1' date_created: 2020-05-03T22:00:48Z date_published: 2022-12-01T00:00:00Z date_updated: 2025-04-14T07:48:36Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s40879-020-00405-0 ec_funded: 1 external_id: arxiv: - '1912.12685' file: - access_level: open_access checksum: f53e71fd03744075adcd0b8fc1b8423d content_type: application/pdf creator: dernst date_created: 2020-05-04T10:33:42Z date_updated: 2020-07-14T12:48:03Z file_id: '7796' file_name: 2020_EuropMathematics_Akopyan.pdf file_size: 263926 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 8' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1309 - 1312 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: European Journal of Mathematics publication_identifier: eissn: - 2199-6768 issn: - 2199-675X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: When different norms lead to same billiard trajectories? 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2022' ... --- _id: '8286' abstract: - lang: eng text: "We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of \U0001D4AA (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. " acknowledgement: The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01). article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 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: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 - first_name: Amirmojtaba full_name: Sabour, Amirmojtaba id: bcc145fd-e77f-11ea-ae8b-80d661dbff67 last_name: Sabour citation: ama: Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2022;84(4):1007-1029. doi:10.1007/s00453-021-00905-9 apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2022). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9' chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2022. https://doi.org/10.1007/s00453-021-00905-9. ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica, vol. 84, no. 4. Springer Nature, pp. 1007–1029, 2022. ista: Alistarh D-A, Nadiradze G, Sabour A. 2022. Dynamic averaging load balancing on cycles. Algorithmica. 84(4), 1007–1029. mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, vol. 84, no. 4, Springer Nature, 2022, pp. 1007–29, doi:10.1007/s00453-021-00905-9. short: D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica 84 (2022) 1007–1029. conference: end_date: 2020-07-11 location: Virtual, Online; Germany name: 'ICALP: Automata, Languages and Programming' start_date: 2020-07-08 date_created: 2020-08-24T06:24:04Z date_published: 2022-04-01T00:00:00Z date_updated: 2025-07-10T11:55:11Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00453-021-00905-9 ec_funded: 1 external_id: arxiv: - '2003.09297' isi: - '000734004600001' file: - access_level: open_access checksum: 21169b25b0c8e17b21e12af22bff9870 content_type: application/pdf creator: cchlebak date_created: 2021-12-27T10:36:40Z date_updated: 2021-12-27T10:36:40Z file_id: '10577' file_name: 2021_Algorithmica_Alistarh.pdf file_size: 525950 relation: main_file success: 1 file_date_updated: 2021-12-27T10:36:40Z has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1007-1029 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.4230/LIPIcs.ICALP.2020.7 record: - id: '15077' relation: earlier_version status: public scopus_import: '1' status: public title: Dynamic averaging load balancing on cycles 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: 84 year: '2022' ...