[{"date_updated":"2024-06-04T09:51:20Z","publication_status":"published","author":[{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"month":"01","_id":"17057","publication":"Journal of Cell Science","language":[{"iso":"eng"}],"title":"Cell scientist to watch – Martin Loose","status":"public","external_id":{"isi":["000762665200015"]},"date_created":"2024-05-28T13:28:30Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Martin Loose studied chemistry at the University of Heidelberg, Germany. He then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for work on self-organization and pattern formation in the bacterial Min protein system. He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular Biology Organization (EMBO) long-term fellowships; there, he discovered that the bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Martin established his independent research group at the Institute of Science and Technology (IST) Austria in 2015, supported by an European Research Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies the self-organization of bacterial cell division and small GTPase networks."}],"volume":135,"isi":1,"year":"2022","day":"19","quality_controlled":"1","date_published":"2022-01-19T00:00:00Z","intvolume":" 135","citation":{"ista":"Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.","chicago":"Loose, Martin. Cell Scientist to Watch – Martin Loose. Journal of Cell Science. Vol. 135. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.259715.","apa":"Loose, M. (2022). Cell scientist to watch – Martin Loose. Journal of Cell Science (Vol. 135). The Company of Biologists. https://doi.org/10.1242/jcs.259715","ieee":"M. Loose, Cell scientist to watch – Martin Loose, vol. 135, no. 2. The Company of Biologists, 2022.","mla":"Loose, Martin. “Cell Scientist to Watch – Martin Loose.” Journal of Cell Science, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:10.1242/jcs.259715.","short":"M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022.","ama":"Loose M. Cell Scientist to Watch – Martin Loose. Vol 135. The Company of Biologists; 2022. doi:10.1242/jcs.259715"},"department":[{"_id":"MaLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","publisher":"The Company of Biologists","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"article_processing_charge":"No","article_number":"jcs259715","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.259715"}],"type":"other_academic_publication","oa":1,"doi":"10.1242/jcs.259715"},{"corr_author":"1","doi":"10.4064/aa210430-1-7","oa":1,"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"intvolume":" 204","date_published":"2022-08-22T00:00:00Z","quality_controlled":"1","arxiv":1,"day":"22","article_processing_charge":"No","publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"TiBr"}],"citation":{"mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” Acta Arithmetica, vol. 204, no. 4, Institute of Mathematics, 2022, pp. 317–46, doi:10.4064/aa210430-1-7.","ista":"Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 204(4), 317–346.","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” Acta Arithmetica. Institute of Mathematics, 2022. https://doi.org/10.4064/aa210430-1-7.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” Acta Arithmetica, vol. 204, no. 4. Institute of Mathematics, pp. 317–346, 2022.","apa":"Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. Institute of Mathematics. https://doi.org/10.4064/aa210430-1-7","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 2022;204(4):317-346. doi:10.4064/aa210430-1-7","short":"A.L. Shute, Acta Arithmetica 204 (2022) 317–346."},"publisher":"Institute of Mathematics","issue":"4","oa_version":"Preprint","external_id":{"arxiv":["2104.14946"],"isi":["000844789100001"]},"related_material":{"record":[{"id":"12077","relation":"earlier_version","status":"public"}]},"date_created":"2024-05-28T13:39:26Z","isi":1,"volume":204,"year":"2022","page":"317-346","abstract":[{"text":"We compare the Manin-type conjecture for Campana points recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not agree, and we discuss whether thin sets could explain this discrepancy. Motivated by this, we provide a counterexample to the Manin-type conjecture for Campana points, by considering orbifolds corresponding to squareful values of binary quadratic forms.","lang":"eng"}],"author":[{"full_name":"Shute, Alec L","orcid":"0000-0002-1812-2810","first_name":"Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"month":"08","date_updated":"2025-09-10T09:57:03Z","publication_status":"published","title":"On the leading constant in the Manin-type conjecture for Campana points","scopus_import":"1","status":"public","article_type":"original","publication":"Acta Arithmetica","language":[{"iso":"eng"}],"_id":"17058"},{"oa_version":"Published Version","external_id":{"isi":["000922378801029"]},"date_created":"2024-05-28T13:45:20Z","year":"2022","volume":162,"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"isi":1,"ec_funded":1,"abstract":[{"lang":"eng","text":"The recent focus on the efficiency of deep neural networks (DNNs) has led to significant work on model compression approaches, of which weight pruning is one of the most popular. At the same time, there is rapidly-growing computational support for efficiently executing the unstructured-sparse models obtained via pruning. Yet, most existing pruning methods minimize just the number of remaining weights, i.e. the size of the model, rather than optimizing for inference time. We address this gap by introducing SPDY, a new compression method which automatically determines layer-wise sparsity targets achieving a desired inference speedup on a given system, while minimizing accuracy loss. SPDY is the composition of two new techniques. The first is an efficient and general dynamic programming algorithm for solving constrained layer-wise compression problems, given a set of layer-wise error scores. The second technique is a local search procedure for automatically determining such scores in an accurate and robust manner. Experiments across popular vision and language models show that SPDY guarantees speedups while recovering higher accuracy relative to existing strategies, both for one-shot and gradual pruning scenarios, and is compatible with most existing pruning approaches. We also extend our approach to the recently-proposed task of pruning with very little data, where we achieve the best known accuracy recovery when pruning to the GPU-supported 2:4 sparsity pattern."}],"page":"6726-6743","author":[{"first_name":"Elias","full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"month":"07","ddc":["000"],"publication_status":"published","date_updated":"2025-04-14T07:49:14Z","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2022_PMLR_Frantar.pdf","creator":"dernst","file_id":"17440","success":1,"date_created":"2024-08-19T06:54:41Z","date_updated":"2024-08-19T06:54:41Z","file_size":615916,"checksum":"5179a1e4dfc0fbfab6674907299e414a"}],"scopus_import":"1","status":"public","title":"SPDY: Accurate pruning with speedup guarantees","_id":"17059","language":[{"iso":"eng"}],"publication":"39th International Conference on Machine Learning","corr_author":"1","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No 805223 ScaleML),\r\nas well as computational support from AWS EC2. We thank Eldar Kurtic for code and hyper-parameters for BERT pruning, and the Neural Magic Team, notably Michael Goin and\r\nMark Kurtz, for support with their software.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"conference":{"location":"Baltimore, MD, United States","end_date":"2022-07-23","name":"ICML: International Conference on Machine Learning","start_date":"2022-07-17"},"type":"conference","file_date_updated":"2024-08-19T06:54:41Z","date_published":"2022-07-20T00:00:00Z","intvolume":" 162","day":"20","quality_controlled":"1","article_processing_charge":"Yes","publisher":"ML Research Press","citation":{"mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” 39th International Conference on Machine Learning, vol. 162, ML Research Press, 2022, pp. 6726–43.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” In 39th International Conference on Machine Learning, 162:6726–43. ML Research Press, 2022.","apa":"Frantar, E., & Alistarh, D.-A. (2022). SPDY: Accurate pruning with speedup guarantees. In 39th International Conference on Machine Learning (Vol. 162, pp. 6726–6743). Baltimore, MD, United States: ML Research Press.","ieee":"E. Frantar and D.-A. Alistarh, “SPDY: Accurate pruning with speedup guarantees,” in 39th International Conference on Machine Learning, Baltimore, MD, United States, 2022, vol. 162, pp. 6726–6743.","ista":"Frantar E, Alistarh D-A. 2022. SPDY: Accurate pruning with speedup guarantees. 39th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 162, 6726–6743.","ama":"Frantar E, Alistarh D-A. SPDY: Accurate pruning with speedup guarantees. In: 39th International Conference on Machine Learning. Vol 162. ML Research Press; 2022:6726-6743.","short":"E. Frantar, D.-A. Alistarh, in:, 39th International Conference on Machine Learning, ML Research Press, 2022, pp. 6726–6743."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"}],"alternative_title":["PMLR"]},{"publication_identifier":{"isbn":["9781450398619"]},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"KrPi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Tiwari, Samarth, et al. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–31, doi:10.1145/3558535.3559775.","ista":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. 2022. Wiser: Increasing throughput in payment channel networks with transaction aggregation. Proceedings of the 4th ACM Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, 217–231.","ieee":"S. Tiwari, M. X. Yeo, Z. Avarikioti, I. Salem, K. Z. Pietrzak, and S. Schmid, “Wiser: Increasing throughput in payment channel networks with transaction aggregation,” in Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Cambridge, MA, United States, 2022, pp. 217–231.","chicago":"Tiwari, Samarth, Michelle X Yeo, Zeta Avarikioti, Iosif Salem, Krzysztof Z Pietrzak, and Stefan Schmid. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” In Proceedings of the 4th ACM Conference on Advances in Financial Technologies, 217–31. Association for Computing Machinery, 2022. https://doi.org/10.1145/3558535.3559775.","apa":"Tiwari, S., Yeo, M. X., Avarikioti, Z., Salem, I., Pietrzak, K. Z., & Schmid, S. (2022). Wiser: Increasing throughput in payment channel networks with transaction aggregation. In Proceedings of the 4th ACM Conference on Advances in Financial Technologies (pp. 217–231). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/3558535.3559775","ama":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. Wiser: Increasing throughput in payment channel networks with transaction aggregation. In: Proceedings of the 4th ACM Conference on Advances in Financial Technologies. Association for Computing Machinery; 2022:217-231. doi:10.1145/3558535.3559775","short":"S. Tiwari, M.X. Yeo, Z. Avarikioti, I. Salem, K.Z. Pietrzak, S. Schmid, in:, Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–231."},"publisher":"Association for Computing Machinery","date_published":"2022-09-19T00:00:00Z","arxiv":1,"day":"19","quality_controlled":"1","oa":1,"doi":"10.1145/3558535.3559775","conference":{"end_date":"2022-09-21","location":"Cambridge, MA, United States","start_date":"2022-09-19","name":"AFT: Conference on Advances in Financial Technologies"},"file_date_updated":"2024-08-19T06:45:21Z","type":"conference","has_accepted_license":"1","acknowledgement":"This work was supported partially by ERC Starting Grant QIP–805241, by the Vienna business agency (Wirtschaftsagentur) through the Vienna Cybersecurity and Privacy Research Center\r\n(ViSP) and by the Austrian Science Fund (FWF) project I 4800-N (ADVISE).\r\nThe first author would like to thank Daniel Dadush for suggesting the use of discrepancy techniques to solve the transaction aggregation problem.","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Wiser: Increasing throughput in payment channel networks with transaction aggregation","file":[{"file_id":"17439","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_AFT_Tiwari.pdf","file_size":574728,"checksum":"54a7d405f8e57dba24728599ca63818c","date_created":"2024-08-19T06:45:21Z","success":1,"date_updated":"2024-08-19T06:45:21Z"}],"scopus_import":"1","status":"public","_id":"17060","language":[{"iso":"eng"}],"publication":"Proceedings of the 4th ACM Conference on Advances in Financial Technologies","author":[{"last_name":"Tiwari","full_name":"Tiwari, Samarth","first_name":"Samarth"},{"first_name":"Michelle X","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"},{"last_name":"Avarikioti","first_name":"Zeta","full_name":"Avarikioti, Zeta"},{"last_name":"Salem","first_name":"Iosif","full_name":"Salem, Iosif"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"month":"09","ddc":["000"],"date_updated":"2025-09-10T09:57:48Z","publication_status":"published","isi":1,"year":"2022","abstract":[{"lang":"eng","text":"Payment channel networks (PCNs) are one of the most prominent solutions to the limited transaction throughput of blockchains. Nevertheless, PCNs suffer themselves from a throughput limitation due to the capital constraints of their channels. A similar dependence on high capital is also found in inter-bank payment settlements, where the so-called netting technique is used to mitigate liquidity demands.\r\nIn this work, we alleviate this limitation by introducing the notion of transaction aggregation: instead of executing transactions sequentially through a PCN, we enable senders to aggregate multiple transactions and execute them simultaneously to benefit from several amounts that may \"cancel out\". Two direct advantages of our proposal is the decrease in intermediary fees paid by senders as well as the obfuscation of the transaction data from the intermediaries.\r\nWe formulate the transaction aggregation as a computational problem, a generalization of the Bank Clearing Problem. We present a generic framework for the transaction aggregation execution, and thereafter we propose Wiser as an implementation of this framework in a specific hub-based setting. To overcome the NP-hardness of the transaction aggregation problem, in Wiser we propose a fixed-parameter linear algorithm for a special case of transaction aggregation as well as the Bank Clearing Problem. Wiser can also be seen as a modern variant of the Hawala money transfer system, as well as a decentralized implementation of the overseas remittance service of Wise."}],"page":"217-231","oa_version":"Published Version","external_id":{"arxiv":["2205.11597"],"isi":["001041852800015"]},"date_created":"2024-05-28T13:58:35Z"},{"type":"journal_article","pmid":1,"file_date_updated":"2024-08-06T07:33:30Z","oa":1,"doi":"10.1093/pnasnexus/pgac141","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).","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"pgac141","publisher":"Oxford University Press","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","short":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022).","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.","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."},"department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["2752-6542"]},"article_processing_charge":"Yes","arxiv":1,"day":"01","quality_controlled":"1","date_published":"2022-09-01T00:00:00Z","intvolume":" 1","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"year":"2022","volume":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"external_id":{"arxiv":["2105.06199"],"pmid":["36714856"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/alexmcavoy/fmtl/"}]},"date_created":"2024-05-28T14:23:12Z","oa_version":"Published Version","_id":"17061","publication":"PNAS Nexus","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","status":"public","file":[{"date_updated":"2024-08-06T07:33:30Z","success":1,"date_created":"2024-08-06T07:33:30Z","checksum":"79a8e3e4be7e8a2b407b4efddd65f3f3","file_size":2410962,"file_name":"2022_PNASNexus_McAvoy.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17400","creator":"dernst"}],"title":"Evolutionary instability of selfish learning in repeated games","ddc":["000"],"publication_status":"published","date_updated":"2025-06-11T13:54:20Z","month":"09","author":[{"first_name":"Alex","full_name":"McAvoy, Alex","last_name":"McAvoy"},{"last_name":"Kates-Harbeck","full_name":"Kates-Harbeck, Julian","first_name":"Julian"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X"}]},{"article_number":"159","date_created":"2024-05-29T05:38:47Z","related_material":{"record":[{"status":"public","id":"10123","relation":"earlier_version"}]},"acknowledgement":"Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF “Lise Meitner Fellowship”","corr_author":"1","oa_version":"Published Version","type":"conference_abstract","conference":{"name":"SNI: Semiconductor Nanocrystals","start_date":"2022-03-07","location":"Spain/Virtual","end_date":"2022-03-11"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.29363/nanoge.nsm.2022.159"}],"doi":"10.29363/nanoge.nsm.2022.159","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"year":"2022","oa":1,"date_updated":"2025-04-15T06:54:34Z","publication_status":"published","quality_controlled":"1","day":"07","month":"02","author":[{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"orcid":"0000-0003-4566-5877","first_name":"Mariano","full_name":"Calcabrini, Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-02-07T00:00:00Z","publication":"Proceedings of the nanoGe Spring Meeting 2022","language":[{"iso":"eng"}],"citation":{"short":"M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting 2022, Fundació Scito, 2022.","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","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.","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.","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."},"_id":"17062","department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Fundació Scito","title":"The importance of surface adsorbates in solution-processed thermoelectric materials","article_processing_charge":"No","status":"public"},{"author":[{"last_name":"Arnaud","full_name":"Arnaud, Marie-Claude","first_name":"Marie-Claude"},{"first_name":"Helmut W.","full_name":"Hofer, Helmut W.","last_name":"Hofer"},{"last_name":"Hutchings","first_name":"Michael","full_name":"Hutchings, Michael"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"month":"11","date_updated":"2024-08-06T07:28:50Z","publication_status":"published","article_type":"original","title":"Dynamische Systeme","scopus_import":"1","status":"public","_id":"17063","publication":"Oberwolfach Reports","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2024-05-29T06:01:19Z","volume":18,"year":"2022","abstract":[{"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.","lang":"eng"}],"page":"1735-1803","date_published":"2022-11-26T00:00:00Z","intvolume":" 18","day":"26","quality_controlled":"1","publication_identifier":{"issn":["1660-8933"],"eissn":["1660-8941"]},"article_processing_charge":"No","department":[{"_id":"VaKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803.","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","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.","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.","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."},"issue":"3","publisher":"European Mathematical Society","corr_author":"1","oa":1,"doi":"10.4171/owr/2021/33","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.4171/OWR/2021/33"}],"type":"journal_article"},{"article_number":"32","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.","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12265","open_access":"1"}],"doi":"10.1145/3508499","oa":1,"quality_controlled":"1","day":"09","arxiv":1,"intvolume":" 41","date_published":"2022-03-09T00:00:00Z","citation":{"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.","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.","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.","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.","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","short":"H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz, ACM Transactions on Graphics 41 (2022)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeBi"}],"issue":"3","publisher":"Association for Computing Machinery","article_processing_charge":"No","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"external_id":{"arxiv":["2107.12265"]},"date_created":"2024-05-29T06:09:23Z","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":41,"year":"2022","date_updated":"2024-08-06T07:03:14Z","publication_status":"published","author":[{"last_name":"Zhao","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","orcid":"0000-0002-6389-1045","first_name":"Haisen","full_name":"Zhao, Haisen"},{"full_name":"Willsey, Max","first_name":"Max","last_name":"Willsey"},{"full_name":"Zhu, Amy","first_name":"Amy","last_name":"Zhu"},{"last_name":"Nandi","first_name":"Chandrakana","full_name":"Nandi, Chandrakana"},{"first_name":"Zachary","full_name":"Tatlock, Zachary","last_name":"Tatlock"},{"last_name":"Solomon","full_name":"Solomon, Justin","first_name":"Justin"},{"last_name":"Schulz","full_name":"Schulz, Adriana","first_name":"Adriana"}],"month":"03","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","_id":"17065","title":"Co-optimization of design and fabrication plans for carpentry","status":"public","scopus_import":"1","article_type":"original"},{"file_date_updated":"2024-08-06T07:07:52Z","pmid":1,"type":"journal_article","oa":1,"doi":"10.1371/journal.pbio.3001786","has_accepted_license":"1","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","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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","short":"A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt, PLOS Biology 20 (2022).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"issue":"10","publisher":"Public Library of Science","publication_identifier":{"issn":["1545-7885"]},"article_processing_charge":"Yes","day":"06","quality_controlled":"1","date_published":"2022-10-06T00:00:00Z","intvolume":" 20","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."}],"volume":20,"year":"2022","external_id":{"pmid":["36201522"]},"date_created":"2024-05-29T06:09:34Z","oa_version":"Published Version","_id":"17066","publication":"PLOS Biology","language":[{"iso":"eng"}],"article_type":"original","title":"A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans","scopus_import":"1","file":[{"file_name":"2022_PlosBio_Sethi.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"17399","date_updated":"2024-08-06T07:07:52Z","success":1,"date_created":"2024-08-06T07:07:52Z","file_size":2515388,"checksum":"a7b46460b7819c196028481cc18a7c85"}],"status":"public","ddc":["570"],"date_updated":"2024-08-06T07:08:54Z","publication_status":"published","author":[{"last_name":"Sethi","full_name":"Sethi, Aditya","first_name":"Aditya"},{"last_name":"Wei","first_name":"Hai","full_name":"Wei, Hai"},{"full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","first_name":"Nikhil","last_name":"Mishra","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E"},{"last_name":"Segos","full_name":"Segos, Ioannis","first_name":"Ioannis"},{"full_name":"Lambie, Eric J.","first_name":"Eric J.","last_name":"Lambie"},{"last_name":"Zanin","first_name":"Esther","full_name":"Zanin, Esther"},{"first_name":"Barbara","full_name":"Conradt, Barbara","last_name":"Conradt"}],"month":"10"},{"file_date_updated":"2024-08-06T06:54:24Z","pmid":1,"type":"journal_article","doi":"10.1016/j.nbd.2022.105702","oa":1,"article_number":"105702","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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","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)."},"department":[{"_id":"SiHi"}],"publisher":"Elsevier","article_processing_charge":"Yes","publication_identifier":{"issn":["0969-9961"]},"quality_controlled":"1","day":"15","intvolume":" 168","date_published":"2022-06-15T00:00:00Z","abstract":[{"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.","lang":"eng"}],"volume":168,"year":"2022","external_id":{"pmid":["35339680"]},"date_created":"2024-05-29T06:10:05Z","oa_version":"Published Version","publication":"Neurobiology of Disease","language":[{"iso":"eng"}],"_id":"17067","title":"Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells","status":"public","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2022_NeurobioDisease_Stouffer.pdf","creator":"dernst","file_id":"17398","success":1,"date_created":"2024-08-06T06:54:24Z","date_updated":"2024-08-06T06:54:24Z","file_size":8890818,"checksum":"b705d3d23d0b424ba29920be7ab64c23"}],"scopus_import":"1","article_type":"original","date_updated":"2024-08-06T06:57:39Z","publication_status":"published","ddc":["570"],"month":"06","author":[{"last_name":"Stouffer","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Stouffer, Melissa A"},{"full_name":"Khalaf-Nazzal, R.","first_name":"R.","last_name":"Khalaf-Nazzal"},{"last_name":"Cifuentes-Diaz","full_name":"Cifuentes-Diaz, C.","first_name":"C."},{"last_name":"Albertini","full_name":"Albertini, G.","first_name":"G."},{"first_name":"E.","full_name":"Bandet, E.","last_name":"Bandet"},{"last_name":"Grannec","full_name":"Grannec, G.","first_name":"G."},{"first_name":"V.","full_name":"Lavilla, V.","last_name":"Lavilla"},{"first_name":"J.-F.","full_name":"Deleuze, J.-F.","last_name":"Deleuze"},{"last_name":"Olaso","first_name":"R.","full_name":"Olaso, R."},{"full_name":"Nosten-Bertrand, M.","first_name":"M.","last_name":"Nosten-Bertrand"},{"last_name":"Francis","first_name":"F.","full_name":"Francis, F."}]},{"volume":3,"year":"2022","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","external_id":{"pmid":["35529945"]},"date_created":"2024-05-29T06:10:22Z","title":"TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1","scopus_import":"1","status":"public","file":[{"file_name":"2022_PlantComm_Navarrete.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"17393","date_updated":"2024-08-05T10:26:29Z","date_created":"2024-08-05T10:26:29Z","success":1,"checksum":"1eeb6ee65419e4aa34627fea6857f343","file_size":3216686}],"article_type":"original","publication":"Plant Communications","language":[{"iso":"eng"}],"_id":"17068","month":"03","author":[{"full_name":"Navarrete, Fernando","first_name":"Fernando","last_name":"Navarrete"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Kornienko, Aleksandra E.","first_name":"Aleksandra E.","last_name":"Kornienko"},{"last_name":"Saado","first_name":"Indira","full_name":"Saado, Indira"},{"last_name":"Khan","full_name":"Khan, Mamoona","first_name":"Mamoona"},{"full_name":"Chia, Khong-Sam","first_name":"Khong-Sam","last_name":"Chia"},{"full_name":"Darino, Martin A.","first_name":"Martin A.","last_name":"Darino"},{"last_name":"Bindics","first_name":"Janos","full_name":"Bindics, Janos"},{"last_name":"Djamei","first_name":"Armin","full_name":"Djamei, Armin"}],"date_updated":"2024-08-05T10:27:03Z","publication_status":"published","ddc":["580"],"doi":"10.1016/j.xplc.2021.100269","oa":1,"file_date_updated":"2024-08-05T10:26:29Z","type":"journal_article","pmid":1,"article_number":"100269","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","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_processing_charge":"Yes","publication_identifier":{"issn":["2590-3462"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","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).","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.","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."},"department":[{"_id":"JiFr"}],"publisher":"Elsevier","issue":"2","intvolume":" 3","date_published":"2022-03-14T00:00:00Z","quality_controlled":"1","day":"14"},{"quality_controlled":"1","day":"20","OA_place":"repository","intvolume":" 375","date_published":"2022-01-20T00:00:00Z","issue":"6578","publisher":"American Association for the Advancement of Science","department":[{"_id":"JiFr"}],"citation":{"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.","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","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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"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).","type":"journal_article","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003","open_access":"1"}],"doi":"10.1126/science.abl4683","oa":1,"publication_status":"published","date_updated":"2025-04-24T11:39:46Z","OA_type":"green","month":"01","author":[{"last_name":"Zhong","full_name":"Zhong, Sheng","first_name":"Sheng"},{"last_name":"Li","full_name":"Li, Ling","first_name":"Ling"},{"last_name":"Wang","full_name":"Wang, Zhijuan","first_name":"Zhijuan"},{"full_name":"Ge, Zengxiang","first_name":"Zengxiang","orcid":"0000-0001-9381-3577","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge"},{"full_name":"Li, Qiyun","first_name":"Qiyun","last_name":"Li"},{"last_name":"Bleckmann","first_name":"Andrea","full_name":"Bleckmann, Andrea"},{"full_name":"Wang, Jizong","first_name":"Jizong","last_name":"Wang"},{"first_name":"Zihan","full_name":"Song, Zihan","last_name":"Song"},{"last_name":"Shi","full_name":"Shi, Yihao","first_name":"Yihao"},{"last_name":"Liu","first_name":"Tianxu","full_name":"Liu, Tianxu"},{"last_name":"Li","first_name":"Luhan","full_name":"Li, Luhan"},{"first_name":"Huabin","full_name":"Zhou, Huabin","last_name":"Zhou"},{"last_name":"Wang","first_name":"Yanyan","full_name":"Wang, Yanyan"},{"full_name":"Zhang, Li","first_name":"Li","last_name":"Zhang"},{"first_name":"Hen-Ming","full_name":"Wu, Hen-Ming","last_name":"Wu"},{"last_name":"Lai","first_name":"Luhua","full_name":"Lai, Luhua"},{"last_name":"Gu","full_name":"Gu, Hongya","first_name":"Hongya"},{"last_name":"Dong","first_name":"Juan","full_name":"Dong, Juan"},{"last_name":"Cheung","full_name":"Cheung, Alice Y.","first_name":"Alice Y."},{"first_name":"Thomas","full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus"},{"last_name":"Qu","full_name":"Qu, Li-Jia","first_name":"Li-Jia"}],"publication":"Science","language":[{"iso":"eng"}],"_id":"17069","scopus_import":"1","status":"public","title":"RALF peptide signaling controls the polytubey block in Arabidopsis","article_type":"original","external_id":{"pmid":["35050671"]},"date_created":"2024-05-29T06:11:10Z","oa_version":"Submitted Version","page":"290-296","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."}],"year":"2022","volume":375},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"083030","has_accepted_license":"1","type":"journal_article","file_date_updated":"2024-07-31T12:13:16Z","doi":"10.1088/1367-2630/ac836c","oa":1,"quality_controlled":"1","arxiv":1,"day":"08","intvolume":" 24","date_published":"2022-09-08T00:00:00Z","publisher":"IOP Publishing","issue":"8","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","short":"S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour, New Journal of Physics 24 (2022).","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.","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.","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.","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","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."},"department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","publication_identifier":{"issn":["1367-2630"]},"date_created":"2024-05-29T06:11:35Z","external_id":{"arxiv":["2204.10960"]},"oa_version":"Published Version","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."}],"year":"2022","volume":24,"publication_status":"published","date_updated":"2024-07-31T12:14:55Z","ddc":["530"],"author":[{"last_name":"Mistakidis","full_name":"Mistakidis, S I","first_name":"S I"},{"full_name":"Koutentakis, Georgios","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis"},{"first_name":"F","full_name":"Grusdt, F","last_name":"Grusdt"},{"last_name":"Schmelcher","first_name":"P","full_name":"Schmelcher, P"},{"full_name":"Sadeghpour, H R","first_name":"H R","last_name":"Sadeghpour"}],"month":"09","publication":"New Journal of Physics","language":[{"iso":"eng"}],"_id":"17070","file":[{"file_name":"2022_NewJournPhysics_Mistakidis.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17358","creator":"dernst","date_updated":"2024-07-31T12:13:16Z","success":1,"date_created":"2024-07-31T12:13:16Z","file_size":4201283,"checksum":"85776a9d3abe163b33b322c8e346752a"}],"scopus_import":"1","status":"public","title":"Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron","article_type":"original"},{"month":"06","author":[{"last_name":"Mosalaganti","first_name":"Shyamal","full_name":"Mosalaganti, Shyamal"},{"full_name":"Obarska-Kosinska, Agnieszka","first_name":"Agnieszka","last_name":"Obarska-Kosinska"},{"last_name":"Siggel","full_name":"Siggel, Marc","first_name":"Marc"},{"last_name":"Taniguchi","first_name":"Reiya","full_name":"Taniguchi, Reiya"},{"full_name":"Turoňová, Beata","first_name":"Beata","last_name":"Turoňová"},{"last_name":"Zimmerli","full_name":"Zimmerli, Christian E.","first_name":"Christian E."},{"last_name":"Buczak","first_name":"Katarzyna","full_name":"Buczak, Katarzyna"},{"first_name":"Florian","full_name":"Schmidt, Florian","id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt"},{"last_name":"Margiotta","full_name":"Margiotta, Erica","first_name":"Erica"},{"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"},{"last_name":"Hummer","first_name":"Gerhard","full_name":"Hummer, Gerhard"},{"first_name":"Jan","full_name":"Kosinski, Jan","last_name":"Kosinski"},{"last_name":"Beck","full_name":"Beck, Martin","first_name":"Martin"}],"publication_status":"published","date_updated":"2024-07-31T12:10:32Z","article_type":"original","status":"public","scopus_import":"1","title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores","_id":"17071","language":[{"iso":"eng"}],"publication":"Science","oa_version":"None","date_created":"2024-05-29T06:12:02Z","external_id":{"pmid":["35679397"]},"year":"2022","volume":376,"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."}],"date_published":"2022-06-10T00:00:00Z","intvolume":" 376","day":"10","quality_controlled":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_processing_charge":"No","publisher":"American Association for the Advancement of Science","issue":"6598","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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.","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.","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).","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"},"department":[{"_id":"MaJö"}],"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","doi":"10.1126/science.abm9506","type":"journal_article","pmid":1},{"quality_controlled":"1","day":"01","intvolume":" 8","date_published":"2022-03-01T00:00:00Z","publisher":"American Association for the Advancement of Science","issue":"9","citation":{"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).","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","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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"}],"article_processing_charge":"Yes","publication_identifier":{"issn":["2375-2548"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"eabl6293","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).","has_accepted_license":"1","type":"journal_article","pmid":1,"file_date_updated":"2024-07-31T12:01:51Z","doi":"10.1126/sciadv.abl6293","oa":1,"publication_status":"published","date_updated":"2024-08-05T08:30:29Z","ddc":["570"],"author":[{"first_name":"Mohsin M.","full_name":"Naqvi, Mohsin M.","last_name":"Naqvi"},{"id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","last_name":"Avellaneda Sarrió","first_name":"Mario","orcid":"0000-0001-6406-524X","full_name":"Avellaneda Sarrió, Mario"},{"first_name":"Andrew","full_name":"Roth, Andrew","last_name":"Roth"},{"last_name":"Koers","full_name":"Koers, Eline J.","first_name":"Eline J."},{"last_name":"Roland","first_name":"Antoine","full_name":"Roland, Antoine"},{"full_name":"Sunderlikova, Vanda","first_name":"Vanda","last_name":"Sunderlikova"},{"last_name":"Kramer","full_name":"Kramer, Günter","first_name":"Günter"},{"full_name":"Rye, Hays S.","first_name":"Hays S.","last_name":"Rye"},{"first_name":"Sander J.","full_name":"Tans, Sander J.","last_name":"Tans"}],"month":"03","language":[{"iso":"eng"}],"publication":"Science Advances","_id":"17072","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_ScienceAdv_Naqvi.pdf","file_id":"17357","creator":"dernst","success":1,"date_created":"2024-07-31T12:01:51Z","date_updated":"2024-07-31T12:01:51Z","checksum":"9511579306cce7e04107d3d6389ed614","file_size":2404150}],"status":"public","title":"Protein chain collapse modulation and folding stimulation by GroEL-ES","article_type":"original","date_created":"2024-05-29T06:12:19Z","external_id":{"pmid":["35245117"]},"oa_version":"Published Version","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."}],"year":"2022","volume":8},{"page":"291-312","edition":"2","type":"book_chapter","abstract":[{"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).","lang":"eng"}],"place":"Cham","doi":"10.1007/978-3-030-67727-5_18","year":"2022","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.","date_created":"2024-05-29T06:13:04Z","oa_version":"None","language":[{"iso":"eng"}],"publication":"Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases","publisher":"Springer Nature","department":[{"_id":"GaNo"}],"_id":"17075","citation":{"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.","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.","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","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.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_processing_charge":"No","scopus_import":"1","title":"Amino Acid Transport Defects","publication_identifier":{"isbn":["9783030677268"],"eisbn":["9783030677275"]},"quality_controlled":"1","publication_status":"published","editor":[{"last_name":"Blau","first_name":"Nenad","full_name":"Blau, Nenad"},{"last_name":"Vici","first_name":"Carlo Dionisi","full_name":"Vici, Carlo Dionisi"},{"last_name":"Ferreira","full_name":"Ferreira, Carlos R. ","first_name":"Carlos R. "},{"full_name":"Vianey-Saban, Christine","first_name":"Christine","last_name":"Vianey-Saban"},{"first_name":"Clara D.M.","full_name":"van Karnebeek, Clara D.M.","last_name":"van Karnebeek"}],"date_updated":"2024-07-31T11:45:50Z","day":"22","author":[{"last_name":"Palacín","first_name":"Manuel","full_name":"Palacín, Manuel"},{"last_name":"Bröer","first_name":"Stefan","full_name":"Bröer, Stefan"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia"}],"month":"02","date_published":"2022-02-22T00:00:00Z"},{"article_number":"e12280","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","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].","file_date_updated":"2024-07-31T11:27:29Z","type":"journal_article","pmid":1,"doi":"10.1002/dad2.12280","oa":1,"quality_controlled":"1","day":"20","intvolume":" 14","date_published":"2022-04-20T00:00:00Z","department":[{"_id":"MaRo"}],"citation":{"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.","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.","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","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.","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","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","issue":"1","article_processing_charge":"Yes","publication_identifier":{"eissn":["2352-8729"]},"external_id":{"pmid":["35475137"]},"date_created":"2024-05-29T06:13:25Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":14,"year":"2022","date_updated":"2024-07-31T11:33:50Z","publication_status":"published","ddc":["570"],"month":"04","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"},{"last_name":"McCartney","full_name":"McCartney, Daniel L.","first_name":"Daniel L."},{"first_name":"Liu","full_name":"Shi, Liu","last_name":"Shi"},{"last_name":"Campbell","full_name":"Campbell, Archie","first_name":"Archie"},{"last_name":"Walker","first_name":"Rosie M.","full_name":"Walker, Rosie M."},{"first_name":"Craig W.","full_name":"Ritchie, Craig W.","last_name":"Ritchie"},{"full_name":"Deary, Ian J.","first_name":"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"},{"last_name":"Hayward","full_name":"Hayward, Caroline","first_name":"Caroline"},{"full_name":"Porteous, David J.","first_name":"David J.","last_name":"Porteous"},{"first_name":"Andrew M.","full_name":"McIntosh, Andrew M.","last_name":"McIntosh"},{"last_name":"Lovestone","first_name":"Simon","full_name":"Lovestone, Simon"},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"publication":"Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring","language":[{"iso":"eng"}],"_id":"17076","title":"Genome‐ and epigenome‐wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk","status":"public","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2023_AlzheimersDementia_Hillary.pdf","creator":"dernst","file_id":"17356","date_created":"2024-07-31T11:27:29Z","success":1,"date_updated":"2024-07-31T11:27:29Z","checksum":"49c8597b588ef1c63897703a32b7967b","file_size":975181}],"scopus_import":"1","article_type":"original"},{"page":"380-416","abstract":[{"text":"Resolving a conjecture of Füredi from 1988, we prove that with high probability, the random graph 𝔾(𝑛, 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\n𝑛 − 𝑜(𝑛) 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.","lang":"eng"}],"volume":2,"year":"2022","external_id":{"arxiv":["2105.13337"]},"date_created":"2024-05-29T06:13:37Z","oa_version":"Published Version","publication":"Communications of the American Mathematical Society","language":[{"iso":"eng"}],"_id":"17077","title":"Friendly bisections of random graphs","file":[{"date_updated":"2024-07-12T12:55:02Z","success":1,"date_created":"2024-07-12T12:55:02Z","checksum":"719861e76f5bce3d0362d8171daa26fc","file_size":335965,"file_name":"2022_CommAMS_Ferber.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"17230","creator":"cchlebak"}],"status":"public","article_type":"original","date_updated":"2024-07-15T08:06:05Z","publication_status":"published","ddc":["500"],"month":"12","author":[{"last_name":"Ferber","full_name":"Ferber, Asaf","first_name":"Asaf"},{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan"},{"first_name":"Bhargav","full_name":"Narayanan, Bhargav","last_name":"Narayanan"},{"last_name":"Sah","first_name":"Ashwin","full_name":"Sah, Ashwin"},{"last_name":"Sawhney","full_name":"Sawhney, Mehtaab","first_name":"Mehtaab"}],"file_date_updated":"2024-07-12T12:55:02Z","type":"journal_article","doi":"10.1090/cams/13","oa":1,"license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"has_accepted_license":"1","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.","corr_author":"1","department":[{"_id":"MaKw"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","short":"A. Ferber, M.A. Kwan, B. Narayanan, A. Sah, M. Sawhney, Communications of the American Mathematical Society 2 (2022) 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.","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.","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","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."},"issue":"10","publisher":"American Mathematical Society","article_processing_charge":"No","publication_identifier":{"issn":["2692-3688"]},"quality_controlled":"1","arxiv":1,"day":"20","intvolume":" 2","date_published":"2022-12-20T00:00:00Z"},{"department":[{"_id":"HeEd"},{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"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","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.","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.","ieee":"O. Aichholzer et al., “Hardness of token swapping on trees,” in 30th Annual European Symposium on Algorithms, Berlin/Potsdam, Germany, 2022, vol. 244.","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.","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","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."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"Yes","quality_controlled":"1","arxiv":1,"day":"01","intvolume":" 244","date_published":"2022-09-01T00:00:00Z","file_date_updated":"2024-08-12T08:51:44Z","type":"conference","conference":{"start_date":"2022-09-05","name":"ESA: European Symposium on Algorithms","end_date":"2022-09-09","location":"Berlin/Potsdam, Germany"},"doi":"10.4230/LIPIcs.ESA.2022.3","oa":1,"article_number":"3","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","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.","corr_author":"1","language":[{"iso":"eng"}],"publication":"30th Annual European Symposium on Algorithms","_id":"17084","title":"Hardness of token swapping on trees","status":"public","file":[{"creator":"dernst","file_id":"17420","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2022_LIPIcS_Aichholzer.pdf","checksum":"a1fbd3e7baad510fbcb998cf4a7d9f7f","file_size":1406071,"date_created":"2024-08-12T08:51:44Z","success":1,"date_updated":"2024-08-12T08:51:44Z"}],"scopus_import":"1","date_updated":"2025-04-15T07:16:56Z","publication_status":"published","ddc":["510"],"author":[{"last_name":"Aichholzer","full_name":"Aichholzer, Oswin","first_name":"Oswin"},{"first_name":"Erik D.","full_name":"Demaine, Erik D.","last_name":"Demaine"},{"first_name":"Matias","full_name":"Korman, Matias","last_name":"Korman"},{"full_name":"Lubiw, Anna","first_name":"Anna","last_name":"Lubiw"},{"last_name":"Lynch","first_name":"Jayson","full_name":"Lynch, Jayson"},{"full_name":"Masárová, Zuzana","first_name":"Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová"},{"full_name":"Rudoy, Mikhail","first_name":"Mikhail","last_name":"Rudoy"},{"last_name":"Vassilevska Williams","full_name":"Vassilevska Williams, Virginia","first_name":"Virginia"},{"full_name":"Wein, Nicole","first_name":"Nicole","last_name":"Wein"}],"month":"09","abstract":[{"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.","lang":"eng"}],"volume":244,"project":[{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","call_identifier":"FWF","grant_number":"Z00342"}],"year":"2022","date_created":"2024-05-29T06:27:16Z","external_id":{"arxiv":["2103.06707"]},"oa_version":"Published Version"},{"article_processing_charge":"No","status":"public","title":"Mosses: Accessible Systems for Plant Development Studies","publication_identifier":{"isbn":["9781839697500"]},"publication":"Model Organisms in Plant Genetics","language":[{"iso":"eng"}],"publisher":"IntechOpen","department":[{"_id":"JiFr"}],"_id":"17085","citation":{"short":"J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022.","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","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","author":[{"first_name":"Jordi","full_name":"Floriach-Clark, Jordi","last_name":"Floriach-Clark"},{"full_name":"Tang, Han","first_name":"Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","last_name":"Tang"},{"full_name":"Willemsen, Viola","first_name":"Viola","last_name":"Willemsen"}],"date_published":"2022-06-23T00:00:00Z","publication_status":"published","quality_controlled":"1","editor":[{"first_name":"Ibrokhim Y.","full_name":"Abdurakhmonov, Ibrokhim Y.","last_name":"Abdurakhmonov"}],"date_updated":"2025-05-14T11:20:40Z","day":"23","doi":"10.5772/intechopen.100535","oa":1,"year":"2022","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"type":"book_chapter","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5772/intechopen.100535"}],"ec_funded":1,"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."}],"oa_version":"Published Version","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.","date_created":"2024-05-29T06:35:13Z"}]